2SCU

A detailed description of the structure of Succinyl-COA synthetase from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A detailed structural description of Escherichia coli succinyl-CoA synthetase.

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

(1999) J.Mol.Biol. 285: 1633-1653

  • DOI: 10.1006/jmbi.1998.2324

  • PubMed Abstract: 
  • Succinyl-CoA synthetase (SCS) carries out the substrate-level phosphorylation of GDP or ADP in the citric acid cycle. A molecular model of the enzyme from Escherichia coli, crystallized in the presence of CoA, has been refined against data collected ...

    Succinyl-CoA synthetase (SCS) carries out the substrate-level phosphorylation of GDP or ADP in the citric acid cycle. A molecular model of the enzyme from Escherichia coli, crystallized in the presence of CoA, has been refined against data collected to 2.3 A resolution. The crystals are of space group P4322, having unit cell dimensions a=b=98.68 A, c=403.76 A and the data set includes the data measured from 23 crystals. E. coli SCS is an (alphabeta)2-tetramer; there are two copies of each subunit in the asymmetric unit of the crystals. The crystal packing leaves two choices for which pair of alphabeta-dimers form the physiologically relevant tetramer. The copies of the alphabeta-dimer are similar, each having one active site where the phosphorylated histidine residue and the thiol group of CoA are found. CoA is bound in an extended conformation to the nucleotide-binding motif in the N-terminal domain of the alpha-subunit. The phosphoryl group of the phosphorylated histidine residue is positioned at the amino termini of two alpha-helices, one from the C-terminal domain of the alpha-subunit and the other from the C-terminal domain of the beta-subunit. These two domains have similar topologies, despite only 14 % sequence identity. By analogy to other nucleotide-binding proteins, the binding site for the nucleotide may reside in the N-terminal domain of the beta-subunit. If this is so, the catalytic histidine residue would have to move about 35 A to react with the nucleotide.


    Related Citations: 
    • Crystallization of Succinyl-Coa Synthetase from Escherichia Coli
      Wolodko, W.T.,James, M.N.G.,Bridger, W.A.
      (1984) J.Biol.Chem. 259: 5316
    • A Dimeric Form of Escherichia Coli Succinyl-Coa Synthetase Produced by Site- Directed Mutagenesis
      Bailey, D.L.,Fraser, M.E.,Bridger, W.A.,James, M.N.G.,Wolodko, W.T.
      (1999) J.Mol.Biol. 285: 1655
    • The Crystal Structure of Succinyl-Coa Synthetase from Escherichia Coli at 2.5 Angstroms Resolution
      Wolodko, W.T.,Fraser, M.E.,James, M.N.G.,Bridger, W.A.
      (1994) J.Biol.Chem. 269: 10883


    Organizational Affiliation

    Department of Biochemistry, University of Alberta, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (SUCCINYL-COA LIGASE)
A, D
288Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: sucD
EC: 6.2.1.5
Find proteins for P0AGE9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AGE9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (SUCCINYL-COA LIGASE)
B, E
388Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: sucC
EC: 6.2.1.5
Find proteins for P0A836 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A836
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
COA
Query on COA

Download SDF File 
Download CCD File 
A, D
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NEP
Query on NEP
A, D
L-PEPTIDE LINKINGC6 H10 N3 O5 PHIS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.195 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 98.680α = 90.00
b = 98.680β = 90.00
c = 403.760γ = 90.00
Software Package:
Software NamePurpose
BIOMOLdata scaling
WEISdata reduction
KBAPLY)data scaling
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-08-02
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance