1BGJ

P-HYDROXYBENZOATE HYDROXYLASE (PHBH) MUTANT WITH CYS 116 REPLACED BY SER (C116S) AND HIS 162 REPLACED BY ARG (H162R), IN COMPLEX WITH FAD AND 4-HYDROXYBENZOIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Work: 0.128 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Interdomain binding of NADPH in p-hydroxybenzoate hydroxylase as suggested by kinetic, crystallographic and modeling studies of histidine 162 and arginine 269 variants.

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

(1998) J.Biol.Chem. 273: 21031-21039

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The conserved residues His-162 and Arg-269 of the flavoprotein p-hydroxybenzoate hydroxylase (EC 1.14.13.2) are located at the entrance of the interdomain cleft that leads toward the active site. To study their putative role in NADPH binding, His-162 ...

    The conserved residues His-162 and Arg-269 of the flavoprotein p-hydroxybenzoate hydroxylase (EC 1.14.13.2) are located at the entrance of the interdomain cleft that leads toward the active site. To study their putative role in NADPH binding, His-162 and Arg-269 were selectively changed by site-specific mutagenesis. The catalytic properties of H162R, H162Y, and R269K were similar to the wild-type enzyme. However, less conservative His-162 and Arg-269 replacements strongly impaired NADPH binding without affecting the conformation of the flavin ring and the efficiency of substrate hydroxylation. The crystal structures of H162R and R269T in complex with 4-hydroxybenzoate were solved at 3.0 and 2.0 A resolution, respectively. Both structures are virtually indistinguishable from the wild-type enzyme-substrate complex except for the substituted side chains. In contrast to wild-type p-hydroxybenzoate hydroxylase, H162R is not inactivated by diethyl pyrocarbonate. NADPH protects wild-type p-hydroxybenzoate hydroxylase from diethylpyrocarbonate inactivation, suggesting that His-162 is involved in NADPH binding. Based on these results and GRID calculations we propose that the side chains of His-162 and Arg-269 interact with the pyrophosphate moiety of NADPH. An interdomain binding mode for NADPH is proposed which takes a novel sequence motif (Eppink, M. H. M., Schreuder, H. A., and van Berkel, W. J. H. (1997) Protein Sci. 6, 2454-2458) into account.


    Related Citations: 
    • 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 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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


    Organizational Affiliation

    Department of Biomolecular Sciences, Laboratory of Biochemistry, Wageningen Agricultural University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
P-HYDROXYBENZOATE HYDROXYLASE
A
394Pseudomonas fluorescensMutation(s): 2 
Gene 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Work: 0.128 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 71.800α = 90.00
b = 146.000β = 90.00
c = 88.300γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
X-PLORmodel building
X-PLORphasing
XSCALEdata scaling
X-PLORrefinement

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: 2017-11-29
    Type: Derived calculations, Other
  • Version 1.4: 2018-04-04
    Type: Data collection