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: 2.20 Å
  • R-Value Work: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.6 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

  • DOI: 10.1046/j.1432-1327.1998.2530194.x
  • Primary Citation of Related Structures:  
    1BF3

  • 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-hydroxybenzoate hydroxylase from Pseudomonas fluorescens by more than two orders of magnitude ...

    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
    • 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
    • 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 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
    • 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 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 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
P-HYDROXYBENZOATE HYDROXYLASEA394Pseudomonas fluorescensMutation(s): 2 
Gene Names: pobA
EC: 1.14.13.2
UniProt
Find proteins for P00438 (Pseudomonas fluorescens)
Explore P00438 
Go to UniProtKB:  P00438
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
PHB
Query on PHB

Download Ideal Coordinates CCD File 
C [auth A]P-HYDROXYBENZOIC ACID
C7 H6 O3
FJKROLUGYXJWQN-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
PHB Binding MOAD:  1BF3 Kd: 1.20e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.175 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.35α = 90
b = 145.9β = 90
c = 88.8γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
XSCALEdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-08-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2014-02-12
    Changes: Refinement description
  • Version 1.4: 2014-04-09
    Changes: Data collection
  • Version 1.5: 2017-11-29
    Changes: Derived calculations, Other
  • Version 1.6: 2018-04-04
    Changes: Data collection