Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 45.31 kDa 
• Atom Count: 3415 
• Residue Count: 394 
• Unique protein chains: 1

1IUX

P-HYDROXYBENZOATE HYDROXYLASE COMPLEXED WITH 4-4-HYDROXYBENZOATE AT PH 9.4

• DOI: 10.2210/pdb1IUX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1995-11-22 Released: 1996-07-11 
• Deposition Author(s): Gatti, D.L., Entsch, B., Ballou, D.P., Ludwig, M.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.173 
• R-Value Observed: 0.173 

Literature

pH-dependent structural changes in the active site of p-hydroxybenzoate hydroxylase point to the importance of proton and water movements during catalysis.

Gatti, D.L., Entsch, B., Ballou, D.P., Ludwig, M.L.

(1996) Biochemistry 35: 567-578

• PubMed: 8555229 
• DOI: 10.1021/bi951344i
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Deprotonation of p-hydroxybenzoate to the phenolate and reprotonation of the hydroxylated dienone intermediate to form the product are essential steps in the reaction catalyzed by p-hydroxybenzoate hydroxylase (PHBH). The mechanism by which protons are transferred in these reactions is not obvious, because the substrate bound in the active site is isolated from solvent. Structure analyses of wild-type and mutant PHBH, with bound p-hydroxybenzoate or p-aminobenzoate, reveal a chain of proton donors and acceptors (the hydroxyl groups of Tyr201 and Tyr385, and two water molecules) that can connect the substrate 4-OH to His72, a surface residue. This chain could provide a pathway for proton transfer to and from the substrate. Using various combinations of pH and substrates, we show that in crystalline PHBH ionizable groups in the chain may rotate and change hydrogen-bond orientation. Molecular dynamics simulations have been used to predict the preferred orientation of hydrogen bonds in the chain as a function of the ionization states of substrate and His72. The calculations suggest that changes in the ionization state of the substrate could be associated with changes in orientation of the hydrogen bonds in the chain. Transfer of water between the chain of proton donors and the solvent also appears to be an essential part of the mechanism that provides reversible transfer of protons during the hydroxylation reaction.

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Related Citations: 

• 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 Structures of Mutant Pseudomonas Aeruginosa P-Hydroxybenzoate Hydroxylases:The Tyr201Phe, Tyr385Phe and Asn300Asp Variants
  Lah, M.S., Palfey, B.A., Schreuder, H.A., Ludwig, M.L.
  (1994) Biochemistry 33: 1555

• Catalytic Function of Tyrosine Residues in Para-Hydroxybenzoate Hydroxylase as Determined by the Study of Site-Directed Mutants
  Entsch, B., Palfey, B.A., Ballou, D.P., Massey, V.
  (1991) J Biol Chem 266: 17341

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Organizational Affiliation: 

Department of Biological Chemistry, University of Michigan, Ann Arbor 48109, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
P-HYDROXYBENZOATE HYDROXYLASE	A	394	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: pobA, PA0247 EC: 1.14.13.2
Find proteins for P20586 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Go to UniProtKB:  P20586

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	A	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
PHB	A	P-HYDROXYBENZOIC ACID C7 H6 O3 FJKROLUGYXJWQN-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
PHB	Kd:  231000   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.173 
• R-Value Observed: 0.173 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.73	α = 90
b = 146.37	β = 90
c = 88.05	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
SDMS	data reduction
SDMS	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-11-22 
• Released Date: 1996-07-11 
Deposition Author(s): Gatti, D.L., Entsch, B., Ballou, D.P., Ludwig, M.L.

Revision History 

• Version 1.0: 1996-07-11
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other