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PDBsum entry 2fp4

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protein ligands metals Protein-protein interface(s) links
Ligase PDB id
2fp4
Jmol
Contents
Protein chains
305 a.a. *
393 a.a. *
Ligands
GTP ×2
Metals
__K
_MG
Waters ×294
* Residue conservation analysis
PDB id:
2fp4
Name: Ligase
Title: Crystal structure of pig gtp-specific succinyl-coa synthetase in complex with gtp
Structure: Succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial. Chain: a. Synonym: succinyl-coa synthetase, alpha chain, scs-alpha. Engineered: yes. Succinyl-coa ligase [gdp-forming] beta-chain, mitochondrial. Chain: b. Synonym: succinyl-coa synthetase, betag chain, scs-betag,
Source: Sus scrofa. Pig. Organism_taxid: 9823. Gene: suclg1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: suclg2.
Biol. unit: Dimer (from PQS)
Resolution:
2.08Å     R-factor:   0.195     R-free:   0.242
Authors: M.E.Fraser
Key ref:
M.E.Fraser et al. (2006). Interactions of GTP with the ATP-grasp domain of GTP-specific succinyl-CoA synthetase. J Biol Chem, 281, 11058-11065. PubMed id: 16481318 DOI: 10.1074/jbc.M511785200
Date:
15-Jan-06     Release date:   21-Feb-06    
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.
305 a.a.*
Protein chain
Pfam   ArchSchema ?
P53590  (SUCB2_PIG) -  Succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial (Fragment)
Seq:
Struc:
433 a.a.
393 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 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
Bound ligand (Het Group name = GTP)
corresponds exactly
+ 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: 10.1074/jbc.M511785200 J Biol Chem 281:11058-11065 (2006)
PubMed id: 16481318  
 
 
Interactions of GTP with the ATP-grasp domain of GTP-specific succinyl-CoA synthetase.
M.E.Fraser, K.Hayakawa, M.S.Hume, D.G.Ryan, E.R.Brownie.
 
  ABSTRACT  
 
Two isoforms of succinyl-CoA synthetase exist in mammals, one specific for ATP and the other for GTP. The GTP-specific form of pig succinyl-CoA synthetase has been crystallized in the presence of GTP and the structure determined to 2.1 A resolution. GTP is bound in the ATP-grasp domain, where interactions of the guanine base with a glutamine residue (Gln-20beta) and with backbone atoms provide the specificity. The gamma-phosphate interacts with the side chain of an arginine residue (Arg-54beta) and with backbone amide nitrogen atoms, leading to tight interactions between the gamma-phosphate and the protein. This contrasts with the structures of ATP bound to other members of the family of ATP-grasp proteins where the gamma-phosphate is exposed, free to react with the other substrate. To test if GDP would interact with GTP-specific succinyl-CoA synthetase in the same way that ADP interacts with other members of the family of ATP-grasp proteins, the structure of GDP bound to GTP-specific succinyl-CoA synthetase was also determined. A comparison of the conformations of GTP and GDP shows that the bases adopt the same position but that changes in conformation of the ribose moieties and the alpha- and beta-phosphates allow the gamma-phosphate to interact with the arginine residue and amide nitrogen atoms in GTP, while the beta-phosphate interacts with these residues in GDP. The complex of GTP with succinyl-CoA synthetase shows that the enzyme is able to protect GTP from hydrolysis when the active-site histidine residue is not in position to be phosphorylated.
 
  Selected figure(s)  
 
Figure 1.
FIGURE 1. A, ribbon diagram of pig GTP-specific SCS showing the location of the GTP-binding site. The -subunit is green, the -subunit is yellow, except for the T-loop, which is highlighted in magenta. GTP, the potassium ion, and the side chain of the phosphorylated histidine residue, His-259 , are drawn as stick models and colored according to atom type: red for oxygen, yellow for carbon, blue for nitrogen, green for phosphorus, and turquoise for potassium. B, stereo view of the electron density for GTP and the potassium ion, including nearby residues of the ATP-grasp domain of pig GTP-specific SCS. The F[o] - F[c], [c] electron density map calculated without GTP and the potassium ion is contoured at 3 . C, stereo view of the electron density for GDP and the potassium ion, including nearby residues of the ATP-grasp domain of pig GTP-specific SCS. The F[o] - F[c], [c] electron density map calculated without GDP and the potassium ion is contoured at 3 . The same atom colors were used in B and C as described for A. All parts of the figure were drawn using the program RASTER3D (58), and B and C also used the program XFIT (47).
Figure 3.
FIGURE 3. Stereo views of the superpositions of GTP bound to pig GTP-specific SCS (black) with ADP bound to E. coli SCS (gray) (Protein Data Bank (43) identifier 1cqi (7)) (A), GDP bound to pig GTP-specific SCS (gray) (B), and ATP bound to glycinamide ribonucleotide transformylase (gray) (PDB identifier 1kj8) (54) (C). The superpositions were based on structurally similar residues and performed using the program O (51) with a cutoff of 3.8 Å. Possible hydrogen-bonding interactions and ionic interactions between GTP and the pig GTP-specific SCS are represented by black dashed lines.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 11058-11065) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19809498 R.Singh, J.Lemire, R.J.Mailloux, D.Chénier, R.Hamel, and V.D.Appanna (2009).
An ATP and oxalate generating variant tricarboxylic acid cycle counters aluminum toxicity in pseudomonas fluorescens.
  PLoS One, 4, e7344.  
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
  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.  
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.