2FPG | pdb_00002fpg

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

PDB DOI: https://doi.org/10.2210/pdb2FPG/pdb

Classification: LIGASE
Organism(s): Sus scrofa
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.96 Å
R-Value Free:
0.275 (Depositor), 0.270 (DCC)
R-Value Work:
0.201 (Depositor), 0.200 (DCC)
R-Value Observed:
0.205 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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 Biological Chem 281: 11058-11065

PubMed: 16481318 Search on PubMed
DOI: https://doi.org/10.1074/jbc.M511785200
Primary Citation of Related Structures:
2FP4, 2FPG, 2FPI, 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. 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

Macromolecule Content

Total Structure Weight: 75.3 kDa
Atom Count: 5,265
Modelled Residue Count: 698
Deposited Residue Count: 700
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinyl-CoA ligase [GDP-forming] alpha-chain, mitochondrial	A	305	Sus scrofa	Mutation(s): 0 Gene Names: SUCLG1 EC: 6.2.1.4 (PDB Primary Data), 6.2.1.5 (UniProt)
UniProt
Find proteins for O19069 (Sus scrofa) Explore O19069 Go to UniProtKB: O19069
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O19069
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinyl-CoA ligase [GDP-forming] beta-chain, mitochondrial	B	395	Sus scrofa	Mutation(s): 0 Gene Names: SUCLG2 EC: 6.2.1.4
UniProt
Find proteins for P53590 (Sus scrofa) Explore P53590 Go to UniProtKB: P53590
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53590
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.96 Å
R-Value Free: 0.275 (Depositor), 0.270 (DCC)
R-Value Work: 0.201 (Depositor), 0.200 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.78	α = 90
b = 133.78	β = 90
c = 73.09	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

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
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2024-02-14
Changes: Data collection, Database references, Derived calculations