3OXO

Succinyl-CoA:3-ketoacid CoA transferase from pig heart covalently bound to CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Catalytic role of the conformational change in succinyl-CoA:3-oxoacid CoA transferase on binding CoA.

Fraser, M.E.Hayakawa, K.Brown, W.D.

(2010) Biochemistry 49: 10319-10328

  • DOI: 10.1021/bi100659s

  • PubMed Abstract: 
  • Catalysis by succinyl-CoA:3-oxoacid CoA transferase proceeds through a thioester intermediate in which CoA is covalently linked to the enzyme. To determine the conformation of the thioester intermediate, crystals of the pig enzyme were grown in the p ...

    Catalysis by succinyl-CoA:3-oxoacid CoA transferase proceeds through a thioester intermediate in which CoA is covalently linked to the enzyme. To determine the conformation of the thioester intermediate, crystals of the pig enzyme were grown in the presence of the substrate acetoacetyl-CoA. X-ray diffraction data show the enzyme in both the free form and covalently bound to CoA via Glu305. In the complex, the protein adopts a conformation in which residues 267-275, 280-287, 357-373, and 398-477 have shifted toward Glu305, closing the enzyme around the thioester. Enzymes provide catalysis by stabilizing the transition state relative to complexes with substrates or products. In this case, the conformational change allows the enzyme to interact with parts of CoA distant from the reactive thiol while the thiol is covalently linked to the enzyme. The enzyme forms stabilizing interactions with both the nucleotide and pantoic acid portions of CoA, while the interactions with the amide groups of the pantetheine portion are poor. The results shed light on how the enzyme uses the binding energy for groups remote from the active center of CoA to destabilize atoms closer to the active center, leading to acceleration of the reaction by the enzyme.


    Organizational Affiliation

    Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada. frasm@ucalgary.ca




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial
A, B, C, D, E, F, G, H
488Sus scrofaMutation(s): 0 
Gene Names: OXCT1 (OXCT, SCOT)
EC: 2.8.3.5
Find proteins for Q29551 (Sus scrofa)
Go to Gene View: OXCT1
Go to UniProtKB:  Q29551
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
COA
Query on COA

Download SDF File 
Download CCD File 
E, F, G, H
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.245 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 69.121α = 89.60
b = 107.133β = 80.21
c = 134.565γ = 75.13
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-09-21 
  • Released Date: 2010-11-10 
  • Deposition Author(s): Fraser, M.E.

Revision History 

  • Version 1.0: 2010-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance