1PDH

CRYSTAL STRUCTURE OF P-HYDROXYBENZOATE HYDROXYLASE RECONSTITUTED WITH THE MODIFIED FAD PRESENT IN ALCOHOL OXIDASE FROM METHYLOTROPHIC YEASTS: EVIDENCE FOR AN ARABINOFLAVIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 2245-2253

  • DOI: 10.1002/pro.5560031210

  • PubMed Abstract: 
  • The flavin prosthetic group (FAD) of p-hydroxybenzoate hydroxylase from Pseudomonas fluorescens was replaced by a stereochemical analog, which is spontaneously formed from natural FAD in alcohol oxidases from methylotrophic yeasts. Reconstitution of ...

    The flavin prosthetic group (FAD) of p-hydroxybenzoate hydroxylase from Pseudomonas fluorescens was replaced by a stereochemical analog, which is spontaneously formed from natural FAD in alcohol oxidases from methylotrophic yeasts. Reconstitution of p-hydroxybenzoate hydroxylase from apoprotein and modified FAD is a rapid process complete within seconds. Crystals of the enzyme-substrate complex of modified FAD-containing p-hydroxybenzoate hydroxylase diffract to 2.1 A resolution. The crystal structure provides direct evidence for the presence of an arabityl sugar chain in the modified form of FAD. The isoalloxazine ring of the arabinoflavin adenine dinucleotide (a-FAD) is located in a cleft outside the active site as recently observed in several other p-hydroxybenzoate hydroxylase complexes. Like the native enzyme, a-FAD-containing p-hydroxybenzoate hydroxylase preferentially binds the phenolate form of the substrate (pKo = 7.2). The substrate acts as an effector highly stimulating the rate of enzyme reduction by NADPH (kred > 500 s-1). The oxidative part of the catalytic cycle of a-FAD-containing p-hydroxybenzoate hydroxylase differs from native enzyme. Partial uncoupling of hydroxylation results in the formation of about 0.3 mol of 3,4-dihydroxybenzoate and 0.7 mol of hydrogen peroxide per mol NADPH oxidized. It is proposed that flavin motion in p-hydroxybenzoate hydroxylase is important for efficient reduction and that the flavin "out" conformation is associated with the oxidase activity.


    Related Citations: 
    • Crystal Structure of Wild-Type P-Hydroxybenzoate Hydroxylase Complexed with 4-Aminobenzoate, 2,4-Dihydroxybenzoate and 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.J.,Van Der Bolt, F.,Van Berkel, W.J.H.
      (1994) Biochemistry 33: 10161
    • 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
    • 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
    • Crystal Structure of the Reduced Form of P-Hydroxybenzoate Hydroxylase Refine 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
    • Crystal Structure of the P-Hydroxybenzoate 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
    • The Coenzyme Analogue Adenosine 5-Diphosphoribose Displaces the Fad from 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
    • 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
    • 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.,Schultz, G.E.
      (1983) J.Mol.Biol. 167: 725
    • 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
    • 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


    Organizational Affiliation

    Department of Biochemistry, Agricultural University, Wageningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
P-HYDROXYBENZOATE HYDROXYLASE
A
394Pseudomonas fluorescensMutation(s): 0 
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
FAS
Query on FAS

Download SDF File 
Download CCD File 
A
ARABINO-FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-WCVIGVMNSA-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: 2.1 Å
  • R-Value Work: 0.179 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 72.100α = 90.00
b = 146.400β = 90.00
c = 88.450γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-03-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other