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PDBsum entry 1eud

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protein ligands Protein-protein interface(s) links
Ligase PDB id
1eud
Jmol
Contents
Protein chains
306 a.a. *
395 a.a. *
Ligands
SO4 ×2
Waters ×188
* Residue conservation analysis
PDB id:
1eud
Name: Ligase
Title: Crystal structure of phosphorylated pig heart, gtp-specific succinyl-coa synthetase
Structure: Succinyl-coa synthetase, alpha chain. Chain: a. Synonym: scs-alpha. Engineered: yes. Succinyl-coa synthetase, beta chain. Chain: b. Synonym: scs-beta. Engineered: yes. Mutation: yes
Source: Sus scrofa. Pig. Organism_taxid: 9823. Tissue: heart. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.10Å     R-factor:   0.156     R-free:   0.215
Authors: M.E.Fraser,M.N.G.James,W.A.Bridger,W.T.Wolodko
Key ref:
M.E.Fraser et al. (2000). Phosphorylated and dephosphorylated structures of pig heart, GTP-specific succinyl-CoA synthetase. J Mol Biol, 299, 1325-1339. PubMed id: 10873456 DOI: 10.1006/jmbi.2000.3807
Date:
14-Apr-00     Release date:   27-Jul-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O19069  (SUCA_PIG) -  Succinyl-CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial
Seq:
Struc:
346 a.a.
306 a.a.*
Protein chain
Pfam   ArchSchema ?
P53590  (SUCB2_PIG) -  Succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial (Fragment)
Seq:
Struc:
433 a.a.
395 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 1: Chains A, B: E.C.6.2.1.4  - Succinate--CoA ligase (GDP-forming).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Citric acid cycle
      Reaction: GTP + succinate + CoA = GDP + phosphate + succinyl-CoA
GTP
+ succinate
+ CoA
= GDP
+ phosphate
+ succinyl-CoA
   Enzyme class 2: Chain A: E.C.6.2.1.5  - Succinate--CoA ligase (ADP-forming).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + succinate + CoA = ADP + phosphate + succinyl-CoA
ATP
+ succinate
+ CoA
= ADP
+ phosphate
+ succinyl-CoA
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     mitochondrion   1 term 
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     9 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.2000.3807 J Mol Biol 299:1325-1339 (2000)
PubMed id: 10873456  
 
 
Phosphorylated and dephosphorylated structures of pig heart, GTP-specific succinyl-CoA synthetase.
M.E.Fraser, M.N.James, W.A.Bridger, W.T.Wolodko.
 
  ABSTRACT  
 
Succinyl-CoA synthetase (SCS) catalyzes the reversible phosphorylation/dephosphorylation reaction:¿¿¿rm succinyl ¿hbox ¿-¿CoA+NDP+P_i¿leftrightarrow succinate+CoA+NTP¿¿where N denotes adenosine or guanosine. In the course of the reaction, an essential histidine residue is transiently phosphorylated. We have crystallized and solved the structure of the GTP-specific isoform of SCS from pig heart (EC 6.2.1.4) in both the dephosphorylated and phosphorylated forms. The structures were refined to 2.1 A resolution. In the dephosphorylated structure, the enzyme is stabilized via coordination of a phosphate ion by the active-site histidine residue and the two "power" helices, one contributed by each subunit of the alphabeta-dimer. Small changes in the conformations of residues at the amino terminus of the power helix contributed by the alpha-subunit allow the enzyme to accommodate either the covalently bound phosphoryl group or the free phosphate ion. Structural comparisons are made between the active sites in these two forms of the enzyme, both of which can occur along the catalytic path. Comparisons are also made with the structure of Escherichia coli SCS. The domain that has been shown to bind ADP in E. coli SCS is more open in the pig heart, GTP-specific SCS structure.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Pig heart, GTP-specific SCS. In this three-dimensional ribbon diagram, the a-subunit is white, with light gray for the interior of the helices, and the side-chain of the active site phosphohistidine residue is shown as a ball-and-stick model; the b-subunit is shaded gray, as are the two sulfate ions. The amino and carboxy termini of each subunit are labeled N and C, respectively. This Figure and Figure 2 and Figure 7 were drawn using the program MOLSCRIPT (Kraulis, 1991).
Figure 2.
Figure 2. Stereo diagrams of the regions surrounding the active-site histidine residue. The residues are shown as ball-and-stick models. Hydrogen-bonding interactions with the oxygen atoms of the phosphate ion or the phosporyl group are represented by broken lines. (a) Dephosphorylated pig heart, GTP-specific SCS. (b) Phosphorylated pig heart, GTP-specific SCS.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 299, 1325-1339) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20399182 N.Tanaka, P.Smith, and S.Shuman (2010).
Structure of the RNA 3'-phosphate cyclase-adenylate intermediate illuminates nucleotide specificity and covalent nucleotidyl transfer.
  Structure, 18, 449-457.
PDB code: 3kgd
19527071 D.Phillips, A.M.Aponte, S.A.French, D.J.Chess, and R.S.Balaban (2009).
Succinyl-CoA synthetase is a phosphate target for the activation of mitochondrial metabolism.
  Biochemistry, 48, 7140-7149.  
19627098 Y.Chen, J.Jakoncic, K.A.Parker, N.Carpino, and N.Nassar (2009).
Structures of the phosphorylated and VO(3)-bound 2H-phosphatase domain of Sts-2.
  Biochemistry, 48, 8129-8135.  
18372246 C.Bräsen, M.Schmidt, J.Grötzinger, and P.Schönheit (2008).
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.
  J Biol Chem, 283, 15409-15418.  
18433294 J.R.Hughes, A.M.Meireles, K.H.Fisher, A.Garcia, P.R.Antrobus, A.Wainman, N.Zitzmann, C.Deane, H.Ohkura, and J.G.Wakefield (2008).
A microtubule interactome: complexes with roles in cell cycle and mitosis.
  PLoS Biol, 6, e98.  
18452512 K.Hamblin, D.M.Standley, M.B.Rogers, A.Stechmann, A.J.Roger, R.Maytum, and M.van der Giezen (2008).
Localization and nucleotide specificity of Blastocystis succinyl-CoA synthetase.
  Mol Microbiol, 68, 1395-1405.  
17642514 E.Hidber, E.R.Brownie, K.Hayakawa, and M.E.Fraser (2007).
Participation of Cys123alpha of Escherichia coli succinyl-CoA synthetase in catalysis.
  Acta Crystallogr D Biol Crystallogr, 63, 876-884.
PDB codes: 2nu6 2nu7 2nu8 2nu9 2nua
17640871 K.Shikata, T.Fukui, H.Atomi, and T.Imanaka (2007).
A novel ADP-forming succinyl-CoA synthetase in Thermococcus kodakaraensis structurally related to the archaeal nucleoside diphosphate-forming acetyl-CoA synthetases.
  J Biol Chem, 282, 26963-26970.  
  17565180 M.A.Joyce, E.R.Brownie, K.Hayakawa, and M.E.Fraser (2007).
Cloning, expression, purification, crystallization and preliminary X-ray analysis of Thermus aquaticus succinyl-CoA synthetase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 399-402.  
17403370 R.G.Kibbey, R.L.Pongratz, A.J.Romanelli, C.B.Wollheim, G.W.Cline, and G.I.Shulman (2007).
Mitochondrial GTP regulates glucose-stimulated insulin secretion.
  Cell Metab, 5, 253-264.  
16737961 J.S.Lott, B.Paget, J.M.Johnston, L.T.Delbaere, J.A.Sigrell-Simon, M.J.Banfield, and E.N.Baker (2006).
The structure of an ancient conserved domain establishes a structural basis for stable histidine phosphorylation and identifies a new family of adenosine-specific kinases.
  J Biol Chem, 281, 22131-22141.
PDB codes: 1wvq 2gl0
16481318 M.E.Fraser, K.Hayakawa, M.S.Hume, D.G.Ryan, and E.R.Brownie (2006).
Interactions of GTP with the ATP-grasp domain of GTP-specific succinyl-CoA synthetase.
  J Biol Chem, 281, 11058-11065.
PDB codes: 2fp4 2fpg 2fpi 2fpp
16990267 R.D.Busam, A.G.Thorsell, A.Flores, M.Hammarström, C.Persson, and B.M.Hallberg (2006).
First structure of a eukaryotic phosphohistidine phosphatase.
  J Biol Chem, 281, 33830-33834.
PDB code: 2hw4
14718657 M.Kothe, and S.G.Powers-Lee (2004).
Nucleotide recognition in the ATP-grasp protein carbamoyl phosphate synthetase.
  Protein Sci, 13, 466-475.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.