3K6M

Dynamic domains of Succinyl-CoA:3-ketoacid-coenzyme A transferase from pig heart.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The high-resolution structure of pig heart succinyl-CoA:3-oxoacid coenzyme A transferase.

Coker, S.F.Lloyd, A.J.Mitchell, E.Lewis, G.R.Coker, A.R.Shoolingin-Jordan, P.M.

(2010) Acta Crystallogr D Biol Crystallogr 66: 797-805

  • DOI: 10.1107/S0907444910018366
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The enzyme succinyl-CoA:3-oxoacid coenzyme A transferase (SCOT) participates in the metabolism of ketone bodies in extrahepatic tissues. It catalyses the transfer of coenzyme A (CoA) from succinyl-CoA to acetoacetate with a classical ping-pong mechan ...

    The enzyme succinyl-CoA:3-oxoacid coenzyme A transferase (SCOT) participates in the metabolism of ketone bodies in extrahepatic tissues. It catalyses the transfer of coenzyme A (CoA) from succinyl-CoA to acetoacetate with a classical ping-pong mechanism. There is biochemical evidence that the enzyme undergoes conformational changes during the reaction, but no domain movements have been reported in the available crystal structures. Here, a structure of pig heart SCOT refined at 1.5 A resolution is presented, showing that one of the four enzyme subunits in the crystallographic asymmetric unit has a molecule of glycerol bound in the active site; the glycerol molecule is hydrogen bonded to the conserved catalytic glutamate residue and is likely to occupy the cosubstrate-binding site. The binding of glycerol is associated with a substantial relative movement (a 13 degrees rotation) of two previously undefined domains that close around the substrate-binding site. The binding orientation of one of the cosubstrates, acetoacetate, is suggested based on the glycerol binding and the possibility that this dynamic domain movement is of functional importance is discussed.


    Organizational Affiliation

    Center for Amyloidosis and Acute Phase Proteins, Division of Medicine (Royal Free Campus), University College London, London, England.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrialA, B, C, D481Sus scrofaMutation(s): 0 
Gene Names: OXCT1OXCTSCOT
EC: 2.8.3.5
Find proteins for Q29551 (Sus scrofa)
Explore Q29551 
Go to UniProtKB:  Q29551
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
C
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.715α = 90
b = 133.566β = 104.98
c = 102.23γ = 90
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-07-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2012-03-21
    Changes: Database references