1SCU

THE CRYSTAL STRUCTURE OF SUCCINYL-COA SYNTHETASE FROM ESCHERICHIA COLI AT 2.5 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The crystal structure of succinyl-CoA synthetase from Escherichia coli at 2.5-A resolution.

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

(1994) J.Biol.Chem. 269: 10883-10890


  • PubMed Abstract: 
  • The x-ray crystal structure of succinyl-CoA synthetase (SCS) from Escherichia coli has been determined by the method of multiple isomorphous replacement to a resolution of 2.5 A. Crystals of SCS are tetragonal with a space group of P4(3)22 and unit c ...

    The x-ray crystal structure of succinyl-CoA synthetase (SCS) from Escherichia coli has been determined by the method of multiple isomorphous replacement to a resolution of 2.5 A. Crystals of SCS are tetragonal with a space group of P4(3)22 and unit cell dimensions of a = b = 98.47 A and c = 400.6 A. One molecule of SCS (142 kDa) is contained in the asymmetric unit. The current model has been refined to a conventional R factor of 21.6% with root mean square deviations from ideal stereochemistry of 0.022 A for bond lengths and 3.25 degrees for bond angles. The quaternary organization of the E. coli enzyme is an alpha 2 beta 2 heterotetramer. In this tetramer, the alpha-subunits interact only with the beta-subunits, whereas the beta-subunits interact to form the dimer of alpha beta-dimers. The two active site pockets are located at regions of contact between alpha- and beta-subunits. One molecule of coenzyme A is bound to each alpha-subunit at a typical nucleotide-binding motif, and His-246 of each alpha-subunit is phosphorylated. This phosphohistidine, a catalytic intermediate, is stabilized by two helix dipoles (the "power" helices), one from each of the two subunit types. A short segment of the beta-subunit from one alpha beta-dimer is in close proximity to the CoA-binding site of the other alpha beta-dimer, providing a possible rationale for the overall tetrameric structure.


    Related Citations: 
    • Crystallization of Succinyl-Coa Synthetase from Escherichia Coli
      Wolodko, W.T.,James, M.N.G.,Bridger, W.A.
      (1984) J.Biol.Chem. 249: 5316


    Organizational Affiliation

    Department of Biochemistry, University of Alberta, Edmonton, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SUCCINYL-COA SYNTHETASE, ALPHA SUBUNIT
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
SUCCINYL-COA SYNTHETASE, BETA SUBUNIT
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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: 2.5 Å
  • R-Value Work: 0.216 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 98.470α = 90.00
b = 98.470β = 90.00
c = 400.600γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-04-20
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-07-17
    Type: Data collection, Derived calculations, Other, Refinement description
  • Version 1.4: 2019-08-14
    Type: Data collection, Refinement description