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: 2.5 Å
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.3 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.,Sect.D 56: 1376-1384


  • 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 morpho ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIENELACTONE HYDROLASE
A
232Pseudomonas putidaGene Names: clcD
EC: 3.1.1.45
Find proteins for P0A114 (Pseudomonas putida)
Go to UniProtKB:  P0A114
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEB
Query on SEB
A
L-PEPTIDE LINKINGC10 H13 N O5 SSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.080α = 90.00
b = 51.860β = 90.00
c = 82.610γ = 90.00
Software Package:
Software NamePurpose
MANUFACTURERdata reduction
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-12-13
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Advisory, Refinement description