Добірка наукової літератури з теми "Propionate Kinase (TdcD)"
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Статті в журналах з теми "Propionate Kinase (TdcD)"
Chittori, Sagar, Dhirendra Kumar Simanshu, Sanchari Banerjee, Ambika Mosale Venkatesh Murthy, Subashini Mathivanan, Handanahal Subbarao Savithri, and Mathur Ramabhadrashastry Narasimha Murthy. "Mechanistic features of Salmonella typhimurium propionate kinase (TdcD): Insights from kinetic and crystallographic studies." Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1834, no. 10 (October 2013): 2036–44. http://dx.doi.org/10.1016/j.bbapap.2013.05.020.
Повний текст джерелаSimanshu, Dhirendra K., and M. R. N. Murthy. "Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of propionate kinase (TdcD) fromSalmonella typhimurium." Acta Crystallographica Section F Structural Biology and Crystallization Communications 61, no. 1 (October 23, 2004): 52–55. http://dx.doi.org/10.1107/s1744309104026429.
Повний текст джерелаSimanshu, Dhirendra K., H. S. Savithri, and M. R. N. Murthy. "Crystal Structures of ADP and AMPPNP-bound Propionate Kinase (TdcD) from Salmonella typhimurium: Comparison with Members of Acetate and Sugar Kinase/Heat Shock Cognate 70/Actin Superfamily." Journal of Molecular Biology 352, no. 4 (September 2005): 876–92. http://dx.doi.org/10.1016/j.jmb.2005.07.069.
Повний текст джерелаДисертації з теми "Propionate Kinase (TdcD)"
Mathivanan, Subashini. "Structural and Functional Studies on Salmonella typhimurium Propionate Kinase and Photorhabdus luminescens Oxalate Decarboxylase." Thesis, 2016. https://etd.iisc.ac.in/handle/2005/4371.
Повний текст джерелаChittori, Sagar. "Metabolic Adaptation For Utilization Of Short-Chain Fatty Acids In Salmonella Typhimurium : Structural And Functional Studies On 2-methylcitrate Synthase, Acetate And Propionate Kinases." Thesis, 2011. https://etd.iisc.ac.in/handle/2005/2209.
Повний текст джерелаList of Publications with Abstract 1. Preliminary X-ray crystallographic studies on acetate kinase (AckA) from Salmonella typhimurium in two crystal forms. Chittori S, Savithri HS, Murthy MR. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Dec 1;67(Pt 12):1658-61. Acetate kinase (AckA) catalyzes the reversible transfer of a phosphate group from acetyl phosphate to ADP, generating acetate and ATP, and plays a central role in carbon metabolism. In the present work, the gene corresponding to AckA from Salmonella typhimurium (StAckA) was cloned in the IPTG-inducible pRSET C vector, resulting in the attachment of a hexahistidine tag to the N-terminus of the expressed enzyme. The recombinant protein was overexpressed, purified and crystallized in two different crystal forms using the microbatch-under-oil method. Form I crystals diffracted to 2.70 Å resolution when examined using X-rays from a rotating-anode X-ray generator and belonged to the monoclinic space group C2, with unit-cell parameters a = 283.16, b = 62.17, c = 91.69 Å, β =93.57°. Form II crystals, which diffracted to a higher resolution of 2.35 Å on the rotating-anode X-ray generator and to 1.90 Å on beamline BM14 of the ESRF, Grenoble, also belonged to space group C2 but with smaller unit-cell parameters (a = 151.01, b = 78.50, c = 97.48 Å, β = 116.37°). Calculation of Matthews coefficients for the two crystal forms suggested the presence of four and two protomers of StAckA in the asymmetric units of forms I and II, respectively. Initial phases for the form I diffraction data were obtained by molecular replacement using the coordinates of Thermotoga maritima AckA (TmAckA) as the search model. The form II structure was phased using a monomer of form I as the phasing model. Inspection of the initial electron-density maps suggests dramatic conformational differences between residues 230 and 300 of the two crystal forms and warrants further investigation. Link for the complete article: http://www.ncbi.nlm.nih.gov/pubmed/22139191 2. Crystal structure of Salmonella typhimurium 2-methylcitrate synthase: Insights on domain movement and substrate specificity. Chittori S, Savithri HS, Murthy MR. J Struct Biol. 2011 Apr;174(1):58-68. 