1IUW

P-HYDROXYBENZOATE HYDROXYLASE COMPLEXED WITH 4-4-HYDROXYBENZOATE AT PH 7.4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

pH-dependent structural changes in the active site of p-hydroxybenzoate hydroxylase point to the importance of proton and water movements during catalysis.

Gatti, D.L.Entsch, B.Ballou, D.P.Ludwig, M.L.

(1996) Biochemistry 35: 567-578

  • DOI: 10.1021/bi951344i
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Deprotonation of p-hydroxybenzoate to the phenolate and reprotonation of the hydroxylated dienone intermediate to form the product are essential steps in the reaction catalyzed by p-hydroxybenzoate hydroxylase (PHBH). The mechanism by which protons a ...

    Deprotonation of p-hydroxybenzoate to the phenolate and reprotonation of the hydroxylated dienone intermediate to form the product are essential steps in the reaction catalyzed by p-hydroxybenzoate hydroxylase (PHBH). The mechanism by which protons are transferred in these reactions is not obvious, because the substrate bound in the active site is isolated from solvent. Structure analyses of wild-type and mutant PHBH, with bound p-hydroxybenzoate or p-aminobenzoate, reveal a chain of proton donors and acceptors (the hydroxyl groups of Tyr201 and Tyr385, and two water molecules) that can connect the substrate 4-OH to His72, a surface residue. This chain could provide a pathway for proton transfer to and from the substrate. Using various combinations of pH and substrates, we show that in crystalline PHBH ionizable groups in the chain may rotate and change hydrogen-bond orientation. Molecular dynamics simulations have been used to predict the preferred orientation of hydrogen bonds in the chain as a function of the ionization states of substrate and His72. The calculations suggest that changes in the ionization state of the substrate could be associated with changes in orientation of the hydrogen bonds in the chain. Transfer of water between the chain of proton donors and the solvent also appears to be an essential part of the mechanism that provides reversible transfer of protons during the hydroxylation reaction.


    Related Citations: 
    • Catalytic Function of Tyrosine Residues in Para-Hydroxybenzoate Hydroxylase as Determined by the Study of Site-Directed Mutants
      Entsch, B.,Palfey, B.A.,Ballou, D.P.,Massey, V.
      (1991) J.Biol.Chem. 266: 17341
    • Crystal Structures of Wild-Type P-Hydroxybenzoate Hydroxylase Complexed with 4-Aminobenzoate,2,4-Dihydroxybenzoate, and 2-Hydroxy-4-Aminobenzoate and of the Tyr222Ala Mutant Complexed with 2-Hydroxy-4-Aminobenzoate. Evidence for a Proton Channel and a New Binding Mode of the Flavin Ring
      Schreuder, H.A.,Mattevi, A.,Obmolova, G.,Kalk, K.H.,Hol, W.G.,Van Der Bolt, F.J.,Van Berkel, W.J.
      (1994) Biochemistry 33: 10161
    • Crystal Structures of Mutant Pseudomonas Aeruginosa P-Hydroxybenzoate Hydroxylases:The Tyr201Phe, Tyr385Phe and Asn300Asp Variants
      Lah, M.S.,Palfey, B.A.,Schreuder, H.A.,Ludwig, M.L.
      (1994) Biochemistry 33: 1555


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
P-HYDROXYBENZOATE HYDROXYLASE
A
394Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

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

Download SDF File 
Download CCD File 
A
P-HYDROXYBENZOIC ACID
C7 H6 O3
FJKROLUGYXJWQN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PHBKd: 18000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.172 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 71.790α = 90.00
b = 146.590β = 90.00
c = 88.120γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
SDMSdata scaling
X-PLORrefinement
SDMSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-07-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other