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PDBsum entry 1pbc

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Oxidoreductase PDB id
1pbc
Jmol
Contents
Protein chain
391 a.a. *
Ligands
FAD
BHA
Waters ×208
* Residue conservation analysis
PDB id:
1pbc
Name: Oxidoreductase
Title: Crystal structures of wild-type p-hydroxybenzoate hydroxylas complexed with 4-aminobenzoate, 2,4-dihydroxybenzoate and 2 4-aminobenzoate and of the try222ala mutant, complexed with hydroxy-4-aminobenzoate. Evidence for a proton channel and binding mode of the flavin ring
Structure: P-hydroxybenzoate hydroxylase. Chain: a. Engineered: yes
Source: Pseudomonas fluorescens. Organism_taxid: 294
Biol. unit: Dimer (from PQS)
Resolution:
2.80Å     R-factor:   0.145    
Authors: H.A.Schreuder,F.J.T.Van Der Bolt,W.J.H.Van Berkel
Key ref:
H.A.Schreuder et al. (1994). 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. Biochemistry, 33, 10161-10170. PubMed id: 7520279 DOI: 10.1021/bi00199a044
Date:
06-Jul-94     Release date:   30-Sep-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00438  (PHHY_PSEFL) -  p-hydroxybenzoate hydroxylase
Seq:
Struc:
394 a.a.
391 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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 = BHA)
matches with 75.00% 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/bi00199a044 Biochemistry 33:10161-10170 (1994)
PubMed id: 7520279  
 
 
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.
H.A.Schreuder, A.Mattevi, G.Obmolova, K.H.Kalk, W.G.Hol, F.J.van der Bolt, W.J.van Berkel.
 
  ABSTRACT  
 
The crystal structures of wild-type p-hydroxybenzoate hydroxylase from Pseudomonas fluorescens, complexed with the substrate analogues 4-aminobenzoate, 2,4-dihydroxybenzoate, and 2-hydroxy-4-aminobenzoate have been determined at 2.3-, 2.5-, and 2.8-A resolution, respectively. In addition, the crystal structure of a Tyr222Ala mutant, complexed with 2-hydroxy-4-aminobenzoate, has been determined at 2.7-A resolution. The structures have been refined to R factors between 14.5% and 15.8% for data between 8.0 A and the high-resolution limit. The differences between these complexes and the wild-type enzyme-substrate complex are all concentrated in the active site region. Binding of substrate analogues bearing a 4-amino group (4-aminobenzoate and 2-hydroxy-4-aminobenzoate) leads to binding of a water molecule next to the active site Tyr385. As a result, a continuous hydrogen-bonding network is present between the 4-amino group of the substrate analogue and the side chain of His72. It is likely that this hydrogen-bonding network is transiently present during normal catalysis, where it may or may not function as a proton channel assisting the deprotonation of the 4-hydroxyl group of the normal substrate upon binding to the active site. Binding of substrate analogues bearing a hydroxyl group at the 2-position (2,4-dihydroxybenzoate and 2-hydroxy-4-aminobenzoate) leads to displacement of the flavin ring from the active site. The flavin is no longer in the active site (the "in" conformation) but is in the cleft leading to the active site instead (the "out" conformation). It is proposed that movement of the FAD out of the active site may provide an entrance for the substrate to enter the active site and an exit for the product to leave.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20949369 S.Sah, and P.S.Phale (2011).
1-Naphthol 2-hydroxylase from Pseudomonas sp. strain C6: purification, characterization and chemical modification studies.
  Biodegradation, 22, 517-526.  
21183988 Y.W.Tan, and H.Yang (2011).
Seeing the forest for the trees: fluorescence studies of single enzymes in the context of ensemble experiments.
  Phys Chem Chem Phys, 13, 1709-1721.  
18176933 E.V.Kudryashova, A.J.Visser, and W.J.van Berkel (2008).
Monomer formation and function of p-hydroxybenzoate hydroxylase in reverse micelles and in dimethylsulfoxide/water mixtures.
  Chembiochem, 9, 413-419.  
  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.  
17582174 T.N.Gustafsson, T.Sandalova, J.Lu, A.Holmgren, and G.Schneider (2007).
High-resolution structures of oxidized and reduced thioredoxin reductase from Helicobacter pylori.
  Acta Crystallogr D Biol Crystallogr, 63, 833-843.
PDB codes: 2q0k 2q0l
16492664 A.H.Westphal, A.Matorin, M.A.Hink, J.W.Borst, W.J.van Berkel, and A.J.Visser (2006).
Real-time enzyme dynamics illustrated with fluorescence spectroscopy of p-hydroxybenzoate hydroxylase.
  J Biol Chem, 281, 11074-11081.  
16275925 C.Siebold, N.Berrow, T.S.Walter, K.Harlos, R.J.Owens, D.I.Stuart, J.R.Terman, A.L.Kolodkin, R.J.Pasterkamp, and E.Y.Jones (2005).
High-resolution structure of the catalytic region of MICAL (molecule interacting with CasL), a multidomain flavoenzyme-signaling molecule.
  Proc Natl Acad Sci U S A, 102, 16836-16841.
PDB codes: 2bry 2c4c
12684497 B.A.Palfey, Y.V.Murthy, and V.Massey (2003).
Altered balance of half-reactions in p-hydroxybenzoate hydroxylase caused by substituting the 2'-carbon of FAD with fluorine.
  J Biol Chem, 278, 22210-22216.  
12912903 D.Leys, J.Basran, and N.S.Scrutton (2003).
Channelling and formation of 'active' formaldehyde in dimethylglycine oxidase.
  EMBO J, 22, 4038-4048.
PDB codes: 1pj5 1pj6 1pj7
12968028 U.Kirchner, A.H.Westphal, R.Müller, and W.J.van Berkel (2003).
Phenol hydroxylase from Bacillus thermoglucosidasius A7, a two-protein component monooxygenase with a dual role for FAD.
  J Biol Chem, 278, 47545-47553.  
11733527 A.Meyer, A.Schmid, M.Held, A.H.Westphal, M.Rothlisberger, H.P.Kohler, W.J.van Berkel, and B.Witholt (2002).
Changing the substrate reactivity of 2-hydroxybiphenyl 3-monooxygenase from Pseudomonas azelaica HBP1 by directed evolution.
  J Biol Chem, 277, 5575-5582.  
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.  
11805318 J.Wang, M.Ortiz-Maldonado, B.Entsch, V.Massey, D.Ballou, and D.L.Gatti (2002).
Protein and ligand dynamics in 4-hydroxybenzoate hydroxylase.
  Proc Natl Acad Sci U S A, 99, 608-613.
PDB codes: 1k0i 1k0j 1k0l
11248022 M.D.Altose, Y.Zheng, J.Dong, B.A.Palfey, and P.R.Carey (2001).
Comparing protein-ligand interactions in solution and single crystals by Raman spectroscopy.
  Proc Natl Acad Sci U S A, 98, 3006-3011.  
11170433 M.Ortiz-Maldonado, D.P.Ballou, and V.Massey (2001).
A rate-limiting conformational change of the flavin in p-hydroxybenzoate hydroxylase is necessary for ligand exchange and catalysis: studies with 8-mercapto- and 8-hydroxy-flavins.
  Biochemistry, 40, 1091-1101.  
10716694 A.A.Raibekas, K.Fukui, and V.Massey (2000).
Design and properties of human D-amino acid oxidase with covalently attached flavin.
  Proc Natl Acad Sci U S A, 97, 3089-3093.  
11082194 M.H.Eppink, E.Cammaart, D.Van Wassenaar, W.J.Middelhoven, and W.J.van Berkel (2000).
Purification and properties of hydroquinone hydroxylase, a FAD-dependent monooxygenase involved in the catabolism of 4-hydroxybenzoate in Candida parapsilosis CBS604.
  Eur J Biochem, 267, 6832-6840.  
10504385 E.Pessione, S.Divari, E.Griva, M.Cavaletto, G.L.Rossi, G.Gilardi, and C.Giunta (1999).
Phenol hydroxylase from Acinetobacter radioresistens is a multicomponent enzyme. Purification and characterization of the reductase moiety.
  Eur J Biochem, 265, 549-555.  
10320359 G.R.Moran, B.Entsch, B.A.Palfey, and D.P.Ballou (1999).
Mechanistic insights into p-hydroxybenzoate hydroxylase from studies of the mutant Ser212Ala.
  Biochemistry, 38, 6292-6299.  
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
10387058 M.Ortiz-Maldonado, D.P.Ballou, and V.Massey (1999).
Use of free energy relationships to probe the individual steps of hydroxylation of p-hydroxybenzoate hydroxylase: studies with a series of 8-substituted flavins.
  Biochemistry, 38, 8124-8137.  
10559214 W.A.Suske, W.J.van Berkel, and H.P.Kohler (1999).
Catalytic mechanism of 2-hydroxybiphenyl 3-monooxygenase, a flavoprotein from Pseudomonas azelaica HBP1.
  J Biol Chem, 274, 33355-33365.  
10606503 Y.Zheng, J.Dong, B.A.Palfey, and P.R.Carey (1999).
Using Raman spectroscopy to monitor the solvent-exposed and "buried" forms of flavin in p-hydroxybenzoate hydroxylase.
  Biochemistry, 38, 16727-16732.  
9546198 A.Mattevi (1998).
The PHBH fold: not only flavoenzymes.
  Biophys Chem, 70, 217-222.  
9634698 C.Enroth, H.Neujahr, G.Schneider, and Y.Lindqvist (1998).
The crystal structure of phenol hydroxylase in complex with FAD and phenol provides evidence for a concerted conformational change in the enzyme and its cofactor during catalysis.
  Structure, 6, 605-617.
PDB code: 1foh
9694855 M.H.Eppink, H.A.Schreuder, and W.J.van Berkel (1998).
Interdomain binding of NADPH in p-hydroxybenzoate hydroxylase as suggested by kinetic, crystallographic and modeling studies of histidine 162 and arginine 269 variants.
  J Biol Chem, 273, 21031-21039.
PDB codes: 1bgj 1bgn
9434899 A.Mattevi, M.A.Vanoni, and B.Curti (1997).
Structure of D-amino acid oxidase: new insights from an old enzyme.
  Curr Opin Struct Biol, 7, 804-810.  
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.  
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.  
8555229 D.L.Gatti, B.Entsch, D.P.Ballou, and M.L.Ludwig (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.
PDB codes: 1ius 1iut 1iuu 1iuv 1iuw 1iux
8647102 F.J.van der Bolt, J.Vervoort, and W.J.van Berkel (1996).
Flavin motion in p-hydroxybenzoate hydroxylase. Substrate and effector specificity of the Tyr22-->Ala mutant.
  Eur J Biochem, 237, 592-600.  
8804824 J.F.Gibrat, T.Madej, and S.H.Bryant (1996).
Surprising similarities in structure comparison.
  Curr Opin Struct Biol, 6, 377-385.  
7628466 M.H.Eppink, H.A.Schreuder, and W.J.Van Berkel (1995).
Structure and function of mutant Arg44Lys of 4-hydroxybenzoate hydroxylase implications for NADPH binding.
  Eur J Biochem, 231, 157-165.
PDB code: 1bkw
7499374 Y.V.Murthy, and V.Massey (1995).
Chemical modification of the N-10 ribityl side chain of flavins. Effects on properties of flavoprotein disulfide oxidoreductases.
  J Biol Chem, 270, 28586-28594.  
  7756982 W.J.van Berkel, M.H.Eppink, and H.A.Schreuder (1994).
Crystal structure of p-hydroxybenzoate hydroxylase reconstituted with the modified FAD present in alcohol oxidase from methylotrophic yeasts: evidence for an arabinoflavin.
  Protein Sci, 3, 2245-2253.
PDB code: 1pdh
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.