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Journal articles on the topic 'Coenzyme A Ligases'

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Published: 4 June 2021

Last updated: 1 February 2022

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1

Villemur, Richard. "Coenzyme A ligases involved in anaerobic biodegradation of aromatic compounds." Canadian Journal of Microbiology 41, no. 10 (October 1, 1995): 855–61. http://dx.doi.org/10.1139/m95-118.

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Bacterial strains and consortia of bacteria have been isolated for their ability to degrade, under anaerobic conditions, homocyclic monoaromatic compounds, such as phenolic compounds, methylbenzenes, and aminobenzenes. As opposed to aerobic conditions where these compounds are degraded via dihydroxyl intermediates introduced by oxygenases, most of aromatic compounds under anaerobic conditions are metabolized via aromatic acid intermediates, such as nitrobenzoates, hydroxybenzoates, or phenylacetate. These aromatic acids are then transformed to benzoate before the reduction and the cleavage of the benzene ring to aliphatic acid products. One step of these catabolic pathways is the addition of a coenzyme A (CoA) residue to the carboxylic group of the aromatic acids by CoA ligases. This addition would facilitate the enzymatic transformation of the aromatic acids to benzoyl-CoA and the subsequent degradation steps of this latter molecule. Aromatic acid – CoA ligases have been characterized or detected from several bacterial strains that were grown under anaerobic conditions and from an anaerobic syntrophic consortium. They are also involved in the degradation of some aromatic compounds under aerobic conditions. They have molecular masses varying between 48 and 61 kDa, require ATP, Mg2+, and CoASH as cofactors, and have an optimum pH of 8.2–9.3. Amino acid sequence analyses of four aromatic acid–CoA ligases have revealed that they are related to an AMP-binding protein family. Aromatic acid – CoA ligases expressed in anaerobically grown bacterial cells are strictly regulated by the anaerobic conditions and the presence of aromatic acids.Key words: aromatic compounds, coenzyme A ligase, anaerobic microorganisms.

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2

Altenschmidt, U., B. Oswald, and G. Fuchs. "Purification and characterization of benzoate-coenzyme A ligase and 2-aminobenzoate-coenzyme A ligases from a denitrifying Pseudomonas sp." Journal of Bacteriology 173, no. 17 (1991): 5494–501. http://dx.doi.org/10.1128/jb.173.17.5494-5501.1991.

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3

Horrobin, David F., and Crispin N. Bennett. "Fatty acid coenzyme a ligases as candidate genes in schizophrenia." Schizophrenia Research 41, no. 1 (January 2000): 99. http://dx.doi.org/10.1016/s0920-9964(00)90540-1.

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4

Di Gioia, Diana, Michelle Peel, Fabio Fava, and R. Campbell Wyndham. "Structures of Homologous Composite Transposons Carrying cbaABC Genes from Europe and North America." Applied and Environmental Microbiology 64, no. 5 (May 1, 1998): 1940–46. http://dx.doi.org/10.1128/aem.64.5.1940-1946.1998.

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ABSTRACT IS1071 is a class II transposable element carrying atnpA gene related to the transposase genes of the Tn3 family. Copies of IS1071 that are conserved with more than 99% nucleotide sequence identity have been found as direct repeats flanking a remarkable variety of catabolic gene sequences worldwide. The sequences of chlorobenzoate catabolic transposons found on pBRC60 (Tn5271) in Niagara Falls, N.Y., and on pCPE3 in Bologna, Italy, show that these transposons were formed from highly homologous IS1071 and cbaABCcomponents (levels of identity, >99.5 and >99.3%, respectively). Nevertheless, the junction sequences between the IS1071Land IS1071R elements and the internal DNA differ by 41 and 927 bp, respectively, suggesting that these transposons were assembled independently on the two plasmids. The formation of the right junction in both transposons truncated an open reading frame for a putative aryl-coenzyme A ligase with sequence similarity to benzoate- andp-hydroxybenzoate-coenzyme A ligases ofRhodopseudomonas palustris.

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5

Nolte, Johannes Christoph, Marc Schürmann, Catherine-Louise Schepers, Elvira Vogel, Jan Hendrik Wübbeler, and Alexander Steinbüchel. "Novel Characteristics of Succinate Coenzyme A (Succinate-CoA) Ligases: Conversion of Malate to Malyl-CoA and CoA-Thioester Formation of Succinate AnaloguesIn Vitro." Applied and Environmental Microbiology 80, no. 1 (October 18, 2013): 166–76. http://dx.doi.org/10.1128/aem.03075-13.

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ABSTRACTThree succinate coenzyme A (succinate-CoA) ligases (SucCD) fromEscherichia coli,Advenella mimigardefordensisDPN7T, andAlcanivorax borkumensisSK2 were characterized regarding their substrate specificity concerning succinate analogues. Previous studies had suggested that SucCD enzymes might be promiscuous toward succinate analogues, such as itaconate and 3-sulfinopropionate (3SP). The latter is an intermediate of the degradation pathway of 3,3′-dithiodipropionate (DTDP), a precursor for the biotechnical production of polythioesters (PTEs) in bacteria. ThesucCDgenes were expressed inE. coliBL21(DE3)/pLysS. The SucCD enzymes ofE. coliandA. mimigardefordensisDPN7Twere purified in the native state using stepwise purification protocols, while SucCD fromA. borkumensisSK2 was equipped with a C-terminal hexahistidine tag at the SucD subunit. Besides the preference for the physiological substrates succinate, itaconate, ATP, and CoA, high enzyme activity was additionally determined for both enantiomeric forms of malate, amounting to 10 to 21% of the activity with succinate.Kmvalues ranged from 2.5 to 3.6 mM forl-malate and from 3.6 to 4.2 mM ford-malate for the SucCD enzymes investigated in this study. Asl-malate-CoA ligase is present in the serine cycle for assimilation of C1compounds in methylotrophs, structural comparison of these two enzymes as members of the same subsubclass suggested a strong resemblance of SucCD tol-malate-CoA ligase and gave rise to the speculation that malate-CoA ligases and succinate-CoA ligases have the same evolutionary origin. Although enzyme activities were very low for the additional substrates investigated, liquid chromatography/electrospray ionization-mass spectrometry analyses proved the ability of SucCD enzymes to form CoA-thioesters of adipate, glutarate, and fumarate. Since all SucCD enzymes were able to activate 3SP to 3SP-CoA, we consequently demonstrated that the activation of 3SP is not a unique characteristic of the SucCD fromA. mimigardefordensisDPN7T. The essential role ofsucCDin the activation of 3SPin vivowas proved by genetic complementation.

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6

Bhushan, Alok, Rajinder Pal Singh, and Inderjit Singh. "Characterization of rat brain microsomal acyl-coenzyme A ligases: Different enzymes for the synthesis of palmitoyl-coenzyme A and lignoceroyl-coenzyme A." Archives of Biochemistry and Biophysics 246, no. 1 (April 1986): 374–80. http://dx.doi.org/10.1016/0003-9861(86)90482-0.

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7

Coleman, James P., L. Lynn Hudson, Susan L. McKnight, John M. Farrow, M. Worth Calfee, Claire A. Lindsey, and Everett C. Pesci. "Pseudomonas aeruginosa PqsA Is an Anthranilate-Coenzyme A Ligase." Journal of Bacteriology 190, no. 4 (December 14, 2007): 1247–55. http://dx.doi.org/10.1128/jb.01140-07.

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ABSTRACT Pseudomonas aeruginosa is an opportunistic human pathogen which relies on several intercellular signaling systems for optimum population density-dependent regulation of virulence genes. The Pseudomonas quinolone signal (PQS) is a 3-hydroxy-4-quinolone with a 2-alkyl substitution which is synthesized by the condensation of anthranilic acid with a 3-keto-fatty acid. The pqsABCDE operon has been identified as being necessary for PQS production, and the pqsA gene encodes a predicted protein with homology to acyl coenzyme A (acyl-CoA) ligases. In order to elucidate the first step of the 4-quinolone synthesis pathway in P. aeruginosa, we have characterized the function of the pqsA gene product. Extracts prepared from Escherichia coli expressing PqsA were shown to catalyze the formation of anthraniloyl-CoA from anthranilate, ATP, and CoA. The PqsA protein was purified as a recombinant His-tagged polypeptide, and this protein was shown to have anthranilate-CoA ligase activity. The enzyme was active on a variety of aromatic substrates, including benzoate and chloro and fluoro derivatives of anthranilate. Inhibition of PQS formation in vivo was observed for the chloro- and fluoroanthranilate derivatives, as well as for several analogs which were not PqsA enzymatic substrates. These results indicate that the PqsA protein is responsible for priming anthranilate for entry into the PQS biosynthetic pathway and that this enzyme may serve as a useful in vitro indicator for potential agents to disrupt quinolone signaling in P. aeruginosa.

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8

El-Said Mohamed, Magdy. "Biochemical and Molecular Characterization of Phenylacetate-Coenzyme A Ligase, an Enzyme Catalyzing the First Step in Aerobic Metabolism of Phenylacetic Acid inAzoarcus evansii." Journal of Bacteriology 182, no. 2 (January 15, 2000): 286–94. http://dx.doi.org/10.1128/jb.182.2.286-294.2000.

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ABSTRACT Phenylacetate-coenzyme A ligase (PA-CoA ligase; AMP forming, EC6.2.1.30 ), the enzyme catalyzing the first step in the aerobic degradation of phenylacetate (PA) in Azoarcus evansii, has been purified and characterized. The gene (paaK) coding for this enzyme was cloned and sequenced. The enzyme catalyzes the reaction of PA with CoA and MgATP to yield phenylacetyl-CoA (PACoA) plus AMP plus PPi. The enzyme was specifically induced after aerobic growth in a chemically defined medium containing PA or phenylalanine (Phe) as the sole carbon source. Growth with 4-hydroxyphenylacetate, benzoate, adipate, or acetate did not induce the synthesis of this enzyme. This enzymatic activity was detected very early in the exponential phase of growth, and a maximal specific activity of 76 nmol min−1mg of cell protein−1 was measured. After 117-fold purification to homogeneity, a specific activity of 48 μmol min−1 mg of protein−1 was achieved with a turnover number (catalytic constant) of 40 s−1. The protein is a monomer of 52 kDa and shows high specificity towards PA; other aromatic or aliphatic acids were not used as substrates. The apparent Km values for PA, ATP, and CoA were 14, 60, and 45 μM, respectively. The PA-CoA ligase has an optimum pH of 8 to 8.5 and a pI of 6.3. The enzyme is labile and requires the presence of glycerol for stabilization. The N-terminal amino acid sequence of the purified protein showed no homology with other reported PA-CoA ligases. The gene encoding this enzyme is 1,320 bp long and codes for a protein of 48.75 kDa (440 amino acids) which shows high similarity with other reported PA-CoA ligases. An amino acid consensus for an AMP binding motif (VX2SSGTTGXP) was identified. The biochemical and molecular characteristics of this enzyme are quite different from those of the isoenzyme catalyzing the same reaction under anaerobic conditions in the same bacterium.

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9

Egland, P. G., J. Gibson, and C. S. Harwood. "Benzoate-coenzyme A ligase, encoded by badA, is one of three ligases able to catalyze benzoyl-coenzyme A formation during anaerobic growth of Rhodopseudomonas palustris on benzoate." Journal of bacteriology 177, no. 22 (1995): 6545–51. http://dx.doi.org/10.1128/jb.177.22.6545-6551.1995.

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10

Li, H., H. Xu, D. E. Graham, and R. H. White. "Glutathione synthetase homologs encode -L-glutamate ligases for methanogenic coenzyme F420 and tetrahydrosarcinapterin biosyntheses." Proceedings of the National Academy of Sciences 100, no. 17 (August 8, 2003): 9785–90. http://dx.doi.org/10.1073/pnas.1733391100.

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11

Rao, Guodong, Xiang Pan, Fang Xu, Yongzhuo Zhang, Shan Cao, Xiangning Jiang, and Hai Lu. "Divergent and Overlapping Function of Five 4-Coumarate/Coenzyme A Ligases from Populus tomentosa." Plant Molecular Biology Reporter 33, no. 4 (September 21, 2014): 841–54. http://dx.doi.org/10.1007/s11105-014-0803-4.

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12

Barragán, María J. López, Manuel Carmona, María T. Zamarro, Bärbel Thiele, Matthias Boll, Georg Fuchs, José L. García, and Eduardo Díaz. "The bzd Gene Cluster, Coding for Anaerobic Benzoate Catabolism, in Azoarcus sp. Strain CIB." Journal of Bacteriology 186, no. 17 (September 1, 2004): 5762–74. http://dx.doi.org/10.1128/jb.186.17.5762-5774.2004.

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ABSTRACT We report here that the bzd genes for anaerobic benzoate degradation in Azoarcus sp. strain CIB are organized as two transcriptional units, i.e., a benzoate-inducible catabolic operon, bzdNOPQMSTUVWXYZA, and a gene, bzdR, encoding a putative transcriptional regulator. The last gene of the catabolic operon, bzdA, has been expressed in Escherichia coli and encodes the benzoate-coenzyme A (CoA) ligase that catalyzes the first step in the benzoate degradation pathway. The BzdA enzyme is able to activate a wider range of aromatic compounds than that reported for other previously characterized benzoate-CoA ligases. The reduction of benzoyl-CoA to a nonaromatic cyclic intermediate is carried out by a benzoyl-CoA reductase (bzdNOPQ gene products) detected in Azoarcus sp. strain CIB extracts. The bzdW, bzdX, and bzdY gene products show significant similarity to the hydratase, dehydrogenase, and ring-cleavage hydrolase that act sequentially on the product of the benzoyl-CoA reductase in the benzoate catabolic pathway of Thauera aromatica. Benzoate-CoA ligase assays and transcriptional analyses based on lacZ-reporter fusions revealed that benzoate degradation in Azoarcus sp. strain CIB is subject to carbon catabolite repression by some organic acids, indicating the existence of a physiological control that connects the expression of the bzd genes to the metabolic status of the cell.

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13

Li, Zhao-Bo, Chang-Fu Li, Jia Li, and Yan-Sheng Zhang. "Molecular Cloning and Functional Characterization of Two Divergent 4-Coumarate : Coenzyme A Ligases from Kudzu (Pueraria lobata)." Biological and Pharmaceutical Bulletin 37, no. 1 (2014): 113–22. http://dx.doi.org/10.1248/bpb.b13-00633.

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14

Gardner, Richard G., Alexander G. Shearer, and Randolph Y. Hampton. "In Vivo Action of the HRD Ubiquitin Ligase Complex: Mechanisms of Endoplasmic Reticulum Quality Control and Sterol Regulation." Molecular and Cellular Biology 21, no. 13 (July 1, 2001): 4276–91. http://dx.doi.org/10.1128/mcb.21.13.4276-4291.2001.

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ABSTRACT Ubiquitination is used to target both normal proteins for specific regulated degradation and misfolded proteins for purposes of quality control destruction. Ubiquitin ligases, or E3 proteins, promote ubiquitination by effecting the specific transfer of ubiquitin from the correct ubiquitin-conjugating enzyme, or E2 protein, to the target substrate. Substrate specificity is usually determined by specific sequence determinants, or degrons, in the target substrate that are recognized by the ubiquitin ligase. In quality control, however, a potentially vast collection of proteins with characteristic hallmarks of misfolding or misassembly are targeted with high specificity despite the lack of any sequence similarity between substrates. In order to understand the mechanisms of quality control ubiquitination, we have focused our attention on the first characterized quality control ubiquitin ligase, the HRD complex, which is responsible for the endoplasmic reticulum (ER)-associated degradation (ERAD) of numerous ER-resident proteins. Using an in vivo cross-linking assay, we directly examined the association of the separate HRDcomplex components with various ERAD substrates. We have discovered that the HRD ubiquitin ligase complex associates with both ERAD substrates and stable proteins, but only mediates ubiquitin-conjugating enzyme association with ERAD substrates. Our studies with the sterol pathway-regulated ERAD substrate Hmg2p, an isozyme of the yeast cholesterol biosynthetic enzyme HMG-coenzyme A reductase (HMGR), indicated that the HRD complex discerns between a degradation-competent “misfolded” state and a stable, tightly folded state. Thus, it appears that the physiologically regulated, HRD-dependent degradation of HMGR is effected by a programmed structural transition from a stable protein to a quality control substrate.

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15

Gazzaniga, Francesca, Rebecca Stebbins, Sheila Z. Chang, Mark A. McPeek, and Charles Brenner. "Microbial NAD Metabolism: Lessons from Comparative Genomics." Microbiology and Molecular Biology Reviews 73, no. 3 (September 2009): 529–41. http://dx.doi.org/10.1128/mmbr.00042-08.

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SUMMARY NAD is a coenzyme for redox reactions and a substrate of NAD-consuming enzymes, including ADP-ribose transferases, Sir2-related protein lysine deacetylases, and bacterial DNA ligases. Microorganisms that synthesize NAD from as few as one to as many as five of the six identified biosynthetic precursors have been identified. De novo NAD synthesis from aspartate or tryptophan is neither universal nor strictly aerobic. Salvage NAD synthesis from nicotinamide, nicotinic acid, nicotinamide riboside, and nicotinic acid riboside occurs via modules of different genes. Nicotinamide salvage genes nadV and pncA, found in distinct bacteria, appear to have spread throughout the tree of life via horizontal gene transfer. Biochemical, genetic, and genomic analyses have advanced to the point at which the precursors and pathways utilized by a microorganism can be predicted. Challenges remain in dissecting regulation of pathways.

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16

Elsabrouty, Rania, Youngah Jo, Tammy T. Dinh, and Russell A. DeBose-Boyd. "Sterol-induced dislocation of 3-hydroxy-3-methylglutaryl coenzyme A reductase from membranes of permeabilized cells." Molecular Biology of the Cell 24, no. 21 (November 2013): 3300–3308. http://dx.doi.org/10.1091/mbc.e13-03-0157.

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The polytopic endoplasmic reticulum (ER)–localized enzyme 3-hydroxy-3-methylglutaryl CoA reductase catalyzes a rate-limiting step in the synthesis of cholesterol and nonsterol isoprenoids. Excess sterols cause the reductase to bind to ER membrane proteins called Insig-1 and Insig-2, which are carriers for the ubiquitin ligases gp78 and Trc8. The resulting gp78/Trc8-mediated ubiquitination of reductase marks it for recognition by VCP/p97, an ATPase that mediates subsequent dislocation of reductase from ER membranes into the cytosol for proteasomal degradation. Here we report that in vitro additions of the oxysterol 25-hydroxycholesterol (25-HC), exogenous cytosol, and ATP trigger dislocation of ubiquitinated and full-length forms of reductase from membranes of permeabilized cells. In addition, the sterol-regulated reaction requires the action of Insigs, is stimulated by reagents that replace 25-HC in accelerating reductase degradation in intact cells, and is augmented by the nonsterol isoprenoid geranylgeraniol. Finally, pharmacologic inhibition of deubiquitinating enzymes markedly enhances sterol-dependent ubiquitination of reductase in membranes of permeabilized cells, leading to enhanced dislocation of the enzyme. Considered together, these results establish permeabilized cells as a viable system in which to elucidate mechanisms for postubiquitination steps in sterol-accelerated degradation of reductase.

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17

Mukhopadhyay, Biswarup, Endang Purwantini, Cynthia L. Kreder, and Ralph S. Wolfe. "Oxaloacetate Synthesis in the Methanarchaeon Methanosarcina barkeri: Pyruvate Carboxylase Genes and a PutativeEscherichia coli-Type Bifunctional Biotin Protein Ligase Gene (bpl/birA) Exhibit a Unique Organization." Journal of Bacteriology 183, no. 12 (June 15, 2001): 3804–10. http://dx.doi.org/10.1128/jb.183.12.3804-3810.2001.

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ABSTRACT Evidence is presented that, in Methanosarcina barkerioxaloacetate synthesis, an essential and major CO2 fixation reaction is catalyzed by an apparent α4β4-type acetyl coenzyme A-independent pyruvate carboxylase (PYC), composed of 64.2-kDa biotinylated and 52.9-kDa ATP-binding subunits. The purified enzyme was most active at 70°C, insensitive to aspartate and glutamate, mildly inhibited by α-ketoglutarate, and severely inhibited by ATP, ADP, and excess Mg2+. It showed negative cooperativity towards bicarbonate at 70°C but not at 37°C. The organism expressed holo-PYC without an external supply of biotin and, thus, synthesized biotin. pycA, pycB, and a putative bpl gene formed a novel operon-like arrangement. Unlike other archaeal homologs, the putative biotin protein ligases (BPLs) of M. barkeri and the closely related euryarchaeon Archaeoglobus fulgidus appeared to be of the Escherichia coli-type (bifunctional, with two activities: BirA or a repressor of the biotin operon and BPL). We found the element Tyr(Phe)ProX 5Phe(Tyr) to be fully conserved in biotin-dependent enzymes; it might function as the hinge for their “swinging arms.”

