3DEA | pdb_00003dea

Glomerella cingulata PETFP-cutinase complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.248 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

Catalysis by Glomerella cingulata Cutinase Requires Conformational Cycling between the Active and Inactive States of Its Catalytic Triad

Nyon, M.P.Rice, D.W.Berrisford, J.M.Hounslow, A.M.Moir, A.J.G.Huang, H.Nathan, S.Mahadi, N.M.Bakar, F.D.A.Craven, C.J.

(2009) J Mol Biology 385: 226-235

  • DOI: https://doi.org/10.1016/j.jmb.2008.10.050
  • Primary Citation Related Structures: 
    3DCN, 3DD5, 3DEA

  • PubMed Abstract: 

    Cutinase belongs to a group of enzymes that catalyze the hydrolysis of esters and triglycerides. Structural studies on the enzyme from Fusarium solani have revealed the presence of a classic catalytic triad that has been implicated in the enzyme's mechanism. We have solved the crystal structure of Glomerella cingulata cutinase in the absence and in the presence of the inhibitors E600 (diethyl p-nitrophenyl phosphate) and PETFP (3-phenethylthio-1,1,1-trifluoropropan-2-one) to resolutions between 2.6 and 1.9 A. Analysis of these structures reveals that the catalytic triad (Ser136, Asp191, and His204) adopts an unusual configuration with the putative essential histidine His204 swung out of the active site into a position where it is unable to participate in catalysis, with the imidazole ring 11 A away from its expected position. Solution-state NMR experiments are consistent with the disrupted configuration of the triad observed crystallographically. H204N, a site-directed mutant, was shown to be catalytically inactive, confirming the importance of this residue in the enzyme mechanism. These findings suggest that, during its catalytic cycle, cutinase undergoes a significant conformational rearrangement converting the loop bearing the histidine from an inactive conformation, in which the histidine of the triad is solvent exposed, to an active conformation, in which the triad assumes a classic configuration.


  • Organizational Affiliation
    • School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Selangor, Malaysia.

Macromolecule Content 

  • Total Structure Weight: 42.69 kDa 
  • Atom Count: 2,936 
  • Modeled Residue Count: 374 
  • Deposited Residue Count: 402 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cutinase
A, B
201Colletotrichum gloeosporioidesMutation(s): 0 
EC: 3.1.1.74
UniProt
Find proteins for P11373 (Colletotrichum gloeosporioides)
Explore P11373 
Go to UniProtKB:  P11373
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11373
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.248 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.32α = 90
b = 88.32β = 90
c = 123.69γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary