2FPI

Crystal structure of pig GTP-specific succinyl-CoA synthetase from polyethylene glycol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.3 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, 2FPG, 2FPP

  • 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. ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Succinyl-CoA ligase [GDP-forming] alpha-chain, mitochondrial
A
305Sus scrofaGene Names: SUCLG1
EC: 6.2.1.4, 6.2.1.5
Find proteins for O19069 (Sus scrofa)
Go to Gene View: SUCLG1
Go to UniProtKB:  O19069
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Succinyl-CoA ligase [GDP-forming] beta-chain, mitochondrial
B
395Sus scrofaGene Names: SUCLG2
EC: 6.2.1.4
Find proteins for P53590 (Sus scrofa)
Go to Gene View: SUCLG2
Go to UniProtKB:  P53590
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NEP
Query on NEP
A
L-PEPTIDE LINKINGC6 H10 N3 O5 PHIS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.215 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 135.790α = 90.00
b = 135.790β = 90.00
c = 77.150γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-01-16 
  • Released Date: 2006-02-21 
  • Deposition Author(s): Fraser, M.E.

Revision History 

  • Version 1.0: 2006-02-21
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description