1DII

CRYSTAL STRUCTURE OF P-CRESOL METHYLHYDROXYLASE AT 2.5 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 

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This is version 2.1 of the entry. See complete history


Literature

Structures of the flavocytochrome p-cresol methylhydroxylase and its enzyme-substrate complex: gated substrate entry and proton relays support the proposed catalytic mechanism.

Cunane, L.M.Chen, Z.W.Shamala, N.Mathews, F.S.Cronin, C.N.McIntire, W.S.

(2000) J Mol Biol 295: 357-374

  • DOI: https://doi.org/10.1006/jmbi.1999.3290
  • Primary Citation of Related Structures:  
    1DII, 1DIQ

  • PubMed Abstract: 

    The degradation of the toxic phenol p-cresol by Pseudomonas bacteria occurs by way of the protocatechuate metabolic pathway. The first enzyme in this pathway, p-cresol methylhydroxylase (PCMH), is a flavocytochrome c. The enzyme first catalyzes the oxidation of p-cresol to p-hydroxybenzyl alcohol, utilizing one atom of oxygen derived from water, and yielding one molecule of reduced FAD. The reducing electron equivalents are then passed one at a time from the flavin cofactor to the heme cofactor by intramolecular electron transfer, and subsequently to cytochrome oxidase within the periplasmic membrane via one or more soluble electron carrier proteins. The product, p-hydroxybenzyl alcohol, can also be oxidized by PCMH to yield p-hydroxybenzaldehyde. The fully refined X-ray crystal structure of PCMH in the native state has been obtained at 2. 5 A resolution on the basis of the gene sequence. The structure of the enzyme-substrate complex has also been refined, at 2.75 A resolution, and reveals significant conformational changes in the active site upon substrate binding. The active site for substrate oxidation is deeply buried in the interior of the PCMH molecule. A route for substrate access to the site has been identified and is shown to be governed by a swinging-gate mechanism. Two possible proton transfer pathways, that may assist in activating the substrate for nucleophilic attack and in removal of protons generated during the reaction, have been revealed. Hydrogen bonding interactions between the flavoprotein and cytochrome subunits that stabilize the intramolecular complex and may contribute to the electron transfer process have been identified.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
P-CRESOL METHYLHYDROXYLASEA,
C [auth B]
521Pseudomonas putidaMutation(s): 0 
EC: 1.17.99.1 (PDB Primary Data), 1.17.9.1 (UniProt)
UniProt
Find proteins for P09788 (Pseudomonas putida)
Explore P09788 
Go to UniProtKB:  P09788
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09788
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
P-CRESOL METHYLHYDROXYLASEB [auth C],
D
80Pseudomonas putidaMutation(s): 0 
EC: 1.17.99.1
UniProt
Find proteins for P09787 (Pseudomonas putida)
Explore P09787 
Go to UniProtKB:  P09787
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09787
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.3α = 90
b = 130.6β = 90
c = 74.1γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
CNSrefinement
SDMSdata reduction
SDMSdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-12-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2021-03-03
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-11-06
    Changes: Data collection, Database references, Structure summary