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18

Peters, Franziska, Michael Rother, and Matthias Boll. "Selenocysteine-Containing Proteins in Anaerobic Benzoate Metabolism of Desulfococcus multivorans." Journal of Bacteriology 186, no. 7 (April 1, 2004): 2156–63. http://dx.doi.org/10.1128/jb.186.7.2156-2163.2004.

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ABSTRACT The sulfate-reducing bacterium Desulfococcus multivorans uses various aromatic compounds as sources of cell carbon and energy. In this work, we studied the initial steps in the aromatic metabolism of this strictly anaerobic model organism. An ATP-dependent benzoate coenzyme A (CoA) ligase (AMP plus PPi forming) composed of a single 59-kDa subunit was purified from extracts of cells grown on benzoate. Specific activity was highest with benzoate and some benzoate derivatives, whereas aliphatic carboxylic acids were virtually unconverted. The N-terminal amino acid sequence showed high similarities with benzoate CoA ligases from Thauera aromatica and Azoarcus evansii. When cultivated on benzoate, cells strictly required selenium and molybdenum, whereas growth on nonaromatic compounds, such as cyclohexanecarboxylate or lactate, did not depend on the presence of the two trace elements. The growth rate on benzoate was half maximal with 1 nM selenite present in the growth medium. In molybdenum- and/or selenium-depleted cultures, growth on benzoate could be induced by addition of the missing trace elements. In extracts of cells grown on benzoate in the presence of [75Se]selenite, three radioactively labeled proteins with molecular masses of ∼100, 30, and 27 kDa were detected by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis. The 100- and 30-kDa selenoproteins were 5- to 10-fold induced in cells grown on benzoate compared to cells grown on lactate. These results suggest that the dearomatization process in D. multivorans is not catalyzed by the ATP-dependent Fe-S enzyme benzoyl-CoA reductase as in facultative anaerobes but rather involves unknown molybdenum- and selenocysteine-containing proteins.

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19

Chen, Hsi-Chuan, Jina Song, Cranos M. Williams, Christopher M. Shuford, Jie Liu, Jack P. Wang, Quanzi Li, et al. "Monolignol Pathway 4-Coumaric Acid:Coenzyme A Ligases in Populus. trichocarpa: Novel Specificity, Metabolic Regulation, and Simulation of Coenzyme A Ligation Fluxes." Plant Physiology 161, no. 3 (January 23, 2013): 1501–16. http://dx.doi.org/10.1104/pp.112.210971.

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20

Bullock, H. A., C. R. Reisch, A. S. Burns, M. A. Moran, and W. B. Whitman. "Regulatory and Functional Diversity of Methylmercaptopropionate Coenzyme A Ligases from the Dimethylsulfoniopropionate Demethylation Pathway in Ruegeria pomeroyi DSS-3 and Other Proteobacteria." Journal of Bacteriology 196, no. 6 (January 17, 2014): 1275–85. http://dx.doi.org/10.1128/jb.00026-14.

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21

Wang, Juan, Ning Ding, Yun Wu, Xiaoping Shi, Bowen Qi, Xiao Liu, Xiaohui Wang, Jun Li, Pengfei Tu, and Shepo Shi. "Enzymatic synthesis of 2-hydroxy-4H-quinolizin-4-one scaffolds by integrating coenzyme a ligases and a type III PKS from Huperzia serrata." RSC Advances 10, no. 40 (2020): 23566–72. http://dx.doi.org/10.1039/d0ra04133e.

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22

Berger, Martine, Nelson L. Brock, Heiko Liesegang, Marco Dogs, Ines Preuth, Meinhard Simon, Jeroen S. Dickschat, and Thorsten Brinkhoff. "Genetic Analysis of the Upper Phenylacetate Catabolic Pathway in the Production of Tropodithietic Acid by Phaeobacter gallaeciensis." Applied and Environmental Microbiology 78, no. 10 (March 9, 2012): 3539–51. http://dx.doi.org/10.1128/aem.07657-11.

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ABSTRACTProduction of the antibiotic tropodithietic acid (TDA) depends on the central phenylacetate catabolic pathway, specifically on the oxygenase PaaABCDE, which catalyzes epoxidation of phenylacetyl-coenzyme A (CoA). Our study was focused on genes of the upper part of this pathway leading to phenylacetyl-CoA as precursor for TDA.Phaeobacter gallaeciensisDSM 17395 encodes two genes with homology to phenylacetyl-CoA ligases (paaK1andpaaK2), which were shown to be essential for phenylacetate catabolism but not for TDA biosynthesis and phenylalanine degradation. Thus, inP. gallaeciensisanother enzyme must produce phenylacetyl-CoA from phenylalanine. Using random transposon insertion mutagenesis of apaaK1-paaK2double mutant we identified a gene (ior1) with similarity toiorAandiorBin archaea, encoding an indolepyruvate:ferredoxin oxidoreductase (IOR). Theior1mutant was unable to grow on phenylalanine, and production of TDA was significantly reduced compared to the wild-type level (60%). Nuclear magnetic resonance (NMR) spectroscopic investigations using13C-labeled phenylalanine isotopomers demonstrated that phenylalanine is transformed into phenylacetyl-CoA by Ior1. Using quantitative real-time PCR, we could show that expression ofior1depends on the adjacent regulator IorR. Growth on phenylalanine promotes production of TDA, induces expression ofior1(27-fold) andpaaK1(61-fold), and regulates the production of TDA. Phylogenetic analysis showed that the aerobic type of IOR as found in many roseobacters is common within a number of different phylogenetic groups of aerobic bacteria such asBurkholderia,Cupriavidis, andRhizobia, where it may also contribute to the degradation of phenylalanine.

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Steidle, Anette, Marie Allesen-Holm, Kathrin Riedel, Gabriele Berg, Michael Givskov, Søren Molin, and Leo Eberl. "Identification and Characterization of an N-Acylhomoserine Lactone-Dependent Quorum-Sensing System in Pseudomonas putida Strain IsoF." Applied and Environmental Microbiology 68, no. 12 (December 2002): 6371–82. http://dx.doi.org/10.1128/aem.68.12.6371-6382.2002.

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ABSTRACT Recent reports have shown that several strains of Pseudomonas putida produce N-acylhomoserine lactones (AHLs). These signal molecules enable bacteria to coordinately express certain phenotypic traits in a density-dependent manner in a process referred to as quorum sensing. In this study we have cloned a genomic region of the plant growth-promoting P. putida strain IsoF that, when present in trans, provoked induction of a bioluminescent AHL reporter plasmid. Sequence analysis identified a gene cluster consisting of four genes: ppuI and ppuR, whose predicted amino acid sequences are highly similar to proteins of the LuxI-LuxR family, an open reading frame (ORF) located in the intergenic region between ppuI and ppuR with significant homology to rsaL from Pseudomonas aeruginosa, and a gene, designated ppuA, present upstream of ppuR, the deduced amino acid sequence of which shows similarity to long-chain fatty acid coenzyme A ligases from various organisms. Using a transcriptional ppuA::luxAB fusion we demonstrate that expression of ppuA is AHL dependent. Furthermore, transcription of the AHL synthase ppuI is shown to be subject to quorum-sensing regulation, creating a positive feedback loop. Sequencing of the DNA regions flanking the ppu gene cluster indicated that the four genes form an island in the suhB-PA3819 intergenic region of the currently sequenced P. putida strain KT2440. Moreover, we provide evidence that the ppu genes are not present in other AHL-producing P. putida strains, indicating that this gene cluster is so far unique for strain IsoF. While the wild-type strain formed very homogenous biofilms, both a ppuI and a ppuA mutant formed structured biofilms with characteristic microcolonies and water-filled channels. These results suggest that the quorum-sensing system influences biofilm structural development.

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Yamini, Lingala, and Manga Vijjulatha. "Inhibitors of Human Dihydrofolate Reductase: A Computational Design and Docking Studies Using Glide." E-Journal of Chemistry 5, no. 2 (2008): 263–70. http://dx.doi.org/10.1155/2008/401738.

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Dihydrofolate reductase (DHFR) plays a vital role in the DNA synthesis by reducing dihydrofolic acid to tetrahydrofolic acid which is an essential component. Synthetic ligands like methotrexate (MTX), aminopterin (AMP) and their analogues act as potential anti metabolites by mimicking the coenzyme dihydrofolic acid (DHFA) they inhibit the activity of DHFR antagonistically. Several ligands which are similar to MTX analogues and 6, 8 substituted 2 – naphthyls (NAP) which can mimic the pteridyl group of DHFA have been computationally designed. These ligands were proposed to hinder the formation N5, N10 methylene tetrahydrofolic acid (THFA) coenzyme, which is essential for the DNA synthesis. The docking studies were done using grid, generated with the 0.9 Vander Waals scaling for non polar bonds in the active site of the receptor. These newly designed ligands such as 14 -21 ,23 and 28 have shown good docking scores and predicted activities when compared to already existing ligands MTX and its analogues.

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Singh, Poonam, Lutz Preu, Till Beuerle, David Kaufholdt, Robert Hänsch, Ludger Beerhues, and Mariam Gaid. "A promiscuous coenzyme A ligase provides benzoyl‐coenzyme A for xanthone biosynthesis in Hypericum." Plant Journal 104, no. 6 (November 3, 2020): 1472–90. http://dx.doi.org/10.1111/tpj.15012.

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Juárez, Javier F., María Teresa Zamarro, María J. L. Barragán, Blas Blázquez, Matthias Boll, Kevin Kuntze, José Luis García, Eduardo Díaz, and Manuel Carmona. "Identification of the Geobacter metallireducens BamVW Two-Component System, Involved in Transcriptional Regulation of Aromatic Degradation." Applied and Environmental Microbiology 76, no. 1 (November 13, 2009): 383–85. http://dx.doi.org/10.1128/aem.02255-09.

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ABSTRACT Regulation of aromatic degradation in obligate anaerobes was studied in the Fe(III)-respiring model organism Geobacter metallireducens GS-15. A two-component system and a σ54-dependent promoter were identified that are both involved in the regulation of the gene coding for benzoate-coenzyme A ligase, catalyzing the initial step of benzoate degradation.

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Schühle, Karola, Johannes Gescher, Ulrich Feil, Michael Paul, Martina Jahn, Hermann Schägger, and Georg Fuchs. "Benzoate-Coenzyme A Ligase from Thauera aromatica: an Enzyme Acting in Anaerobic and Aerobic Pathways." Journal of Bacteriology 185, no. 16 (August 15, 2003): 4920–29. http://dx.doi.org/10.1128/jb.185.16.4920-4929.2003.

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ABSTRACT In the denitrifying member of the β-Proteobacteria Thauera aromatica, the anaerobic metabolism of aromatic acids such as benzoate or 2-aminobenzoate is initiated by the formation of the coenzyme A (CoA) thioester, benzoyl-CoA and 2-aminobenzoyl-CoA, respectively. Both aromatic substrates were transformed to the acyl-CoA intermediate by a single CoA ligase (AMP forming) that preferentially acted on benzoate. This benzoate-CoA ligase was purified and characterized as a 57-kDa monomeric protein. Based on V max/Km , the specificity constant for 2-aminobenzoate was 15 times lower than that for benzoate; this may be the reason for the slower growth on 2-aminobenzoate. The benzoate-CoA ligase gene was cloned and sequenced and was found not to be part of the gene cluster encoding the general benzoyl-CoA pathway of anaerobic aromatic metabolism. Rather, it was located in a cluster of genes coding for a novel aerobic benzoate oxidation pathway. In line with this finding, the same CoA ligase was induced during aerobic growth with benzoate. A deletion mutant not only was unable to grow anaerobically on benzoate or 2-aminobenzoate, but also aerobic growth on benzoate was affected. This suggests that benzoate induces a single benzoate-CoA ligase. The product of benzoate activation, benzoyl-CoA, then acts as inducer of separate anaerobic or aerobic pathways of benzoyl-CoA, depending on whether oxygen is lacking or present.

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Sieweke, Hans-Jürgen, and Eckhard Leistner. "o-Succinylbenzoate: Coenzyme A Ligase, an Enzyme Involved in Menaquinone (Vitamin K2) Biosynthesis, Displays Broad Specificity." Zeitschrift für Naturforschung C 46, no. 7-8 (August 1, 1991): 585–90. http://dx.doi.org/10.1515/znc-1991-7-814.

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o-Succinylbenzoate: coenzyme A ligase, an enzyme involved in menaquinone biosynthesis, was purified from Mycobacterium phlei and characterized with respect to isoelectric point, molecular weight, pH optimum, temperature optimum and kinetic data. The enzyme hydrolyses ATP to AMP. The substrate and cofactor specificity of the enzyme was tested with analogues of o-succinylbenzoic acid, different nucleotides, thiols and divalent cations. The enzyme appears to possess broad specificity for substrates and cofactors.

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Li, Xinfeng, Fang Chen, Jinfeng Xiao, Shan-Ho Chou, Xuming Li, and Jin He. "Genome-wide Analysis of the Distribution of Riboswitches and Function Analyses of the Corresponding Downstream Genes in Prokaryotes." Current Bioinformatics 14, no. 1 (December 6, 2018): 53–61. http://dx.doi.org/10.2174/1574893613666180423145812.

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Background: Riboswitches are structured elements that usually reside in the noncoding regions of mRNAs, with which various ligands bind to control a wide variety of downstream gene expressions. To date, more than twenty different classes of riboswitches have been characterized to sense various metabolites, including purines and their derivatives, coenzymes, amino acids, and metal ions, etc. </P><P> Objective: This study aims to study the genome-wide analysis of the distribution of riboswitches and function analyses of the corresponding downstream genes in prokaryotes. Results: In this study, we have completed a genome context analysis of 27 riboswitches to elucidate their metabolic capacities of riboswitch-mediated gene regulation from the completely-sequenced 3,079 prokaryotic genomes. Furthermore, Cluster of Orthologous Groups of proteins (COG) annotation was applied to predict and classify the possible functions of corresponding downstream genes of these riboswitches. We found that they could all be successfully annotated and grouped into 20 different COG functional categories, in which the two main clusters "coenzyme metabolism [H]" and "amino acid transport and metabolism [E]" were the most significantly enriched. Conclusion: Riboswitches are found to be widespread in bacteria, among which three main classes of TPP-, cobalamin- and SAM-riboswitch were the most widely distributed. We found a wide variety of functions were associated with the corresponding downstream genes, suggesting that a wide extend of regulatory roles were mediated by these riboswitches in prokaryotes.

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30

Xin, Yu, Liushen Lu, Qing Wang, Ling Zhang, Yanjun Tong, and Wu Wang. "Coenzyme-like ligands for affinity isolation of cholesterol oxidase." Journal of Chromatography B 1021 (May 2016): 169–74. http://dx.doi.org/10.1016/j.jchromb.2016.01.043.

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31

Sydor, Tobias, Steffen Schaffer, and Eckhard Boles. "Considerable Increase in Resveratrol Production by Recombinant Industrial Yeast Strains with Use of Rich Medium." Applied and Environmental Microbiology 76, no. 10 (March 26, 2010): 3361–63. http://dx.doi.org/10.1128/aem.02796-09.

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ABSTRACT Resveratrol synthesis from p-coumarate was analyzed in different Saccharomyces cerevisiae strains expressing the 4-coumaroyl-coenzyme A ligase (4CL1) from Arabidopsis thaliana and the stilbene synthase (STS) from Vitis vinifera and compared between yeast cultures growing in rich or synthetic medium. The use of rich medium considerably improved resveratrol production, and resveratrol yields of up to 391 mg/liter could be achieved with an industrial Brazilian sugar cane-fermenting yeast.

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LÖFFLER, Frank, Rudolf MÜLLER, and Franz LINGENS. "Purification and Properties of 4-Halobenzoate-Coenzyme A Ligase fromPseudomonas sp.CBS3." Biological Chemistry Hoppe-Seyler 373, no. 2 (January 1992): 1001–8. http://dx.doi.org/10.1515/bchm3.1992.373.2.1001.

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33

Manandhar, Miglena, and John E. Cronan. "Proofreading of Noncognate Acyl Adenylates by an Acyl-Coenzyme A Ligase." Chemistry & Biology 20, no. 12 (December 2013): 1441–46. http://dx.doi.org/10.1016/j.chembiol.2013.10.010.

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34

Barillas, Wagner, and Ludger Beerhues. "3-Hydroxybenzoate:coenzyme A ligase and 4-coumarate: coenzyme A ligase from cultured cells of Centaurium erythraea." Planta 202, no. 1 (April 30, 1997): 112–16. http://dx.doi.org/10.1007/s004250050109.

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35

Barillas, Wagner, and Ludger Beerhues. "3-Hydroxybenzoate:Coenzyme A Ligase from Cell Cultures of Centaurium erythraea: Isolation and Characterization." Biological Chemistry 381, no. 2 (February 15, 2000): 155–60. http://dx.doi.org/10.1515/bc.2000.021.

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Abstract In xanthone biosynthesis, 3-hydroxybenzoate:coenzyme A ligase (3HBL) supplies the starter substrate for the formation of an intermediate benzophenone. 3HBL from cell cultures of the medicinal plant Centaurium erythraea was purified to apparent homogeneity using a sevenstepprocedure. The enzyme was an AMPforming CoA ligase with a K = 14.7 for 3-hydroxybenzoic acid, 8.5 for coenzyme A and 229 for ATP. The pH and temperature optima were 7.5 and 35C, respectively. In SDSPAGE, two polypeptides of M 41500 and 40500 were detected. Both proteins were structurally related to each other as shown by tryptic digestion. Their Ntermini were blocked. The difference in their apparent molecular masses could not be attributed to glycosylation. 3HBL had a native M of approx. 50000 and is thus active as a monomer.

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36

Kovář, Jan, and Ivana Matysková. "Effect of modification of certain amino acid residues on enzyme activity of D-3-hydroxybutyrate dehydrogenase from bacterium Paracoccus denitrificans." Collection of Czechoslovak Chemical Communications 52, no. 7 (1987): 1872–77. http://dx.doi.org/10.1135/cccc19871872.

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We examined the effect of several modifying reagents on the activity of the title enzyme. The results show that one histidine residue participates in the interaction of the enzyme with the substrate; one cysteine residue binds near to the nicotine amide moiety of the coenzyme molecule and its role is to induce conformational changes leading to the formation of enzyme aggregates with an increased catalytic power. The enzyme does not contain essential tyrosine and tryptophan residues. The results of the experiments with the modification of additional amino acid residues permit us to make preliminary conclusions only based on the knowledge of the protective effect of the individual ligands: One arginine residue may be involved in the binding of the coenzyme, the residues of lysine and serine may be localized in the substrate binding site.

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37

Knights, Kathleen M., Ursula M. Talbot, and Thomas A. Baillie. "Evidence of multiple forms of rat liver microsomal coenzyme A ligase catalysing the formation of 2-arylpropionyl-coenzyme A thioesters." Biochemical Pharmacology 44, no. 12 (December 1992): 2415–17. http://dx.doi.org/10.1016/0006-2952(92)90689-g.

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38

MISHINA, Masayoshi, Rainer ROGGUENKAMP, and Eckhart SCHWEIZER. "Yeast Mutants Defective in Acetyl-Coenzyme A Carboxylase and Biotin: Apocarboxylase Ligase." European Journal of Biochemistry 111, no. 1 (March 3, 2005): 79–87. http://dx.doi.org/10.1111/j.1432-1033.1980.tb06077.x.

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39

Koetsier, Martijn J., Peter A. Jekel, Hein J. Wijma, Roel A. L. Bovenberg, and Dick B. Janssen. "Aminoacyl-coenzyme A synthesis catalyzed by a CoA ligase from Penicillium chrysogenum." FEBS Letters 585, no. 6 (February 18, 2011): 893–98. http://dx.doi.org/10.1016/j.febslet.2011.02.018.

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40

Barthová, Jana, Jana Kučerová, and Sylva Leblová. "Interaction of lactate dehydrogenase isoenzymes with ligands." Collection of Czechoslovak Chemical Communications 53, no. 8 (1988): 1857–61. http://dx.doi.org/10.1135/cccc19881857.

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Isoenzymes of bovine lactate dehydrogenase (H4, H3M, and H2M2) were prepared by affinity chromatography on a 5'-AMP-Sepharose 4B column. The interaction of isoenzymes with two ligands, coenzyme NADH and the competitive inhibitor Cibacron Blue F3GA was followed by means of kinetic measurements and by affinity electrophoresis. The Michaelis constants of NADH were compared with the inhibition constants of Cibacron Blue and dissociation constants of enzyme-inhibitor complexes. It was found that the M subunit of lactate dehydrogenase exhibits always higher affinity both to NADH and Cibacron Blue in comparison to the H subunit. This finding corresponds to the physiological role of lactate dehydrogenase isoenzymes.

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41

Wang, Dong-Dong, Hua Bai, Wei-Qi Chen, Hai Lu, and Xiang-Ning Jiang. "Identifying a Cinnamoyl Coenzyme A Reductase (CCR) Activity with 4-Coumaric Acid: Coenzyme A Ligase (4CL) Reaction Products in Populus tomentosa." Journal of Plant Biology 52, no. 5 (August 22, 2009): 482–91. http://dx.doi.org/10.1007/s12374-009-9062-6.

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42

Wu, Rui, Albert S. Reger, Xuefeng Lu, Andrew M. Gulick, and Debra Dunaway-Mariano. "The Mechanism of Domain Alternation in the Acyl-Adenylate Forming Ligase Superfamily Member 4-Chlorobenzoate: Coenzyme A Ligase,." Biochemistry 48, no. 19 (May 19, 2009): 4115–25. http://dx.doi.org/10.1021/bi9002327.

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43

Anderson, Peter J., Jozsef Lango, Colleen Carkeet, Audrey Britten, Bernhard Kräutler, Bruce D. Hammock, and John R. Roth. "One Pathway Can Incorporate either Adenine or Dimethylbenzimidazole as an α-Axial Ligand of B12 Cofactors in Salmonella enterica." Journal of Bacteriology 190, no. 4 (November 2, 2007): 1160–71. http://dx.doi.org/10.1128/jb.01386-07.

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ABSTRACT Corrinoid (vitamin B12-like) cofactors contain various α-axial ligands, including 5,6-dimethylbenzimidazole (DMB) or adenine. The bacterium Salmonella enterica produces the corrin ring only under anaerobic conditions, but it can form “complete” corrinoids aerobically by importing an “incomplete” corrinoid, such as cobinamide (Cbi), and adding appropriate α- and β-axial ligands. Under aerobic conditions, S. enterica performs the corrinoid-dependent degradation of ethanolamine if given vitamin B12, but it can make B12 from exogenous Cbi only if DMB is also provided. Mutants isolated for their ability to degrade ethanolamine without added DMB converted Cbi to pseudo-B12 cofactors (having adenine as an α-axial ligand). The mutations cause an increase in the level of free adenine and install adenine (instead of DMB) as an α-ligand. When DMB is provided to these mutants, synthesis of pseudo-B12 cofactors ceases and B12 cofactors are produced, suggesting that DMB regulates production or incorporation of free adenine as an α-ligand. Wild-type cells make pseudo-B12 cofactors during aerobic growth on propanediol plus Cbi and can use pseudo-vitamin B12 for all of their corrinoid-dependent enzymes. Synthesis of coenzyme pseudo-B12 cofactors requires the same enzymes (CobT, CobU, CobS, and CobC) that install DMB in the formation of coenzyme B12. Models are described for the mechanism and control of α-axial ligand installation.

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44

Muskal, Steven M., Joe Sliman, John Kokai-Kun, Mark Pimentel, Vince Wacher, and Klaus Gottlieb. "Lovastatin lactone may improve irritable bowel syndrome with constipation (IBS-C) by inhibiting enzymes in the archaeal methanogenesis pathway." F1000Research 5 (April 8, 2016): 606. http://dx.doi.org/10.12688/f1000research.8406.1.

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Methane produced by the methanoarchaeonMethanobrevibacter smithii(M. smithii) has been linked to constipation, irritable bowel syndrome with constipation (IBS-C), and obesity. Lovastatin, which demonstrates a cholesterol-lowering effect by the inhibition of HMG-CoA reductase, may also have an anti-methanogenesis effect through direct inhibition of enzymes in the archaeal methanogenesis pathway. We conducted protein-ligand docking experiments to evaluate this possibility. Results are consistent with recent clinical findings.METHODS: F420-dependent methylenetetrahydromethanopterin dehydrogenase (mtd), a key methanogenesis enzyme with a known sequence but no tertiary protein structural information, was modeled for two different methanogenic archaea:M. smithiiandMethanopyrus kandleri. Once protein models were developed, ligand-binding sites were identified. Multiple ligands and their respective protonation, isomeric and tautomeric representations were docked into each site, including F420-coenzyme (natural ligand), lactone and β-hydroxyacid forms of lovastatin and simvastatin, and other co-complexed ligands found in related crystal structures.RESULTS: 1) Generally, for each modeled site the lactone form of the statins had more favorable site interactions compared to F420; 2) The statin lactone forms generally had the most favorable docking scores, even relative to the native template PDB ligands; and 3) The statin β-hydroxyacid forms had less favorable docking scores, typically scoring in the middle with some of the F420 tautomeric forms. Consistent with these computational results were those from a recent phase II clinical trial (NCT02495623) with a proprietary, modified-release lovastatin-lactone (SYN-010) in patients with IBS-C, which showed a reduction in symptoms and breath methane levels, compared to placebo.CONCLUSION: The lactone form of lovastatin exhibits preferential binding over the native-F420 coenzyme ligandin silicoand thus could inhibit the activity of the keyM. smithiimethanogenesis enzymemtdin vivo. Statin lactones may thus exert a methane-reducing effect that is distinct from cholesterol lowering activity, which requires HMGR inhibition by statin β-hydroxyacid forms.

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45

Muskal, Steven M., Joe Sliman, John Kokai-Kun, Mark Pimentel, Vince Wacher, and Klaus Gottlieb. "Lovastatin lactone may improve irritable bowel syndrome with constipation (IBS-C) by inhibiting enzymes in the archaeal methanogenesis pathway." F1000Research 5 (April 28, 2016): 606. http://dx.doi.org/10.12688/f1000research.8406.2.

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Methane produced by the methanoarchaeonMethanobrevibacter smithii(M. smithii) has been linked to constipation, irritable bowel syndrome with constipation (IBS-C), and obesity. Lovastatin, which demonstrates a cholesterol-lowering effect by the inhibition of HMG-CoA reductase, may also have an anti-methanogenesis effect through direct inhibition of enzymes in the archaeal methanogenesis pathway. We conducted protein-ligand docking experiments to evaluate this possibility. Results are consistent with recent clinical findings.METHODS: F420-dependent methylenetetrahydromethanopterin dehydrogenase (mtd), a key methanogenesis enzyme was modeled for two different methanogenic archaea:M. smithiiandMethanopyrus kandleri. Once protein models were developed, ligand-binding sites were identified. Multiple ligands and their respective protonation, isomeric and tautomeric representations were docked into each site, including F420-coenzyme (natural ligand), lactone and β-hydroxyacid forms of lovastatin and simvastatin, and other co-complexed ligands found in related crystal structures.RESULTS: 1) Generally, for each modeled site the lactone form of the statins had more favorable site interactions compared to F420; 2) The statin lactone forms generally had the most favorable docking scores, even relative to the native template PDB ligands; and 3) The statin β-hydroxyacid forms had less favorable docking scores, typically scoring in the middle with some of the F420 tautomeric forms. Consistent with these computational results were those from a recent phase II clinical trial (NCT02495623) with a proprietary, modified-release lovastatin-lactone (SYN-010) in patients with IBS-C, which showed a reduction in symptoms and breath methane levels, compared to placebo.CONCLUSION: The lactone form of lovastatin exhibits preferential binding over the native-F420 coenzyme ligandin silicoand thus could inhibit the activity of the keyM. smithiimethanogenesis enzymemtdin vivo. Statin lactones may thus exert a methane-reducing effect that is distinct from cholesterol lowering activity, which requires HMGR inhibition by statin β-hydroxyacid forms.

