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PDBsum entry 1cqi

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protein ligands metals Protein-protein interface(s) links
Ligase PDB id
1cqi
Jmol
Contents
Protein chains
286 a.a. *
385 a.a. *
Ligands
PO4 ×2
COA ×2
ADP ×2
Metals
_MG ×2
* Residue conservation analysis
PDB id:
1cqi
Name: Ligase
Title: Crystal structure of the complex of adp and mg2+ with dephosphorylated e. Coli succinyl-coa synthetase
Structure: Protein (succinyl-coa synthetase alpha chain). Chain: a, d. Fragment: alpha subunit. Synonym: scs-alpha. Engineered: yes. Protein (succinyl-coa synthetase beta chain). Chain: b, e. Fragment: beta subunit. Synonym: scs-beta.
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
3.30Å     R-factor:   0.191     R-free:   0.247
Authors: M.A.Joyce,M.E.Fraser,M.N.G.James,W.A.Bridger,W.T.Wolodko
Key ref:
M.A.Joyce et al. (2000). ADP-binding site of Escherichia coli succinyl-CoA synthetase revealed by x-ray crystallography. Biochemistry, 39, 17-25. PubMed id: 10625475 DOI: 10.1021/bi991696f
Date:
06-Aug-99     Release date:   07-Jan-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0AGE9  (SUCD_ECOLI) -  Succinyl-CoA ligase [ADP-forming] subunit alpha
Seq:
Struc:
289 a.a.
286 a.a.
Protein chains
Pfam   ArchSchema ?
P0A836  (SUCC_ECOLI) -  Succinyl-CoA ligase [ADP-forming] subunit beta
Seq:
Struc:
388 a.a.
385 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, D, E: 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
Bound ligand (Het Group name = PO4)
corresponds exactly
+
succinyl-CoA
Bound ligand (Het Group name = COA)
matches with 87.00% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     11 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi991696f Biochemistry 39:17-25 (2000)
PubMed id: 10625475  
 
 
ADP-binding site of Escherichia coli succinyl-CoA synthetase revealed by x-ray crystallography.
M.A.Joyce, M.E.Fraser, M.N.James, W.A.Bridger, W.T.Wolodko.
 
  ABSTRACT  
 
Succinyl-CoA synthetase (SCS) catalyzes the following reversible reaction via a phosphorylated histidine intermediate (His 246alpha): succinyl-CoA + P(i) + NDP <--> succinate + CoA + NTP (N denotes adenosine or guanosine). To determine the structure of the enzyme with nucleotide bound, crystals of phosphorylated Escherichia coli SCS were soaked in successive experiments adopting progressive strategies. In the first experiment, 1 mM ADP (>15 x K(d)) was added; Mg(2+) ions were omitted to preclude the formation of an insoluble precipitate with the phosphate and ammonium ions. X-ray crystallography revealed that the enzyme was dephosphorylated, but the nucleotide did not remain bound to the enzyme (R(working) = 17.2%, R(free) = 22.8% for data to 2.9 A resolution). Catalysis requires Mg(2+) ions; hence, the "true" nucleotide substrate is probably an ADP-Mg(2+) complex. In the successful experiment, the phosphate buffer was exchanged with MOPS, the concentration of sulfate ions was lowered, and the concentrations of ADP and Mg(2+) ions were increased to 10.5 and 50 mM, respectively. X-ray diffraction data revealed an ADP-Mg(2+) complex bound in the ATP-grasp fold of the N-terminal domain of each beta-subunit (R(working) = 19.1%, R(free) = 24.7% for data to 3.3 A resolution). We describe the specific interactions of the nucleotide-Mg(2+) complex with SCS, compare these results with those for other proteins containing the ATP-grasp fold, and present a hypothetical model of the histidine-containing loop in the "down" position where it can interact with the nucleotide approximately 35 A from where His 246alpha is seen in both phosphorylated and dephosphorylated SCS.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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.  
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
16952946 W.Kim, and F.R.Tabita (2006).
Both subunits of ATP-citrate lyase from Chlorobium tepidum contribute to catalytic activity.
  J Bacteriol, 188, 6544-6552.  
15101981 M.Aoshima, M.Ishii, and Y.Igarashi (2004).
A novel enzyme, citryl-CoA synthetase, catalysing the first step of the citrate cleavage reaction in Hydrogenobacter thermophilus TK-6.
  Mol Microbiol, 52, 751-761.  
14718657 M.Kothe, and S.G.Powers-Lee (2004).
Nucleotide recognition in the ATP-grasp protein carbamoyl phosphate synthetase.
  Protein Sci, 13, 466-475.  
12135479 T.Kanao, T.Fukui, H.Atomi, and T.Imanaka (2002).
Kinetic and biochemical analyses on the reaction mechanism of a bacterial ATP-citrate lyase.
  Eur J Biochem, 269, 3409-3416.  
11389851 H.Yamaguchi, M.Matsushita, A.C.Nairn, and J.Kuriyan (2001).
Crystal structure of the atypical protein kinase domain of a TRP channel with phosphotransferase activity.
  Mol Cell, 7, 1047-1057.
PDB codes: 1ia9 1iah 1iaj
11248686 T.Kanao, T.Fukui, H.Atomi, and T.Imanaka (2001).
ATP-citrate lyase from the green sulfur bacterium Chlorobium limicola is a heteromeric enzyme composed of two distinct gene products.
  Eur J Biochem, 268, 1670-1678.  
11063569 J.L.Brosius, and R.F.Colman (2000).
A key role in catalysis for His89 of adenylosuccinate lyase of Bacillus subtilis.
  Biochemistry, 39, 13336-13343.  
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 codes are shown on the right.