1DIQ

CRYSTAL STRUCTURE OF P-CRESOL METHYLHYDROXYLASE WITH SUBSTRATE BOUND


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.133 

wwPDB Validation   3D Report Full Report


This is version 2.0 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: 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 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.


    Related Citations: 
    • Three-dimensional Structure of p-Cresol Methylhydroxylase (Flavocytochrome c) from Pseudomonas putida at 3.0 A Resolution
      Mathews, F.S., Chen, Z.W., Bellamy, H., McIntire, W.S.
      (1991) Biochemistry 30: 238

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
P-CRESOL METHYLHYDROXYLASEA, C [auth B]521Pseudomonas putidaMutation(s): 0 
Gene Names: pchF
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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
P-CRESOL METHYLHYDROXYLASEB [auth C], D80Pseudomonas putidaMutation(s): 0 
Gene Names: pchC
EC: 1.17.99.1
UniProt
Find proteins for P09787 (Pseudomonas putida)
Explore P09787 
Go to UniProtKB:  P09787
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
F [auth A], J [auth B]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
HEC
Query on HEC

Download Ideal Coordinates CCD File 
H [auth C], L [auth D]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
PCR
Query on PCR

Download Ideal Coordinates CCD File 
G [auth A], K [auth B]P-CRESOL
C7 H8 O
IWDCLRJOBJJRNH-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A], I [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.133 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.1α = 90
b = 130.5β = 90
c = 74.4γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
CNSrefinement
SDMSdata reduction
SDMSdata scaling
X-PLORphasing

Structure Validation

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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