1DIN

DIENELACTONE HYDROLASE AT 2.8 ANGSTROMS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Refined structure of dienelactone hydrolase at 1.8 A.

Pathak, D.Ollis, D.

(1990) J Mol Biol 214: 497-525

  • DOI: 10.1016/0022-2836(90)90196-s
  • Primary Citation of Related Structures:  
    1DIN

  • PubMed Abstract: 
  • The structure of dienelactone hydrolase (DLH) from Pseudomonus sp. B13, after stereochemically restrained least-squares refinement at 1.8 A resolution, is described. The final molecular model of DLH has a conventional R value of 0.150 and includes al ...

    The structure of dienelactone hydrolase (DLH) from Pseudomonus sp. B13, after stereochemically restrained least-squares refinement at 1.8 A resolution, is described. The final molecular model of DLH has a conventional R value of 0.150 and includes all but the carboxyl-terminal three residues that are crystallographically disordered. The positions of 279 water molecules are included in the final model. The root-mean-square deviation from ideal bond distances for the model is 0.014 A and the error in atomic co-ordinates is estimated to be 0.15 A. DLH is a monomeric enzyme containing 236 amino acid residues and is a member of the beta-ketoadipate pathway found in bacteria and fungi. DLH is an alpha/beta protein containing seven helices and eight strands of beta-pleated sheet. A single 4-turn 3(10)-helix is seen. The active-site Cys123 residues at the N-terminal end of an alpha-helix that is peculiar in its consisting entirely of hydrophobic residues (except for a C-terminal lysine). The beta-sheet is composed of parallel strands except for strand 2, which gives rise to a short antiparallel region at the N-terminal end of the central beta-sheet. The active-site cysteine residue is part of a triad of residues consisting of Cys123, His202 and Asp171, and is reminiscent of the serine/cysteine proteases. As in papain and actinidin, the active thiol is partially oxidized during X-ray data collection. The positions of both the reduced and the oxidized sulphur are described. The active site geometry suggests that a change in the conformation of the native thiol occurs upon diffusion of substrate into the active site cleft of DLH. This enables nucleophilic attack by the gamma-sulphur to occur on the cyclic ester substrate through a ring-opening reaction.


    Related Citations: 
    • X-Ray Crystallographic Structure of Dienelactone Hydrolase at 2.8 A
      Pathak, D., Ngai, K.L., Ollis, D.
      (1988) J Mol Biol 204: 435
    • Crystallization and Preliminary X-Ray Crystallographic Data of Dienelactone Hydrolase from Pseudomonas Sp. B13
      Ollis, D.L., Ngai, K.L.
      (1985) J Biol Chem 260: 9818

    Organizational Affiliation

    Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, IL 60208.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DIENELACTONE HYDROLASEA236Pseudomonas knackmussiiMutation(s): 1 
Gene Names: CLC D
EC: 3.1.1.45
Find proteins for P0A115 (Pseudomonas knackmussii (strain DSM 6978 / LMG 23759 / B13))
Explore P0A115 
Go to UniProtKB:  P0A115
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
AL-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.9α = 90
b = 71.45β = 90
c = 78.24γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement
TNTrefinement
XENGENdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-08-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance