2SCU

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.195 

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This is version 1.3 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: https://doi.org/10.1006/jmbi.1998.2324
  • Primary Citation of Related Structures:  
    2SCU

  • 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 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.


  • Organizational Affiliation

    Department of Biochemistry, University of Alberta, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (SUCCINYL-COA LIGASE)A,
C [auth D]
288Escherichia coliMutation(s): 1 
EC: 6.2.1.5
UniProt
Find proteins for P0AGE9 (Escherichia coli (strain K12))
Explore P0AGE9 
Go to UniProtKB:  P0AGE9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AGE9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (SUCCINYL-COA LIGASE)B,
D [auth E]
388Escherichia coliMutation(s): 0 
EC: 6.2.1.5
UniProt
Find proteins for P0A836 (Escherichia coli (strain K12))
Explore P0A836 
Go to UniProtKB:  P0A836
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A836
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.195 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.68α = 90
b = 98.68β = 90
c = 403.76γ = 90
Software Package:
Software NamePurpose
TNTrefinement
WEISdata reduction
BIOMOLdata scaling
KBAPLY)data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-08-02
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations