1EUD

CRYSTAL STRUCTURE OF PHOSPHORYLATED PIG HEART, GTP-SPECIFIC SUCCINYL-COA SYNTHETASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Phosphorylated and dephosphorylated structures of pig heart, GTP-specific succinyl-CoA synthetase.

Fraser, M.E.James, M.N.Bridger, W.A.Wolodko, W.T.

(2000) J Mol Biol 299: 1325-1339

  • DOI: 10.1006/jmbi.2000.3807
  • Primary Citation of Related Structures:  
    1EUD, 1EUC

  • PubMed Abstract: 
  • Succinyl-CoA synthetase (SCS) catalyzes the reversible phosphorylation/dephosphorylation reaction:¿¿¿rm succinyl ¿hbox ¿-¿CoA+NDP+P_i¿leftrightarrow succinate+CoA+NTP¿¿where N denotes adenosine or guanosine. In the course of the reaction, an essential histidine residue is transiently phosphorylated ...

    Succinyl-CoA synthetase (SCS) catalyzes the reversible phosphorylation/dephosphorylation reaction:¿¿¿rm succinyl ¿hbox ¿-¿CoA+NDP+P_i¿leftrightarrow succinate+CoA+NTP¿¿where N denotes adenosine or guanosine. In the course of the reaction, an essential histidine residue is transiently phosphorylated. We have crystallized and solved the structure of the GTP-specific isoform of SCS from pig heart (EC 6.2.1.4) in both the dephosphorylated and phosphorylated forms. The structures were refined to 2.1 A resolution. In the dephosphorylated structure, the enzyme is stabilized via coordination of a phosphate ion by the active-site histidine residue and the two "power" helices, one contributed by each subunit of the alphabeta-dimer. Small changes in the conformations of residues at the amino terminus of the power helix contributed by the alpha-subunit allow the enzyme to accommodate either the covalently bound phosphoryl group or the free phosphate ion. Structural comparisons are made between the active sites in these two forms of the enzyme, both of which can occur along the catalytic path. Comparisons are also made with the structure of Escherichia coli SCS. The domain that has been shown to bind ADP in E. coli SCS is more open in the pig heart, GTP-specific SCS structure.


    Organizational Affiliation

    Department of Biochemistry, University of Western Ontario, London, Ontario, Canada N6A 5C1.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SUCCINYL-COA SYNTHETASE, ALPHA CHAINA311Sus scrofaMutation(s): 1 
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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SUCCINYL-COA SYNTHETASE, BETA CHAINB396Sus scrofaMutation(s): 3 
Gene Names: SUCLG2
EC: 6.2.1.4
UniProt
Find proteins for P53590 (Sus scrofa)
Explore P53590 
Go to UniProtKB:  P53590
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth B], D [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
NEP
Query on NEP
AL-PEPTIDE LINKINGC6 H10 N3 O5 PHIS
CME
Query on CME
BL-PEPTIDE LINKINGC5 H11 N O3 S2CYS
CSS
Query on CSS
BL-PEPTIDE LINKINGC3 H7 N O2 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.907α = 90
b = 82.278β = 104.37
c = 50.017γ = 90
Software Package:
Software NamePurpose
CNSrefinement
TNTrefinement
WEISdata reduction
WEISdata scaling
BIOMOLdata scaling
KBAPLY)data scaling
TNTphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-07-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description