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46

Muskal, Steven M., Joe Sliman, John Kokai-Kun, Mark Pimentel, Vince Wacher, and Klaus Gottlieb. "Lovastatin lactone may improve irritable bowel syndrome with constipation (IBS-C) by inhibiting enzymes in the archaeal methanogenesis pathway." F1000Research 5 (June 22, 2016): 606. http://dx.doi.org/10.12688/f1000research.8406.3.

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Methane produced by the methanoarchaeonMethanobrevibacter smithii(M. smithii) has been linked to constipation, irritable bowel syndrome with constipation (IBS-C), and obesity. Lovastatin, which demonstrates a cholesterol-lowering effect by the inhibition of HMG-CoA reductase, may also have an anti-methanogenesis effect through direct inhibition of enzymes in the archaeal methanogenesis pathway. We conducted protein-ligand docking experiments to evaluate this possibility. Results are consistent with recent clinical findings.METHODS: F420-dependent methylenetetrahydromethanopterin dehydrogenase (mtd), a key methanogenesis enzyme was modeled for two different methanogenic archaea:M. smithiiandMethanopyrus kandleri. Once protein models were developed, ligand-binding sites were identified. Multiple ligands and their respective protonation, isomeric and tautomeric representations were docked into each site, including F420-coenzyme (natural ligand), lactone and β-hydroxyacid forms of lovastatin and simvastatin, and other co-complexed ligands found in related crystal structures.RESULTS: 1) Generally, for each modeled site the lactone form of the statins had more favorable site interactions compared to F420; 2) The statin lactone forms generally had the most favorable docking scores, even relative to the native template PDB ligands; and 3) The statin β-hydroxyacid forms had less favorable docking scores, typically scoring in the middle with some of the F420 tautomeric forms. Consistent with these computational results were those from a recent phase II clinical trial (NCT02495623) with a proprietary, modified-release lovastatin-lactone (SYN-010) in patients with IBS-C, which showed a reduction in symptoms and breath methane levels, compared to placebo.CONCLUSION: The lactone form of lovastatin exhibits preferential binding over the native-F420 coenzyme ligandin silicoand thus could inhibit the activity of the keyM. smithiimethanogenesis enzymemtdin vivo. Statin lactones may thus exert a methane-reducing effect that is distinct from cholesterol lowering activity, which requires HMGR inhibition by statin β-hydroxyacid forms.

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47

Adhikari, Kamal, I.-Wen Lo, Chun-Liang Chen, Yung-Lin Wang, Kuan-Hung Lin, Saeid Malek Zadeh, Rajesh Rattinam, Yi-Shan Li, Chang-Jer Wu, and Tsung-Lin Li. "Chemoenzymatic Synthesis and Biological Evaluation for Bioactive Molecules Derived from Bacterial Benzoyl Coenzyme A Ligase and Plant Type III Polyketide Synthase." Biomolecules 10, no. 5 (May 9, 2020): 738. http://dx.doi.org/10.3390/biom10050738.

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Plant type III polyketide synthases produce diverse bioactive molecules with a great medicinal significance to human diseases. Here, we demonstrated versatility of a stilbene synthase (STS) from Pinus Sylvestris, which can accept various non-physiological substrates to form unnatural polyketide products. Three enzymes (4-coumarate CoA ligase, malonyl-CoA synthetase and engineered benzoate CoA ligase) along with synthetic chemistry was practiced to synthesize starter and extender substrates for STS. Of these, the crystal structures of benzoate CoA ligase (BadA) from Rhodopseudomonas palustris in an apo form or in complex with a 2-chloro-1,3-thiazole-5-carboxyl-AMP or 2-methylthiazole-5-carboxyl-AMP intermediate were determined at resolutions of 1.57 Å, 1.7 Å, and 2.13 Å, respectively, which reinforces its capacity in production of unusual CoA starters. STS exhibits broad substrate promiscuity effectively affording structurally diverse polyketide products. Seven novel products showed desired cytotoxicity against a panel of cancer cell lines (A549, HCT116, Cal27). With the treatment of two selected compounds, the cancer cells underwent cell apoptosis in a dose-dependent manner. The precursor-directed biosynthesis alongside structure-guided enzyme engineering greatly expands the pharmaceutical repertoire of lead compounds with promising/enhanced biological activities.

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48

Aronson, Benjamin D., Paula D. Ravnikar, and Ronald L. Somerville. "Nucleotide sequence of the 2-amino-3-ketobutyrate coenzyme A ligase (kbl) gene ofE.coli." Nucleic Acids Research 16, no. 8 (1988): 3586. http://dx.doi.org/10.1093/nar/16.8.3586.

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49

Sieweke, Hans-Jürgen, and Eckhard Leistner. "O-succinylbenzoate: Coenzyme a ligase from anthraquinone producing cell suspension cultures of Galium mollugo." Phytochemistry 31, no. 7 (July 1992): 2329–35. http://dx.doi.org/10.1016/0031-9422(92)83275-4.

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50

Parke, Donna, and L. Nicholas Ornston. "Toxicity Caused by Hydroxycinnamoyl-Coenzyme A Thioester Accumulation in Mutants of Acinetobacter sp. Strain ADP1." Applied and Environmental Microbiology 70, no. 5 (May 2004): 2974–83. http://dx.doi.org/10.1128/aem.70.5.2974-2983.2004.

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ABSTRACT Hydroxycinnamates, aromatic compounds that play diverse roles in plants, are dissimilated by enzymes encoded by the hca genes in the nutritionally versatile, naturally transformable bacterium Acinetobacter sp. strain ADP1. A key step in the hca-encoded pathway is activation of the natural substrates caffeate, p-coumarate, and ferulate by an acyl:coenzyme A (acyl:CoA) ligase encoded by hcaC. As described in this paper, Acinetobacter cells with a knockout of the next enzyme in the pathway, hydroxycinnamoyl-CoA hydratase/lyase (HcaA), are extremely sensitive to the presence of the three natural hydroxycinnamate substrates; Escherichia coli cells carrying a subclone with the hcaC gene are hydroxycinnamate sensitive as well. When the hcaA mutation was combined with a mutation in the repressor HcaR, exposure of the doubly mutated Acinetobacter cells to caffeate, p-coumarate, or ferulate at 10−6 M totally inhibited the growth of cells. The toxicity of p-coumarate and ferulate to a ΔhcaA strain was found to be a bacteriostatic effect. Although not toxic to wild-type cells initially, the diphenolic caffeate was itself converted to a toxin over time in the absence of cells; the converted toxin was bactericidal. In an Acinetobacter strain blocked in hcaA, a secondary mutation in the ligase (HcaC) suppresses the toxic effect. Analysis of suppression due to the mutation of hcaC led to the development of a positive-selection strategy that targets mutations blocking HcaC. An hcaC mutation from one isolate was characterized and was found to result in the substitution of an amino acid that is conserved in a functionally characterized homolog of HcaC.

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