1YKJ

A45G p-hydroxybenzoate hydroxylase with p-hydroxybenzoate bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Removal of a methyl group causes global changes in p-hydroxybenzoate hydroxylase.

Cole, L.J.Gatti, D.L.Entsch, B.Ballou, D.P.

(2005) Biochemistry 44: 8047-8058

  • DOI: 10.1021/bi050108x

  • PubMed Abstract: 
  • p-Hydroxybenzoate hydroxylase (PHBH) is a homodimeric flavoprotein monooxygenase that catalyzes the hydroxylation of p-hydroxybenzoate to form 3,4-dihydroxybenzoate. Controlled catalysis is achieved by movement of the flavin and protein between three ...

    p-Hydroxybenzoate hydroxylase (PHBH) is a homodimeric flavoprotein monooxygenase that catalyzes the hydroxylation of p-hydroxybenzoate to form 3,4-dihydroxybenzoate. Controlled catalysis is achieved by movement of the flavin and protein between three conformations, in, out, and open [Entsch, B., et al. (2005) Arch. Biochem. Biophys. 433, 297-311]. The open conformation is important for substrate binding and product release, the in conformation for reaction with oxygen and hydroxylation, and the out conformation for the reduction of FAD by NADPH. The open conformation is similar to the structure of Arg220Gln-PHBH in which the backbone peptide loop of residues 43-46, located on the si side of the flavin, is rotated. In this paper, we examine the structure and properties of the Ala45Gly-PHBH mutant enzyme. The crystal structure of the Ala45Gly enzyme is an asymmetric dimer, with one monomer similar (but not identical) to wild-type PHBH, while the other monomer has His72 flipped into solvent and replaced with Glu73 as one of several changes in the structure. The two structures correlate with evidence from kinetic studies for two forms of Ala45Gly-PHBH. One form of the enzyme dominates turnover and hydroxylates, while the other contributes little to turnover and fails to hydroxylate. Ala45Gly-PHBH favors the in conformation over alternative conformations. The effect of this mutation on the structure and function of PHBH illustrates the importance of the si side loop in the conformational state of PHBH and, consequently, the function of the enzyme. This work demonstrates some general principles of how enzymes use conformational movements to allow both access and egress of substrates and product, while restricting access to the solvent at a critical stage in catalysis.


    Organizational Affiliation

    Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
P-hydroxybenzoate hydroxylase
A, B
394Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 1 
Gene Names: pobA
EC: 1.14.13.2
Find proteins for P20586 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  P20586
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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
PHB
Query on PHB

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Download CCD File 
A, B
P-HYDROXYBENZOIC ACID
C7 H6 O3
FJKROLUGYXJWQN-UHFFFAOYSA-N
 Ligand Interaction
PSL
Query on PSL

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Download CCD File 
B
PYROSULFATE
O7 S2
VFNGKCDDZUSWLR-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PHBKd: 700 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 69.860α = 90.00
b = 85.897β = 90.00
c = 146.074γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CrystalCleardata reduction
d*TREKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-07-26
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model