1DUB | pdb_00001dub

2-ENOYL-COA HYDRATASE, DATA COLLECTED AT 100 K, PH 6.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.265 (Depositor) 
  • R-Value Work: 
    0.209 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

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This is version 1.3 of the entry. See complete history

Literature

Crystal structure of enoyl-coenzyme A (CoA) hydratase at 2.5 angstroms resolution: a spiral fold defines the CoA-binding pocket.

Engel, C.K.Mathieu, M.Zeelen, J.P.Hiltunen, J.K.Wierenga, R.K.

(1996) EMBO J 15: 5135-5145

  • Primary Citation Related Structures: 
    1DUB

  • PubMed Abstract: 

    The crystal structure of rat liver mitochondrial enoyl-coenzyme A (CoA) hydratase complexed with the potent inhibitor acetoacetyl-CoA has been refined at 2.5 angstroms resolution. This enzyme catalyses the reversible addition of water to alpha,beta-unsaturated enoyl-CoA thioesters, with nearly diffusion-controlled reaction rates for the best substrates. Enoyl-CoA hydratase is a hexamer of six identical subunits of 161 kDa molecular mass for the complex. The hexamer is a dimer of trimers. The monomer is folded into a right-handed spiral of four turns, followed by two small domains which are involved in trimerization. Each turn of the spiral consists of two beta-strands and an alpha-helix. The mechanism for the hydratase/dehydratase reaction follows a syn-stereochemistry, a preference that is opposite to the nonenzymatic reaction. The active-site architecture agrees with this stereochemistry. It confirms the importance of Glu164 as the catalytic acid for providing the alpha-proton during the hydratase reaction. It also shows the importance of Glu144 as the catalytic base for the activation of a water molecule in the hydratase reaction. The comparison of an unliganded and a liganded active site within the same crystal form shows a water molecule in the unliganded subunit. This water molecule is bound between the two catalytic glutamates and could serve as the activated water during catalysis.


  • Organizational Affiliation
    • European Molecular Biology Laboratory, Heidelberg, Germany.

Macromolecule Content 

  • Total Structure Weight: 174.19 kDa 
  • Atom Count: 12,706 
  • Modeled Residue Count: 1,557 
  • Deposited Residue Count: 1,566 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
2-ENOYL-COA HYDRATASE
A, B, C, D, E
A, B, C, D, E, F
261Rattus norvegicusMutation(s): 0 
EC: 4.2.1.17 (PDB Primary Data), 5.3.3.8 (UniProt)
UniProt
Find proteins for P14604 (Rattus norvegicus)
Explore P14604 
Go to UniProtKB:  P14604
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14604
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.265 (Depositor) 
  • R-Value Work:  0.209 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.972α = 90
b = 93.635β = 90
c = 246.818γ = 90
Software Package:
Software NamePurpose
MLPHAREphasing
X-PLORrefinement
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-07-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations