1DIN | pdb_00001din

DIENELACTONE HYDROLASE AT 2.8 ANGSTROMS


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Refined structure of dienelactone hydrolase at 1.8 A.

Pathak, D.Ollis, D.

(1990) J Mol Biology 214: 497-525

  • DOI: https://doi.org/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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DIENELACTONE HYDROLASE236Pseudomonas knackmussiiMutation(s): 1 
Gene Names: CLC D
EC: 3.1.1.45
UniProt
Find proteins for P0A115 (Pseudomonas knackmussii (strain DSM 6978 / CCUG 54928 / LMG 23759 / B13))
Explore P0A115 
Go to UniProtKB:  P0A115
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A115
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSD
Query on CSD
A
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

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

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-06-05
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.4: 2024-10-23
    Changes: Structure summary