1PBE

CRYSTAL STRUCTURE OF THE P-HYDROXYBENZOATE HYDROXYLASE-SUBSTRATE COMPLEX REFINED AT 1.9 ANGSTROMS RESOLUTION. ANALYSIS OF THE ENZYME-SUBSTRATE AND ENZYME-PRODUCT COMPLEXES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 679-696


  • PubMed Abstract: 
  • Using synchrotron radiation, the X-ray diffraction intensities of crystals of p-hydroxy-benzoate hydroxylase, complexed with the substrate p-hydroxybenzoate, were measured to a resolution of 1.9 A. Restrained least-squares refinement alternated with ...

    Using synchrotron radiation, the X-ray diffraction intensities of crystals of p-hydroxy-benzoate hydroxylase, complexed with the substrate p-hydroxybenzoate, were measured to a resolution of 1.9 A. Restrained least-squares refinement alternated with rebuilding in electron density maps yielded an atom model of the enzyme-substrate complex with a crystallographic R-factor of 15.6% for 31,148 reflections between 6.0 and 1.9 A. A total of 330 solvent molecules was located. In the final model, only three residues have deviating phi-psi angle combinations. One of them, the active site residue Arg44, has a well-defined electron density and may be strained to adopt this conformation for efficient catalysis. The mode of binding of FAD is distinctly different for the different components of the coenzyme. The adenine ring is engaged in three water-mediated hydrogen bonds with the protein, while making only one direct hydrogen bond with the enzyme. The pyrophosphate moiety makes five water-mediated versus three direct hydrogen bonds. The ribityl and ribose moieties make only direct hydrogen bonds, in all cases, except one, with side-chain atoms. The isoalloxazine ring also makes only direct hydrogen bonds, but virtually only with main-chain atoms. The conformation of FAD in p-hydroxybenzoate hydroxylase is strikingly similar to that in glutathione reductase, while the riboflavin-binding parts of these two enzymes have no structural similarity at all. The refined 1.9 A structure of the p-hydroxybenzoate hydroxylase-substrate complex was the basis of further refinement of the 2.3 A structure of the enzyme-product complex. The result was a final R-factor of 16.7% for 14,339 reflections between 6.0 and 2.3 A and an improved geometry. Comparison between the complexes indicated only small differences in the active site region, where the product molecule is rotated by 14 degrees compared with the substrate in the enzyme-substrate complex. During the refinements of the enzyme-substrate and enzyme-product complexes, the flavin ring was allowed to bend or twist by imposing planarity restraints on the benzene and pyrimidine ring, but not on the flavin ring as a whole. The observed angle between the benzene ring and the pyrimidine ring was 10 degrees for the enzyme-substrate complex and 19 degrees for the enzyme-product complex. Because of the high temperature factors of the flavin ring in the enzyme-product complex, the latter value should be treated with caution. Six out of eight peptide residues near the flavin ring are oriented with their nitrogen atom pointing towards the ring.(ABSTRACT TRUNCATED AT 400 WORDS)


    Related Citations: 
    • Crystal Structure of the Reduced Form of P-Hydroxybenzoate Hydroxylase Refined at 2.3 Angstroms Resolution
      Schreuder, H.A.,Van Der Laan, J.M.,Swarte, M.B.A.,Kalk, K.H.,Hol, W.G.J.,Drenth, J.
      (1992) Proteins 14: 178
    • Crystallization and Preliminary X-Ray Investigation of P-Hydroxybenzoate Hydroxylase from Pseudomonas Fluorescens
      Drenth, J.,Hol, W.G.J.,Wierenga, R.K.
      (1975) J.Biol.Chem. 250: 5268
    • 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.J.,Drenth, J.
      (1988) J.Mol.Biol. 199: 637
    • The Influence of Purification and Protein Heterogeneity on the Crystallization of P-Hydroxybenzoate Hydroxylase
      Van Der Laan, J.M.,Swarte, M.B.A.,Groendijk, H.,Hol, W.G.J.,Drenth, J.
      (1989) Eur.J.Biochem. 179: 715
    • Analysis of the Active Site of the Flavoprotein P-Hydroxybenzoate Hydroxylase and Some Ideas with Respect to its Reaction Mechanism
      Schreuder, H.A.,Hol, W.G.J.,Drenth, J.
      (1989) Biochemistry 29: 3101
    • 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.A.,Wierenga, R.K.,Kalk, K.H.,Hol, W.G.J.,Drenth, J.
      (1989) Biochemistry 28: 7199
    • Molecular Modeling Reveals the Possible Importance of a Carbonyl Oxygen Binding Pocket for the Catalytic Mechanism of P-Hydroxybenzoate Hydroxylase
      Schreuder, H.A.,Hol, W.G.J.,Drenth, J.
      (1988) J.Biol.Chem. 263: 3131
    • 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
    • Crystal Structure of P-Hydroxybenzoate Hydroxylase
      Wierenga, R.K.,De Jong, R.J.,Kalk, K.H.,Hol, W.G.J.,Drenth, J.
      (1979) J.Mol.Biol. 131: 55


    Organizational Affiliation

    Laboratory of Chemical Physics, University of Groningen, 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 71.500α = 90.00
b = 145.800β = 90.00
c = 88.200γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-09-30
    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