1HNU

CRYSTAL STRUCTURE OF PEROXISOMAL DELTA3-DELTA2-ENOYL-COA ISOMERASE FROM SACCHAROMYCES CEREVISIAE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

The crystal structure of delta(3)-delta(2)-enoyl-CoA isomerase.

Mursula, A.M., van Aalten, D.M., Hiltunen, J.K., Wierenga, R.K.

(2001) J Mol Biol 309: 845-853

  • DOI: 10.1006/jmbi.2001.4671
  • Primary Citation of Related Structures:  
    1HNO, 1HNU

  • PubMed Abstract: 

    • The active-site geometry of the first crystal structure of a Delta(3)-Delta(2)-enoyl-coenzyme A (CoA) isomerase (the peroxisomal enzyme from the yeast Saccharomyces cerevisiae) shows that only one catalytic base, Glu158, is involved in shuttling the proton from the C2 carbon atom of the substrate, Delta(3)-enoyl-CoA, to the C4 atom of the product, Delta(2)-enoyl-CoA ...

    The active-site geometry of the first crystal structure of a Delta(3)-Delta(2)-enoyl-coenzyme A (CoA) isomerase (the peroxisomal enzyme from the yeast Saccharomyces cerevisiae) shows that only one catalytic base, Glu158, is involved in shuttling the proton from the C2 carbon atom of the substrate, Delta(3)-enoyl-CoA, to the C4 atom of the product, Delta(2)-enoyl-CoA. Site-directed mutagenesis has been performed to confirm that this glutamate residue is essential for catalysis. This Delta(3)-Delta(2)-enoyl-CoA isomerase is a hexameric enzyme, consisting of six identical subunits. It belongs to the hydratase/isomerase superfamily of enzymes which catalyze a wide range of CoA-dependent reactions. The members of the hydratase/ isomerase superfamily have only a low level of sequence identity. Comparison of the crystal structure of the Delta(3)-Delta(2)-enoyl-CoA isomerase with the other structures of this superfamily shows only one region of large structural variability, which is in the second turn of the spiral fold and which is involved in defining the shape of the binding pocket.

    Related Citations: 
    • Crystallization and X-ray Diffraction Analysis of Peroxisomal delta3-delta2-enoyl-CoA Isomerase from Saccharomyces cerevisiae
      Mursula, A.M., van Aalten, D.M., Modis, Y., Hiltunen, J.K., Wierenga, R.K.
      (2000) Acta Crystallogr D Biol Crystallogr 56: 1020
    Organizational Affiliation: 

    Biocenter Oulu and Department of Biochemistry, University of Oulu, FIN-90014, Finland.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D3,D2-ENOYL COA ISOMERASE ECI1A280Saccharomyces cerevisiaeMutation(s): 1 
EC: 5.3.3.8
UniProt
Find proteins for Q05871 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q05871 
Go to UniProtKB:  Q05871
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05871
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
REO
Query on REO
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]		PERRHENATE
O4 Re
WPWXHJFQOFOBAC-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.139α = 90
b = 116.139β = 90
c = 123.276γ = 120
Software Package:
Software NamePurpose
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-06-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Data collection, Database references, Derived calculations