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 1.2 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
  • Also Cited By: 1WVE, 1WVF

  • 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 o ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
P-CRESOL METHYLHYDROXYLASE
A, B
521Pseudomonas putidaGene Names: pchF
EC: 1.17.99.1
Find proteins for P09788 (Pseudomonas putida)
Go to UniProtKB:  P09788
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
P-CRESOL METHYLHYDROXYLASE
C, D
80Pseudomonas putidaGene Names: pchC
Find proteins for P09787 (Pseudomonas putida)
Go to UniProtKB:  P09787
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PCR
Query on PCR

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Download CCD File 
A, B
P-CRESOL
C7 H8 O
IWDCLRJOBJJRNH-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
FAD
Query on FAD

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Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 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 = 139.100α = 90.00
b = 130.500β = 90.00
c = 74.400γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
CNSrefinement
SDMSdata scaling
SDMSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-12-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance