Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 74996.70 
• Atom Count: 5235 
• Residue Count: 700 
• Unique protein chains: 2

2FPI

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

• DOI: 10.2210/pdb2FPI/pdb

• Classification: LIGASE
• Organism(s): Sus scrofa
• Expression System: Escherichia coli BL21(DE3)


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

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Experimental Data Snapshot

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

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

• PubMed: 16481318 
• DOI: 10.1074/jbc.M511785200
• Primary Citation of Related Structures:  
  2FPP, 2FPG, 2FP4


• 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. 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.

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Organizational Affiliation: 

Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Succinyl-CoA ligase [GDP-forming] alpha-chain, mitochondrial	A	305	Sus scrofa	Mutation(s): 0  Gene 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
Molecule	Chains	Sequence Length	Organism	Details
Succinyl-CoA ligase [GDP-forming] beta-chain, mitochondrial	B	395	Sus scrofa	Mutation(s): 0  Gene 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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NEP	A	L-PEPTIDE LINKING	C6 H10 N3 O5 P		HIS

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 = 135.790	α = 90.00
b = 135.790	β = 90.00
c = 77.150	γ = 120.00

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

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