2-Methylcitric acid (2-MCA) cycle is one of the well studied pathways for the utilization of propionate as a source of carbon and energy in bacteria such as Salmonella typhimurium and Escherichia coli. 2-Methylcitrate synthase (2-MCS) catalyzes the conversion of oxaloacetate and propionyl-CoA to 2-methylcitrate and CoA in the second step of 2-MCA cycle. Here, we report the X-ray crystal structure of S. typhimurium 2-MCS (StPrpC) at 2.4Å resolution and its functional characterization. StPrpC was found to utilize propionyl-CoA more efficiently than acetyl-CoA or butyryl-CoA. The polypeptide fold and the catalytic residues of StPrpC are conserved in citrate synthases (CSs) suggesting similarities in their functional mechanisms. In the triclinic P1 cell, StPrpC molecules were organized as decamers composed of five identical dimer units. In solution, StPrpC was in a dimeric form at low concentrations and was converted to larger oligomers at higher concentrations. CSs are usually dimeric proteins. In Gram-negative bacteria, a hexameric form, believed to be important for regulation of activity by NADH, is also observed. Structural comparisons with hexameric E. coli CS suggested that the key residues involved in NADH binding are not conserved in StPrpC. Structural comparison with the ligand free and bound states of CSs showed that StPrpC is in a nearly closed conformation despite the absence of bound ligands. It was found that the Tyr197 and Leu324 of StPrpC are structurally equivalent to the ligand binding residues His and Val, respectively, of CSs. These substitutions might determine the specificities for acyl-CoAs of these enzymes. Link for the complete article: http://www.ncbi.nlm.nih.gov/pubmed/20970504 3. Preliminary X-ray crystallographic analysis of 2-methylcitrate synthase from Salmonella typhimurium. Chittori S, Simanshu DK, Savithri HS, Murthy MR. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Apr 1;66(Pt 4):467-70. Analysis of the genomic sequences of Escherichia coli and Salmonella typhimurium has revealed the presence of several homologues of the well studied citrate synthase (CS). One of these homologues has been shown to code for 2-methylcitrate synthase (2-MCS) activity. 2-MCS catalyzes one of the steps in the 2-methylcitric acid cycle found in these organisms for the degradation of propionate to pyruvate and succinate. In the present work, the gene coding for 2-MCS from S. typhimurium (StPrpC) was cloned in pRSET-C vector and overexpressed in E. coli. The protein was purified to homogeneity using Ni-NTA affinity chromatography. The purified protein was crystallized using the microbatch-under-oil method. The StPrpC crystals diffracted X-rays to 2.4 A resolution and belonged to the triclinic space group P1, with unit-cell parameters a = 92.068, b = 118.159, c = 120.659 A, alpha = 60.84, beta = 67.77, gamma = 81.92 degrees . Computation of rotation functions using the X-ray diffraction data shows that the protein is likely to be a decamer of identical subunits, unlike CSs, which are dimers or hexamers. Link for the complete article: http://www.ncbi.nlm.nih.gov/pubmed/20383024 4. Structure and function of enzymes involved in the anaerobic degradation of L-threonine to propionate. Simanshu DK, Chittori S, Savithri HS, Murthy MR. J Biosci. 2007 Sep;32(6):1195-206. In Escherichia coli and Salmonella typhimurium, L-threonine is cleaved non-oxidatively to propionate via 2-ketobutyrate by biodegradative threonine deaminase, 2-ketobutyrate formate-lyase (or pyruvate formate-lyase), phosphotransacetylase and propionate kinase. In the anaerobic condition, L-threonine is converted to the energy-rich keto acid and this is subsequently catabolised to produce ATP via substrate-level phosphorylation, providing a source of energy to the cells. Most of the enzymes involved in the degradation of L-threonine to propionate are encoded by the anaerobically regulated tdc operon. In the recent past, extensive structural and biochemical studies have been carried out on these enzymes by various groups. Besides detailed structural and functional insights, these studies have also shown the similarities and differences between the other related enzymes present in the metabolic network. In this paper, we review the structural and biochemical studies carried out on these enzymes. Link for the complete article: http://www.ncbi.nlm.nih.gov/pubmed/17954980 5. Structure of the putative mutarotase YeaD from Salmonella typhimurium: structural comparison with galactose mutarotases. Chittori S, Simanshu DK, Savithri HS, Murthy MR. Acta Crystallogr D Biol Crystallogr. 2007 Feb;63(Pt 2):197-205. Salmonella typhimurium YeaD (stYeaD), annotated as a putative aldose 1-epimerase, has a very low sequence identity to other well characterized mutarotases. Sequence analysis suggested that the catalytic residues and a few of the substrate-binding residues of galactose mutarotases (GalMs) are conserved in stYeaD. Determination of the crystal structure of stYeaD in an orthorhombic form at 1.9 A resolution and in a monoclinic form at 2.5 A resolution revealed this protein to adopt the beta-sandwich fold similar to GalMs. Structural comparison of stYeaD with GalMs has permitted the identification of residues involved in catalysis and substrate binding. In spite of the similar fold and conservation of catalytic residues, minor but significant differences were observed in the substrate-binding pocket. These analyses pointed out the possible role of Arg74 and Arg99, found only in YeaD-like proteins, in ligand anchoring and suggested that the specificity of stYeaD may be distinct from those of GalMs. Link for the complete article: http://www.ncbi.nlm.nih.gov/pubmed/17242513 6. Crystallization and preliminary X-ray crystallographic analysis of biodegradative threonine deaminase (TdcB) from Salmonella typhimurium. Simanshu DK, Chittori S, Savithri HS, Murthy MR. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Mar 1;62(Pt 3):275-8. Biodegradative threonine deaminase (TdcB) catalyzes the deamination of L-threonine to alpha-ketobutyrate, the first reaction in the anaerobic breakdown of L-threonine to propionate. Unlike the biosynthetic threonine deaminase, TdcB is insensitive to L-isoleucine and is activated by AMP. Here, the cloning of TdcB (molecular weight 36 kDa) from Salmonella typhimurium with an N-terminal hexahistidine affinity tag and its overexpression in Escherichia coli is reported. TdcB was purified to homogeneity using Ni-NTA affinity column chromatography and crystallized using the hanging-drop vapour-diffusion technique in three different crystal forms. Crystal forms I (unit-cell parameters a = 46.32, b = 55.30, c = 67.24 A, alpha = 103.09, beta = 94.70, gamma = 112.94 degrees) and II (a = 56.68, b = 76.83, c = 78.50 A, alpha = 66.12, beta = 89.16, gamma = 77.08 degrees) belong to space group P1 and contain two and four molecules of TdcB, respectively, in the asymmetric unit. Poorly diffracting form III crystals were obtained in space group C2 and based on the unit-cell volume are most likely to contain one molecule per asymmetric unit. Two complete data sets of resolutions 2.2 A (crystal form I) and 1.7 A (crystal form II) were collected at 100 K using an in-house X-ray source. Link for the complete article: http://www.ncbi.nlm.nih.gov/pubmed/16511321 7. Tyrosine 66 of Pepper vein banding virus genome-linked protein is uridylylated by RNA-dependent RNA polymerase. Anindya R, Chittori S, Savithri HS. Virology. 2005 Jun 5;336(2):154-62. Pepper vein banding virus (PVBV), a member of the genus potyvirus, is a single-stranded positive-sense RNA virus and it primarily infects plants of the family Solanaceae. Genome organization and gene expression strategy of the potyviruses are similar to the picornaviruses, although they infect widely different hosts and have distinctly different morphologies. The genomic RNA of PVBV has a viral genome-linked protein (VPg) at the 5'-terminus and a poly(A) tail at the 3'-terminus. In order to establish the role of VPg in the initiation of replication of the virus, recombinant PVBV NIb and VPg were over-expressed in Escherichia coli and purified under non-denaturing conditions. PVBV NIb was found to be active as polymerase and it could uridylylate the VPg in a template independent manner. N- and C-terminal deletion analysis of VPg revealed that N-terminal 21 and C-terminal 92 residues of PVBV VPg are dispensable for in vitro uridylylation. The amino acid residue uridylylated by PVBV NIb was identified to be Tyr 66 by site-directed mutagenesis. It is possible that in potyviruses, replication begins with uridylylation of VPg which acts as primer for progeny RNA synthesis. Link for the complete article: http://www.ncbi.nlm.nih.gov/pubmed/15892957
Chittori, Sagar. "Metabolic Adaptation For Utilization Of Short-Chain Fatty Acids In Salmonella Typhimurium : Structural And Functional Studies On 2-methylcitrate Synthase, Acetate And Propionate Kinases." Thesis, 2011. http://etd.iisc.ernet.in/handle/2005/2209.
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