Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 59.00 kDa 
• Atom Count: 5109 
• Modelled Residue Count: 515 
• Deposited Residue Count: 520 
• Unique protein chains: 1

1WVF

p-Cresol Methylhydroxylase: Alteration of the Structure of the Flavoprotein Subunit upon its Binding to the Cytochrome Subunit

• DOI: 10.2210/pdb1WVF/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-12-15 Released: 2005-03-08 
• Deposition Author(s): Cunane, L.M., Chen, Z.-W., McIntire, W.S., Mathews, F.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.167 
• R-Value Work: 0.146 

Literature

p-Cresol Methylhydroxylase: Alteration of the Structure of the Flavoprotein Subunit upon Its Binding to the Cytochrome Subunit

Cunane, L.M., Chen, Z.-W., McIntire, W.S., Mathews, F.S.

(2005) Biochemistry 44: 2963-2973

• PubMed: 15723539 
• DOI: 10.1021/bi048020r
• Primary Citation of Related Structures:  
  1WVE, 1WVF


• PubMed Abstract: 
  

The structures of two forms of a recombinant flavoprotein have been determined at high resolution and compared. These proteins are (1) the flavocytochrome c p-cresol methylhydroxylase (rPCMH, 1.85 A resolution) and (2) the cytochrome-free flavoprotein subunit of rPCMH (PchF, 1.30 A resolution). A significant conformational difference is observed in a protein segment that is in contact with the re face of the isoalloxazine ring of FAD when the structure of PchF is compared to the subunit in the intact flavocytochrome. This structural change is important for optimum catalytic function of the flavoprotein, which has been shown to be dependent on the presence of the cytochrome subunit. This change results in different protein-flavin and apparently different protein-substrate interactions that have a "tuning effect" on the electronic and redox properties of bound p-cresol and the covalently bound FAD. The conformational change in the segment in the cofactor-binding site is induced by a small rearrangement in the flavoprotein-cytochrome interface region of the flavoprotein.

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Related Citations: 

• 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

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-cresol dehydrogenase [hydroxylating] flavoprotein subunit	A	520	Pseudomonas putida	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	C [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
GOL	F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY	D [auth A], E [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.167 
• R-Value Work: 0.146 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.64	α = 90
b = 116.91	β = 113.18
c = 50.22	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2004-12-15 
• Released Date: 2005-03-08 
Deposition Author(s): Cunane, L.M., Chen, Z.-W., McIntire, W.S., Mathews, F.S.

Revision History  

• Version 1.0: 2005-03-08
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance