1BF3

P-HYDROXYBENZOATE HYDROXYLASE (PHBH) MUTANT WITH CYS 116 REPLACED BY SER (C116S) AND ARG 42 REPLACED BY LYS (R42K), IN COMPLEX WITH FAD AND 4-HYDROXYBENZOIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Lys42 and Ser42 variants of p-hydroxybenzoate hydroxylase from Pseudomonas fluorescens reveal that Arg42 is essential for NADPH binding.

Eppink, M.H.Schreuder, H.A.van Berkel, W.J.

(1998) Eur.J.Biochem. 253: 194-201


  • PubMed Abstract: 
  • The conserved Arg42 of the flavoprotein p-hydroxybenzoate hydroxylase is located at the entrance of the active site in a loop between helix H2 and sheet E1 of the FAD-binding domain. Replacement of Arg42 by Lys or Ser decreases the turnover rate of p ...

    The conserved Arg42 of the flavoprotein p-hydroxybenzoate hydroxylase is located at the entrance of the active site in a loop between helix H2 and sheet E1 of the FAD-binding domain. Replacement of Arg42 by Lys or Ser decreases the turnover rate of p-hydroxybenzoate hydroxylase from Pseudomonas fluorescens by more than two orders of magnitude. Rapid reaction kinetics show that the low activity of the Arg42 variants results from impaired binding of NADPH. In contrast to an earlier conclusion drawn for p-hydroxybenzoate hydroxylase from Acinetobacter calcoaceticus, substitution of Arg42 with Ser42 in the enzyme from P. fluorescens hardly disturbs the binding of FAD. Crystals of [Lys42]p-hydroxybenzoate hydroxylase complexed with 4-hydroxybenzoate diffract to 0.22-nm resolution. The structure of the Lys42 variant is virtually indistinguishable from the native enzyme with the flavin ring occupying the interior position within the active site. Lys42 in the mutant structure interacts indirectly via a solvent molecule with the 3-OH of the adenosine ribose moiety of FAD. Substrate perturbation difference spectra suggest that the Arg42 replacements influence the solvent accessibility of the flavin ring in the oxidized enzyme. In spite of this, the Arg42 variants fully couple enzyme reduction to substrate hydroxylation. Sequence-comparison studies suggest that Arg42 is involved in binding of the 2'-phosphoadenosine moiety of NADPH.


    Related Citations: 
    • Crystal Structure of P-Hydroxybenzoate Hydroxylase Reconstituted with the Modified Fad Present in Alcohol Oxidase from Methylotrophic Yeasts: Evidence for an Arabinoflavin
      Van Berkel, W.J.,Eppink, M.H.,Schreuder, H.A.
      (1994) Protein Sci. 3: 2245
    • 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
    • The Coenzyme Analogue Adenosine 5-Diphosphoribose Displaces Fad in the Active Site of P-Hydroxybenzoate Hydroxylase. An X-Ray Crystallographic Investigation
      Van Der Laan, J.M.,Schreuder, H.A.,Swarte, M.B.,Wierenga, R.K.,Kalk, K.H.,Hol, W.G.,Drenth, J.
      (1989) Biochemistry 28: 7199
    • Crystal Structure of the P-Hydroxybenzoate Hydroxylase-Substrate Complex Refined at 1.9 A Resolution. Analysis of the Enzyme-Substrate and Enzyme-Product Complexes
      Schreuder, H.A.,Prick, P.A.,Wierenga, R.K.,Vriend, G.,Wilson, K.S.,Hol, W.G.,Drenth, J.
      (1989) J.Mol.Biol. 208: 679
    • Engineering of Microheterogeneity-Resistant P-Hydroxybenzoate Hydroxylase from Pseudomonas Fluorescens
      Eschrich, K.,Van Berkel, W.J.,Westphal, A.H.,De Kok, A.,Mattevi, A.,Obmolova, G.,Kalk, K.H.,Hol, W.G.
      (1990) FEBS Lett. 277: 197
    • Crystal Structure of P-Hydroxybenzoate Hydroxylase Complexed with its Reaction Product 3,4-Dihydroxybenzoate
      Schreuder, H.A.,Van Der Laan, J.M.,Hol, W.G.,Drenth, J.
      (1988) J.Mol.Biol. 199: 637
    • Crystal Structure of the Reduced Form of P-Hydroxybenzoate Hydroxylase Refined at 2.3 A Resolution
      Schreuder, H.A.,Van Der Laan, J.M.,Swarte, M.B.,Kalk, K.H.,Hol, W.G.,Drenth, J.
      (1992) Proteins 14: 178
    • Crystal Structure of P-Hydroxybenzoate Hydroxylase
      Wierenga, R.K.,De Jong, R.J.,Kalk, K.H.,Hol, W.G.,Drenth, J.
      (1979) J.Mol.Biol. 131: 55
    • Crystallization and Preliminary X-Ray Investigation of P-Hydroxybenzoate Hydroxylase from Pseudomonas Fluorescens
      Drenth, J.,Hol, W.G.,Wierenga, R.K.
      (1975) J.Biol.Chem. 250: 5268


    Organizational Affiliation

    Department of Biomolecular Sciences, Wageningen Agricultural University, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
P-HYDROXYBENZOATE HYDROXYLASE
A
394Pseudomonas fluorescensGene Names: pobA
EC: 1.14.13.2
Find proteins for P00438 (Pseudomonas fluorescens)
Go to UniProtKB:  P00438
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: 120000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.175 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 71.350α = 90.00
b = 145.900β = 90.00
c = 88.800γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
XDSdata reduction
X-PLORrefinement
XSCALEdata scaling
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-08-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2014-02-12
    Type: Refinement description
  • Version 1.4: 2014-04-09
    Type: Data collection
  • Version 1.5: 2017-11-29
    Type: Derived calculations, Other