2scu › Citations

A detailed structural description of Escherichia coli succinyl-CoA synthetase.

Fraser ME, James MN, Bridger WA, Wolodko WT
J Mol Biol 285 1633-53 (1999)
Cited: 50 times
EuropePMC logo PMID: 9917402

Abstract

Succinyl-CoA synthetase (SCS) carries out the substrate-level phosphorylation of GDP or ADP in the citric acid cycle. A molecular model of the enzyme from Escherichia coli, crystallized in the presence of CoA, has been refined against data collected to 2.3 A resolution. The crystals are of space group P4322, having unit cell dimensions a=b=98.68 A, c=403.76 A and the data set includes the data measured from 23 crystals. E. coli SCS is an (alphabeta)2-tetramer; there are two copies of each subunit in the asymmetric unit of the crystals. The crystal packing leaves two choices for which pair of alphabeta-dimers form the physiologically relevant tetramer. The copies of the alphabeta-dimer are similar, each having one active site where the phosphorylated histidine residue and the thiol group of CoA are found. CoA is bound in an extended conformation to the nucleotide-binding motif in the N-terminal domain of the alpha-subunit. The phosphoryl group of the phosphorylated histidine residue is positioned at the amino termini of two alpha-helices, one from the C-terminal domain of the alpha-subunit and the other from the C-terminal domain of the beta-subunit. These two domains have similar topologies, despite only 14 % sequence identity. By analogy to other nucleotide-binding proteins, the binding site for the nucleotide may reside in the N-terminal domain of the beta-subunit. If this is so, the catalytic histidine residue would have to move about 35 A to react with the nucleotide.

Reviews - 2scu mentioned but not cited (1)

  1. Principles and characteristics of biological assemblies in experimentally determined protein structures. Xu Q, Dunbrack RL. Curr Opin Struct Biol 55 34-49 (2019)

Articles - 2scu mentioned but not cited (3)

  1. Identification of the citrate-binding site of human ATP-citrate lyase using X-ray crystallography. Sun T, Hayakawa K, Bateman KS, Fraser ME. J Biol Chem 285 27418-27428 (2010)
  2. Structure of GTP-specific succinyl-CoA synthetase in complex with CoA. Huang J, Malhi M, Deneke J, Fraser ME. Acta Crystallogr F Struct Biol Commun 71 1067-1071 (2015)
  3. Modelling and Recognition of Protein Contact Networks by Multiple Kernel Learning and Dissimilarity Representations. Martino A, De Santis E, Giuliani A, Rizzi A. Entropy (Basel) 22 E794 (2020)


Reviews citing this publication (9)

  1. Metabolic control and regulation of the tricarboxylic acid cycle in photosynthetic and heterotrophic plant tissues. Araújo WL, Nunes-Nesi A, Nikoloski Z, Sweetlove LJ, Fernie AR. Plant Cell Environ 35 1-21 (2012)
  2. Acylation of Biomolecules in Prokaryotes: a Widespread Strategy for the Control of Biological Function and Metabolic Stress. Hentchel KL, Escalante-Semerena JC. Microbiol Mol Biol Rev 79 321-346 (2015)
  3. The disulfide proteome and other reactive cysteine proteomes: analysis and functional significance. Lindahl M, Mata-Cabana A, Kieselbach T. Antioxid Redox Signal 14 2581-2642 (2011)
  4. The enzymes of oxalate metabolism: unexpected structures and mechanisms. Svedruzić D, Jónsson S, Toyota CG, Reinhardt LA, Ricagno S, Lindqvist Y, Richards NG. Arch Biochem Biophys 433 176-192 (2005)
  5. Histidine kinases and two-component signal transduction systems. Pirrung MC. Chem Biol 6 R167-75 (1999)
  6. The use of hyperpolarized carbon-13 magnetic resonance for molecular imaging. Siddiqui S, Kadlecek S, Pourfathi M, Xin Y, Mannherz W, Hamedani H, Drachman N, Ruppert K, Clapp J, Rizi R. Adv Drug Deliv Rev 113 3-23 (2017)
  7. Mitochondrial encephalomyopathy and retinoblastoma explained by compound heterozygosity of SUCLA2 point mutation and 13q14 deletion. Matilainen S, Isohanni P, Euro L, Lönnqvist T, Pihko H, Kivelä T, Knuutila S, Suomalainen A. Eur J Hum Genet 23 325-330 (2015)
  8. Bacterial protein complexes investigation using blue native PAGE. Dresler J, Klimentova J, Stulik J. Microbiol Res 166 47-62 (2011)
  9. Succinyl-CoA Synthetase Dysfunction as a Mechanism of Mitochondrial Encephalomyopathy: More than Just an Oxidative Energy Deficit. Lancaster MS, Graham BH. Int J Mol Sci 24 10725 (2023)

Articles citing this publication (37)

  1. Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition. Silva JC, Gorenstein MV, Li GZ, Vissers JP, Geromanos SJ. Mol Cell Proteomics 5 144-156 (2006)
  2. Protein thiol modifications visualized in vivo. Leichert LI, Jakob U. PLoS Biol 2 e333 (2004)
  3. Molecular characterization of a heteromeric ATP-citrate lyase that generates cytosolic acetyl-coenzyme A in Arabidopsis. Fatland BL, Ke J, Anderson MD, Mentzen WI, Cui LW, Allred CC, Johnston JL, Nikolau BJ, Wurtele ES. Plant Physiol 130 740-756 (2002)
  4. The geometry of domain combination in proteins. Bashton M, Chothia C. J Mol Biol 315 927-939 (2002)
  5. A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis. Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M. Electrophoresis 27 3306-3321 (2006)
  6. Early lateral transfer of genes encoding malic enzyme, acetyl-CoA synthetase and alcohol dehydrogenases from anaerobic prokaryotes to Entamoeba histolytica. Field J, Rosenthal B, Samuelson J. Mol Microbiol 38 446-455 (2000)
  7. An allosteric mechanism for potent inhibition of human ATP-citrate lyase. Wei J, Leit S, Kuai J, Therrien E, Rafi S, Harwood HJ, DeLaBarre B, Tong L. Nature 568 566-570 (2019)
  8. Proteomics in Myzus persicae: effect of aphid host plant switch. Francis F, Gerkens P, Harmel N, Mazzucchelli G, De Pauw E, Haubruge E. Insect Biochem Mol Biol 36 219-227 (2006)
  9. Structures of the noncanonical RNA ligase RtcB reveal the mechanism of histidine guanylylation. Desai KK, Bingman CA, Phillips GN, Raines RT. Biochemistry 52 2518-2525 (2013)
  10. Phosphorylated and dephosphorylated structures of pig heart, GTP-specific succinyl-CoA synthetase. Fraser ME, James MN, Bridger WA, Wolodko WT. J Mol Biol 299 1325-1339 (2000)
  11. Reaction mechanism and structural model of ADP-forming Acetyl-CoA synthetase from the hyperthermophilic archaeon Pyrococcus furiosus: evidence for a second active site histidine residue. Bräsen C, Schmidt M, Grötzinger J, Schönheit P. J Biol Chem 283 15409-15418 (2008)
  12. A novel ADP-forming succinyl-CoA synthetase in Thermococcus kodakaraensis structurally related to the archaeal nucleoside diphosphate-forming acetyl-CoA synthetases. Shikata K, Fukui T, Atomi H, Imanaka T. J Biol Chem 282 26963-26970 (2007)
  13. Identification and characterisation of the alpha and beta subunits of succinyl CoA ligase of tomato. Studart-Guimarães C, Gibon Y, Frankel N, Wood CC, Zanor MI, Fernie AR, Carrari F. Plant Mol Biol 59 781-791 (2005)
  14. Identification of (eta6-arene)ruthenium(II) protein binding sites in E. coli cells by combined multidimensional liquid chromatography and ESI tandem mass spectrometry: specific binding of [(eta6-p-cymene)RuCl2 (DMSO)] to stress-regulated proteins and to helicases. Will J, Kyas A, Sheldrick WS, Wolters D. J Biol Inorg Chem 12 883-894 (2007)
  15. Analysis of the Flavobacterium psychrophilum outer-membrane subproteome and identification of new antigenic targets for vaccine by immunomics. Dumetz F, Duchaud E, Claverol S, Orieux N, Papillon S, Lapaillerie D, Le Hénaff M. Microbiology (Reading) 154 1793-1801 (2008)
  16. Structure of the RNA 3'-phosphate cyclase-adenylate intermediate illuminates nucleotide specificity and covalent nucleotidyl transfer. Tanaka N, Smith P, Shuman S. Structure 18 449-457 (2010)
  17. Structure of NDP-forming Acetyl-CoA synthetase ACD1 reveals a large rearrangement for phosphoryl transfer. Weiße RH, Faust A, Schmidt M, Schönheit P, Scheidig AJ. Proc Natl Acad Sci U S A 113 E519-28 (2016)
  18. Structural basis for the binding of succinate to succinyl-CoA synthetase. Huang J, Fraser ME. Acta Crystallogr D Struct Biol 72 912-921 (2016)
  19. Binding of hydroxycitrate to human ATP-citrate lyase. Hu J, Komakula A, Fraser ME. Acta Crystallogr D Struct Biol 73 660-671 (2017)
  20. Crystal structure of a lysine biosynthesis enzyme, LysX, from Thermus thermophilus HB8. Sakai H, Vassylyeva MN, Matsuura T, Sekine Si, Gotoh K, Nishiyama M, Terada T, Shirouzu M, Kuramitsu S, Vassylyev DG, Yokoyama S. J Mol Biol 332 729-740 (2003)
  21. Novel characteristics of succinate coenzyme A (Succinate-CoA) ligases: conversion of malate to malyl-CoA and CoA-thioester formation of succinate analogues in vitro. Nolte JC, Schürmann M, Schepers CL, Vogel E, Wübbeler JH, Steinbüchel A. Appl Environ Microbiol 80 166-176 (2014)
  22. Both subunits of ATP-citrate lyase from Chlorobium tepidum contribute to catalytic activity. Kim W, Tabita FR. J Bacteriol 188 6544-6552 (2006)
  23. Identification of the kinetic mechanism of succinyl-CoA synthetase. Li X, Wu F, Beard DA. Biosci Rep 33 145-163 (2013)
  24. X-ray crystal structure of teicoplanin A₂-2 bound to a catalytic peptide sequence via the carrier protein strategy. Han S, Le BV, Hajare HS, Baxter RH, Miller SJ. J Org Chem 79 8550-8556 (2014)
  25. Evolutionary Changes after Translational Challenges Imposed by Horizontal Gene Transfer. Bedhomme S, Amorós-Moya D, Valero LM, Bonifaci N, Pujana MÀ, Bravo IG. Genome Biol Evol 11 814-831 (2019)
  26. Sample preparation for two-dimensional blue native/SDS polyacrylamide gel electrophoresis in the identification of Streptomyces coelicolor cytoplasmic protein complexes. Wang ZJ, Xu XP, Fan KQ, Jia CJ, Yang KQ. J Biochem Biophys Methods 70 565-572 (2007)
  27. Biochemical and kinetic characterization of the recombinant ADP-forming acetyl coenzyme A synthetase from the amitochondriate protozoan Entamoeba histolytica. Jones CP, Ingram-Smith C. Eukaryot Cell 13 1530-1537 (2014)
  28. A positive selection approach identifies residues important for folding of Salmonella enterica Pat, an N(ε)-lysine acetyltransferase that regulates central metabolism enzymes. Thao S, Escalante-Semerena JC. Res Microbiol 163 427-435 (2012)
  29. Identification of the active site residues in ATP-citrate lyase's carboxy-terminal portion. Nguyen VH, Singh N, Medina A, Usón I, Fraser ME. Protein Sci 28 1840-1849 (2019)
  30. Nucleotide recognition in the ATP-grasp protein carbamoyl phosphate synthetase. Kothe M, Powers-Lee SG. Protein Sci 13 466-475 (2004)
  31. Potential Role of Acetyl-CoA Synthetase (acs) and Malate Dehydrogenase (mae) in the Evolution of the Acetate Switch in Bacteria and Archaea. Barnhart EP, McClure MA, Johnson K, Cleveland S, Hunt KA, Fields MW. Sci Rep 5 12498 (2015)
  32. Tartryl-CoA inhibits succinyl-CoA synthetase. Huang J, Fraser ME. Acta Crystallogr F Struct Biol Commun 76 302-308 (2020)
  33. Natural Selection in Virulence Genes of Francisella tularensis. Gunnell MK, Robison RA, Adams BJ. J Mol Evol 82 264-278 (2016)
  34. Second distinct conformation of the phosphohistidine loop in succinyl-CoA synthetase. Huang J, Fraser ME. Acta Crystallogr D Struct Biol 77 357-368 (2021)
  35. Investigating the mechanism of ADP-forming acetyl-CoA synthetase from the protozoan parasite Entamoeba histolytica. Jones CP, Khan K, Ingram-Smith C. FEBS Lett 591 603-612 (2017)
  36. Structural basis of CoA recognition by the Pyrococcus single-domain CoA-binding proteins. Hiyama TB, Zhao M, Kitago Y, Yao M, Sekine S, Terada T, Kuroishi C, Liu ZJ, Rose JP, Kuramitsu S, Shirouzu M, Watanabe N, Yokoyama S, Tanaka I, Wang BC. J Struct Funct Genomics 7 119-129 (2006)
  37. mRNA levels of tricarboxylic acid cycle genes in Streptomyces coelicolor M145 cultured on glucose. Takahashi-Iñiguez T, Flores ME. Mol Biol Rep 50 719-730 (2023)


Related citations provided by authors (3)

  1. The Crystal Structure of Succinyl-Coa Synthetase from Escherichia Coli at 2.5 Angstroms Resolution. Wolodko WT, Fraser ME, James MNG, Bridger WA J. Biol. Chem. 269 10883-10890 (1994)
  2. Crystallization of Succinyl-Coa Synthetase from Escherichia Coli. Wolodko WT, James MNG, Bridger WA J. Biol. Chem. 259 5316- (1984)
  3. A Dimeric Form of Escherichia Coli Succinyl-Coa Synthetase Produced by Site- Directed Mutagenesis. Bailey DL, Fraser ME, Bridger WA, James MNG, Wolodko WT J. Mol. Biol. 285 1655-1666 (1999)

Quick links