2PHH

THE COENZYME ANALOGUE ADENOSINE 5-DIPHOSPHORIBOSE DISPLACES FAD IN THE ACTIVE SITE OF P-HYDROXYBENZOATE HYDROXYLASE. AN X-RAY CRYSTALLOGRAPHIC INVESTIGATION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Observed: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 7199-7205

  • DOI: 10.1021/bi00444a011
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • p-Hydroxybenzoate hydroxylase (PHBH) is an NADPH-dependent enzyme. To locate the NADPH binding site, the enzyme was crystallized under anaerobic conditions in the presence of the substrate p-hydroxybenzoate, the coenzyme analogue adenosine 5-diphosph ...

    p-Hydroxybenzoate hydroxylase (PHBH) is an NADPH-dependent enzyme. To locate the NADPH binding site, the enzyme was crystallized under anaerobic conditions in the presence of the substrate p-hydroxybenzoate, the coenzyme analogue adenosine 5-diphosphoribose (ADPR), and sodium dithionite. This yielded colorless crystals that were suitable for X-ray analysis. Diffraction data were collected up to 2.7-A resolution. A difference Fourier between data from these colorless crystals and data from yellow crystals of the enzyme-substrate complex showed that in the colorless crystals the flavin ring was absent. The adenosine 5'-diphosphate moiety, which is the common part between FAD and ADPR, was still present. After restrained least-squares refinement of the enzyme-substrate complex with the riboflavin omitted from the model, additional electron density appeared near the pyrophosphate, which indicated the presence of an ADPR molecule in the FAD binding site of PHBH. The complete ADPR molecule was fitted to the electron density, and subsequent least-squares refinement resulted in a final R factor of 16.8%. Replacement of bound FAD by ADPR was confirmed by equilibrium dialysis, where it was shown that ADPR can effectively remove FAD from the enzyme under mild conditions in 0.1 M potassium phosphate buffer, pH 8.0. The empty pocket left by the flavin ring is filled by solvent, leaving the architecture of the active site and the binding of the substrate largely unaffected.


    Related Citations: 
    • The Influence of Purification and Protein Heterogeneity on the Crystallization of P-Hydroxybenzoate Hydroxylase
      Van Derlaan, J.M., Swarte, M.B.A., Groendijk, H., Hol, W.G.J., Drenth, J.
      (1989) Eur J Biochem 179: 715
    • Crystal Structure of the P-Hydroxylase-Substrate Complex Refined at 1.9 Angstroms Resolution
      Schreuder, H.A., Prick, P.A.J., Wierenga, R.K., Vriend, G., Wilson, K.S., Hol, W.G.J., Drenth, J.
      (1989) J Mol Biol 208: 679
    • Crystal Structure of P-Hydroxybenzoate Hydroxylas Complexed with its Reaction Product 3,4-Dihydroxybenzoate
      Schreuder, H.A., Van Derlaan, J.M., Hol, W.G.J., Drenth, J.
      (1988) J Mol Biol 199: 637
    • 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
    • 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
    • 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
    • The Amino-Acid Sequence of the Three Smallest Cnbr Peptides from P-Hydroxybenzoate Hydroxylase from Pseudomonas Florescens
      Vereijken, J.M., Hofsteenge, J., Bak, H.J., Beintema, J.J.
      (1980) Eur J Biochem 113: 151
    • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APR
Query on APR

Download CCD File 
A
ADENOSINE-5-DIPHOSPHORIBOSE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-KEOHHSTQSA-N
 Ligand Interaction
PHB
Query on PHB

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: 2.70 Å
  • R-Value Observed: 0.168 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.7α = 90
b = 146.4β = 90
c = 89.2γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1990-10-15
    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