4C2J

Crystal structure of human mitochondrial 3-ketoacyl-CoA thiolase in complex with CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Crystal Structure of Human Mitochondrial 3-Ketoacyl-Coa Thiolase (T1): Insight Into the Reaction Mechanism of its Thiolase and Thioesterase Activities

Kiema, T.-R.Harijan, R.K.Strozyk, M.Fukao, T.Alexson, S.E.H.Wierenga, R.K.

(2014) Acta Crystallogr D Biol Crystallogr 70: 3212

  • DOI: 10.1107/S1399004714023827
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Crystal structures of human mitochondrial 3-ketoacyl-CoA thiolase (hT1) in the apo form and in complex with CoA have been determined at 2.0 Å resolution. The structures confirm the tetrameric quaternary structure of this degradative thiolase. The act ...

    Crystal structures of human mitochondrial 3-ketoacyl-CoA thiolase (hT1) in the apo form and in complex with CoA have been determined at 2.0 Å resolution. The structures confirm the tetrameric quaternary structure of this degradative thiolase. The active site is surprisingly similar to the active site of the Zoogloea ramigera biosynthetic tetrameric thiolase (PDB entries 1dm3 and 1m1o) and different from the active site of the peroxisomal dimeric degradative thiolase (PDB entries 1afw and 2iik). A cavity analysis suggests a mode of binding for the fatty-acyl tail in a tunnel lined by the Nβ2-Nα2 loop of the adjacent subunit and the Lα1 helix of the loop domain. Soaking of the apo hT1 crystals with octanoyl-CoA resulted in a crystal structure in complex with CoA owing to the intrinsic acyl-CoA thioesterase activity of hT1. Solution studies confirm that hT1 has low acyl-CoA thioesterase activity for fatty acyl-CoA substrates. The fastest rate is observed for the hydrolysis of butyryl-CoA. It is also shown that T1 has significant biosynthetic thiolase activity, which is predicted to be of physiological importance.


    Organizational Affiliation

    Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, PO Box 3000, FIN-90014 Oulu, Finland.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-KETOACYL-COA THIOLASE, MITOCHONDRIAL
A, B, C, D
417HOMO SAPIENSMutation(s): 0 
Gene Names: ACAA2
EC: 2.3.1.16 (PDB Primary Data), 2.3.1.9 (UniProt), 3.1.2 (UniProt), 3.1.2.1 (UniProt), 3.1.2.2 (UniProt)
Find proteins for P42765 (Homo sapiens)
Go to UniProtKB:  P42765
NIH Common Fund Data Resources
PHAROS  P42765
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download CCD File 
A, B, C, D
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A,B,C,D
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.65α = 90
b = 197.16β = 103.72
c = 79.95γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Database references
  • Version 1.2: 2015-02-25
    Changes: Database references