Crystal structure of 2-enoyl-CoA hydratase 2 domain of Candida tropicalis multifunctional enzyme type 2 complexed with (3R)-hydroxydecanoyl-CoA.

Experimental Data Snapshot

  • Resolution: 2.35 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 

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This is version 1.5 of the entry. See complete history


A Two-domain Structure of One Subunit Explains Unique Features of Eukaryotic Hydratase 2.

Koski, M.K.Haapalainen, A.M.Hiltunen, J.K.Glumoff, T.

(2004) J Biol Chem 279: 24666-24672

  • DOI: https://doi.org/10.1074/jbc.M400293200
  • Primary Citation of Related Structures:  
    1PN2, 1PN4

  • PubMed Abstract: 

    2-Enoyl-CoA hydratase 2, a part from multifunctional enzyme type 2, hydrates trans-2-enoyl-CoA to 3-hydroxyacyl-CoA in the (3R)-hydroxy-dependent route of peroxisomal beta-oxidation of fatty acids. Unliganded and (3R)-hydroxydecanoyl coenzyme A-complexed crystal structures of 2-enoyl-CoA hydratase 2 from Candida tropicalis multifunctional enzyme type 2 were solved to 1.95- and 2.35-A resolution, respectively. 2-Enoyl-CoA hydratase 2 is a dimeric, alpha+beta protein with a novel quaternary structure. The overall structure of the two-domain subunit of eukaryotic 2-enoyl-CoA hydratase 2 resembles the homodimeric, hot dog fold structures of prokaryotic (R)-specific 2-enoyl-CoA hydratase and beta-hydroxydecanoyl thiol ester dehydrase. Importantly, though, the eukaryotic hydratase 2 has a complete hot dog fold only in its C-domain, whereas the N-domain lacks a long central alpha-helix, thus creating space for bulkier substrates in the binding pocket and explaining the observed difference in substrate preference between eukaryotic and prokaryotic enzymes. Although the N- and C-domains have an identity of <10% at the amino acid level, they share a 50% identity at the nucleotide level and fold similarly. We suggest that a subunit of 2-enoyl-CoA hydratase 2 has evolved via a gene duplication with the concomitant loss of one catalytic site. The hydrogen bonding network of the active site of 2-enoyl-CoA hydratase 2 resembles the active site geometry of mitochondrial (S)-specific 2-enoyl-CoA hydratase 1, although in a mirror image fashion. This arrangement allows the reaction to occur by similar mechanism, supported by mutagenesis and mechanistic studies, although via reciprocal stereochemistry.

  • Organizational Affiliation

    Department of Biochemistry and Biocenter Oulu, University of Oulu, P. O. Box 3000, FIN-90014 University of Oulu, Finland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisomal hydratase-dehydrogenase-epimerase
A, B, C, D
280Candida tropicalisMutation(s): 2 
Gene Names: FOX2
EC: 4.2.1 (PDB Primary Data), (UniProt), 1.1.1 (UniProt)
Find proteins for P22414 (Candida tropicalis)
Explore P22414 
Go to UniProtKB:  P22414
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22414
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.35 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.64α = 90
b = 151.29β = 90.5
c = 81.62γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
DENZOdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-04-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Advisory, Data collection, Refinement description
  • Version 1.4: 2021-10-27
    Changes: Advisory, Database references, Derived calculations
  • Version 1.5: 2023-08-16
    Changes: Data collection, Refinement description