1PHH

CRYSTAL STRUCTURE OF P-HYDROXYBENZOATE HYDROXYLASE COMPLEXED WITH ITS REACTION PRODUCT 3,4-DIHYDROXYBENZOATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Observed: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 637-648

  • DOI: 10.1016/0022-2836(88)90307-5
  • Primary Citation of Related Structures:  
    1PHH

  • PubMed Abstract: 
  • Crystals of the flavin-containing enzyme p-hydroxybenzoate hydroxylase (PHBHase) complexed with its reaction product were investigated in order to obtain insight into the catalytic cycle of this enzyme involving two substrates and two cofactors. PHBH ...

    Crystals of the flavin-containing enzyme p-hydroxybenzoate hydroxylase (PHBHase) complexed with its reaction product were investigated in order to obtain insight into the catalytic cycle of this enzyme involving two substrates and two cofactors. PHBHase was crystallized initially with its substrate, p-hydroxybenzoate and the substrate was then converted into the product 3,4-dihydroxybenzoate by allowing the catalytic reaction to proceed in the crystals. In addition, crystals were soaked in mother liquor containing a high concentration of this product. Data up to 2.3 A (1 A = 0.1 nm) were collected by the oscillation method and the structure of the enzyme product complex was refined by alternate restrained least-squares procedures and model building by computer graphics techniques. A total of 273 solvent molecules could be located, four of them being presumably sulfate ions. The R-factor for 14,339 reflections between 6.0 A and 2.3 A is 19.3%. The 3-hydroxyl group of the product introduced by the enzyme is clearly visible in the electron density, showing unambiguously which carbon atom of the substrate is hydroxylated. A clear picture of the hydroxylation site is obtained. The plane of the product is rotated 21 degrees with respect to the plane of the substrate in the current model of enzyme-substrate complex. The 4-hydroxyl group of the product is hydrogen bonded to the hydroxyl group of Tyr201, its carboxyl group is interacting with the side-chains of Tyr222, Arg214 and Ser212, while the newly introduced 3-hydroxyl group makes a hydrogen bond with the backbone carbonyl oxygen of Pro293.


    Related Citations: 
    • P-Hydroxybenzoate Hydroxylase from Pseudomonas Fluorescens. 2. Fitting of the Amino-Acid Sequence to the Tertiary Structure
      Weijer, W.J., Hofsteenge, J., Beintema, J.J., Wierenga, R.K., Drenth, J.
      (1983) Eur J Biochem 133: 109
    • P-Hydroxybenzoate Hydroxylase from Pseudomonas Fluorescens. 1. Completion of the Elucidation of the Primary Structure
      Hofsteenge, J., Weijer, W.J., Jekel, P.A., Beintema, J.J.
      (1983) Eur J Biochem 133: 91
    • Comparison of the Three-Dimensional Protein and Nucleotide Structure of the Fad-Binding Domain of P-Hydroxybenzoate Hydroxylase with the Fad-as Well as Nadph-Binding Domains of Glutathione Reductase
      Wierenga, R.K., Drenth, J., Schulz, G.E.
      (1983) J Mol Biol 167: 725
    • Primary and Tertiary Structure Studies of P-Hydroxybenzoate Hydroxylase from Pseudomonas Fluorescens. Isolation and Alignment of the Cnbr Peptides. Interactions of the Protein with Flavin Adenine Dinucleotide
      Hofsteenge, J., Vereijken, J.M., Weijer, W.J., Beintema, J.J., Wierenga, R.K., Drenth, J.
      (1980) Eur J Biochem 113: 141
    • Crystal Structure of P-Hydroxybenzoate Hydroxylase
      Wierenga, R.K., Dejong, R.J., Kalk, K.H., Hol, W.G.J., Drenth, J.
      (1979) J Mol Biol 131: 55
    • Crystallization and Preliminary X-Ray Investigation of P-Hydrobenzoate Hydroxylase from Pseudomonas Fluorescens
      Drenth, J., Hol, W.G.J., Wierenga, R.K.
      (1975) J Biol Chem 250: 5268

    Organizational Affiliation

    Laboratory of Chemical Physics, University of Groningen, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
P-HYDROXYBENZOATE HYDROXYLASEA394Pseudomonas fluorescensMutation(s): 0 
Gene Names: pobA
EC: 1.14.13.2
Find proteins for P00438 (Pseudomonas fluorescens)
Explore P00438 
Go to UniProtKB:  P00438
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

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

Download CCD File 
A
3,4-DIHYDROXYBENZOIC ACID
C7 H6 O4
YQUVCSBJEUQKSH-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DHBKi:  470000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Observed: 0.193 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.9α = 90
b = 146.3β = 90
c = 88.9γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1988-04-16
    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