2FP4

Crystal structure of pig GTP-specific succinyl-CoA synthetase in complex with GTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Interactions of GTP with the ATP-grasp Domain of GTP-specific Succinyl-CoA Synthetase

Fraser, M.E.Hayakawa, K.Hume, M.S.Ryan, D.G.Brownie, E.R.

(2006) J Biol Chem 281: 11058-11065

  • DOI: 10.1074/jbc.M511785200
  • Primary Citation of Related Structures:  
    2FP4, 2FPP, 2FPI, 2FPG

  • PubMed 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 ...

    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.


    Organizational Affiliation

    Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada. frasm@ucalgary.ca



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Succinyl-CoA ligase [GDP-forming] alpha-chain, mitochondrialA305Sus scrofaMutation(s): 1 
Gene Names: SUCLG1
EC: 6.2.1.4 (PDB Primary Data), 6.2.1.5 (UniProt)
Find proteins for O19069 (Sus scrofa)
Explore O19069 
Go to UniProtKB:  O19069
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Succinyl-CoA ligase [GDP-forming] beta-chain, mitochondrialB395Sus scrofaMutation(s): 0 
Gene Names: SUCLG2
EC: 6.2.1.4
Find proteins for P53590 (Sus scrofa)
Explore P53590 
Go to UniProtKB:  P53590
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
E [auth B], F [auth B]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
C [auth B]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NEP
Query on NEP
AL-PEPTIDE LINKINGC6 H10 N3 O5 PHIS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.214 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.61α = 90
b = 132.61β = 90
c = 72.53γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2006-01-15 
  • Released Date: 2006-02-21 
  • Deposition Author(s): Fraser, M.E.

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-21
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance