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PDBsum entry 1iut

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Oxidoreductase PDB id
1iut
Jmol
Contents
Protein chain
394 a.a. *
Ligands
FAD
PAB
Waters ×228
* Residue conservation analysis
PDB id:
1iut
Name: Oxidoreductase
Title: P-hydroxybenzoate hydroxylase complexed with 4-aminobenzoate
Structure: P-hydroxybenzoate hydroxylase. Chain: a. Synonym: phbh. Engineered: yes. Other_details: ph 7.4 structure
Source: Pseudomonas aeruginosa. Organism_taxid: 287
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.166    
Authors: D.L.Gatti,B.Entsch,D.P.Ballou,M.L.Ludwig
Key ref:
D.L.Gatti et al. (1996). pH-dependent structural changes in the active site of p-hydroxybenzoate hydroxylase point to the importance of proton and water movements during catalysis. Biochemistry, 35, 567-578. PubMed id: 8555229 DOI: 10.1021/bi951344i
Date:
22-Nov-95     Release date:   03-Apr-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P20586  (PHHY_PSEAE) -  p-hydroxybenzoate hydroxylase
Seq:
Struc:
394 a.a.
394 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.14.13.2  - 4-hydroxybenzoate 3-monooxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Benzoate Metabolism
      Reaction: 4-hydroxybenzoate + NADPH + O2 = protocatechuate + NADP+ + H2O
4-hydroxybenzoate
Bound ligand (Het Group name = PAB)
matches with 81.82% similarity
+ NADPH
+ O(2)
= protocatechuate
+ NADP(+)
+ H(2)O
      Cofactor: FAD
FAD
Bound ligand (Het Group name = FAD) corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   5 terms 
  Biochemical function     oxidoreductase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi951344i Biochemistry 35:567-578 (1996)
PubMed id: 8555229  
 
 
pH-dependent structural changes in the active site of p-hydroxybenzoate hydroxylase point to the importance of proton and water movements during catalysis.
D.L.Gatti, B.Entsch, D.P.Ballou, M.L.Ludwig.
 
  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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19620242 Y.Chen, E.Wendt-Pienkoski, S.R.Rajski, and B.Shen (2009).
In vivo investigation of the roles of FdmM and FdmM1 in fredericamycin biosynthesis unveiling a new family of oxygenases.
  J Biol Chem, 284, 24735-24743.  
17377583 M.E.Taga, N.A.Larsen, A.R.Howard-Jones, C.T.Walsh, and G.C.Walker (2007).
BluB cannibalizes flavin to form the lower ligand of vitamin B12.
  Nature, 446, 449-453.
PDB codes: 2isj 2isk 2isl
  18007046 S.Y.Kwon, B.S.Kang, G.H.Kim, and K.J.Kim (2007).
Expression, purification, crystallization and initial crystallographic characterization of the p-hydroxybenzoate hydroxylase from Corynebacterium glutamicum.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 944-946.  
15010540 E.Hitt, and M.L.Ludwig (2004).
Biography of Martha L. Ludwig.
  Proc Natl Acad Sci U S A, 101, 3727-3728.  
12105208 A.Meyer, M.Würsten, A.Schmid, H.P.Kohler, and B.Witholt (2002).
Hydroxylation of indole by laboratory-evolved 2-hydroxybiphenyl 3-monooxygenase.
  J Biol Chem, 277, 34161-34167.  
12081493 B.A.Palfey, R.Basu, K.K.Frederick, B.Entsch, and D.P.Ballou (2002).
Role of protein flexibility in the catalytic cycle of p-hydroxybenzoate hydroxylase elucidated by the Pro293Ser mutant.
  Biochemistry, 41, 8438-8446.  
10600126 M.Ortiz-Maldonado, D.Gatti, D.P.Ballou, and V.Massey (1999).
Structure-function correlations of the reaction of reduced nicotinamide analogues with p-hydroxybenzoate hydroxylase substituted with a series of 8-substituted flavins.
  Biochemistry, 38, 16636-16647.
PDB code: 1d7l
9369493 F.J.van der Bolt, R.H.van den Heuvel, J.Vervoort, and W.J.van Berkel (1997).
19F NMR study on the regiospecificity of hydroxylation of tetrafluoro-4-hydroxybenzoate by wild-type and Y385F p-hydroxybenzoate hydroxylase: evidence for a consecutive oxygenolytic dehalogenation mechanism.
  Biochemistry, 36, 14192-14201.  
9200706 G.R.Moran, B.Entsch, B.A.Palfey, and D.P.Ballou (1997).
Electrostatic effects on substrate activation in para-hydroxybenzoate hydroxylase: studies of the mutant lysine 297 methionine.
  Biochemistry, 36, 7548-7556.  
9395318 L.Banci, G.Gori-Savellini, and P.Turano (1997).
A molecular dynamics study in explicit water of the reduced and oxidized forms of yeast iso-1-cytochrome c--solvation and dynamic properties of the two oxidation states.
  Eur J Biochem, 249, 716-723.  
15012448 M.Gutman, and E.Nachliel (1997).
Time-resolved dynamics of proton transfer in proteinous systems.
  Annu Rev Phys Chem, 48, 329-356.  
8706756 B.Seibold, M.Matthes, M.H.Eppink, F.Lingens, W.J.Van Berkel, and R.Müller (1996).
4-Hydroxybenzoate hydroxylase from Pseudomonas sp. CBS3. Purification, characterization, gene cloning, sequence analysis and assignment of structural features determining the coenzyme specificity.
  Eur J Biochem, 239, 469-478.  
8703933 G.R.Moran, B.Entsch, B.A.Palfey, and D.P.Ballou (1996).
Evidence for flavin movement in the function of p-hydroxybenzoate hydroxylase from studies of the mutant Arg220Lys.
  Biochemistry, 35, 9278-9285.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.