1GGV

CRYSTAL STRUCTURE OF THE C123S MUTANT OF DIENELACTONE HYDROLASE (DLH) BOUND WITH THE PMS MOIETY OF THE PROTEASE INHIBITOR, PHENYLMETHYLSULFONYL FLUORIDE (PMSF)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.151 
  • R-Value Observed: 0.151 

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This is version 1.4 of the entry. See complete history


Literature

Structure of the C123S mutant of dienelactone hydrolase (DLH) bound with the PMS moiety of the protease inhibitor phenylmethylsulfonyl fluoride (PMSF).

Robinson, A.Edwards, K.J.Carr, P.D.Barton, J.D.Ewart, G.D.Ollis, D.L.

(2000) Acta Crystallogr D Biol Crystallogr 56: 1376-1384

  • DOI: https://doi.org/10.1107/s0907444900010647
  • Primary Citation of Related Structures:  
    1GGV

  • PubMed Abstract: 

    The structure of DLH (C123S) with PMS bound was solved to 2.5 A resolution (R factor = 15.1%). PMSF in 2-propanol was delivered directly to crystals in drops and unexpectedly caused the crystals to dissolve. New crystals displaying a different morphology emerged within 2 h in situ, a phenomenon that appears to be described for the first time. The changed crystal form reflected altered crystal-packing arrangements elicited by structural changes to the DLH (C123S) molecule on binding inhibitor. The new unit cell remained in the P2(1)2(1)2(1) space group but possessed different dimensions. The structure showed that PMS binding in DLH (C123S) caused conformational changes in the active site and in four regions of the polypeptide chain that contain reverse turns. In the active site, residues with aromatic side chains were repositioned in an edge-to-face cluster around the PMS phenyl ring. Their redistribution prevented restabilization of the triad His202 side chain, which was disordered in electron-density maps. Movements of other residues in the active site were shown to be related to the four displaced regions of the polypeptide chain. Their implied synergy suggests that DLH may be able to accommodate and catalyse a range of compounds unrelated to the natural substrate owing to an inherent coordinated flexibility in its overall structure. Implications for mechanism and further engineering studies are discussed.


  • Organizational Affiliation

    Centre for Molecular Structure and Function, Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia. anna.robinson@bigpond.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DIENELACTONE HYDROLASE232Pseudomonas putidaMutation(s): 0 
EC: 3.1.1.45
UniProt
Find proteins for P0A114 (Pseudomonas putida)
Explore P0A114 
Go to UniProtKB:  P0A114
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A114
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEB
Query on SEB
A
L-PEPTIDE LINKINGC10 H13 N O5 SSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.151 
  • R-Value Observed: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.08α = 90
b = 51.86β = 90
c = 82.61γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MANUFACTURERdata reduction
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-12-13
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Advisory, Refinement description
  • Version 1.4: 2023-12-27
    Changes: Advisory, Data collection, Database references, Derived calculations