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PDBsum entry 1foh

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protein ligands Protein-protein interface(s) links
Flavin PDB id
1foh
Jmol
Contents
Protein chains
649 a.a. *
Ligands
FAD ×4
IPH ×4
Waters ×1189
* Residue conservation analysis
PDB id:
1foh
Name: Flavin
Title: Phenol hydroxylase from trichosporon cutaneum
Structure: Phenol hydroxylase. Chain: a, b, c, d. Engineered: yes
Source: Trichosporon cutaneum. Organism_taxid: 5554. Cell_line: 293. Collection: atcc 46490. Gene: phya. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
2.40Å     R-factor:   0.217     R-free:   0.278
Authors: C.Enroth,H.Neujahr,G.Schneider,Y.Lindqvist
Key ref:
C.Enroth et al. (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. PubMed id: 9634698 DOI: 10.1016/S0969-2126(98)00062-8
Date:
26-Mar-98     Release date:   17-Jun-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P15245  (PH2M_TRICU) -  Phenol 2-monooxygenase
Seq:
Struc:
 
Seq:
Struc:
665 a.a.
649 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.1.14.13.7  - Phenol 2-monooxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Phenol + NADPH + O2 = catechol + NADP+ + H2O
Phenol
Bound ligand (Het Group name = IPH)
corresponds exactly
+ NADPH
+ O(2)
= catechol
+ 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!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     oxidoreductase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(98)00062-8 Structure 6:605-617 (1998)
PubMed id: 9634698  
 
 
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.
C.Enroth, H.Neujahr, G.Schneider, Y.Lindqvist.
 
  ABSTRACT  
 
BACKGROUND: The synthesis of phenolic compounds as by-products of industrial reactions poses a serious threat to the environment. Understanding the enzymatic reactions involved in the degradation and detoxification of these compounds is therefore of much interest. Soil-living yeasts use flavin adenine dinucleotide (FAD)-containing enzymes to hydroxylate phenols. This reaction initiates a metabolic sequence permitting utilisation of the aromatic compound as a source of carbon and energy. The phenol hydroxylase from Trichosporon cutaneum hydroxylates phenol to catechol. Phenol is the best substrate, but the enzyme also accepts simple hydroxyl-, amino-, halogen- or methyl-substituted phenols. RESULTS: The crystal structure of phenol hydroxylase in complex with FAD and phenol has been determined at 2.4 A resolution. The structure was solved by the MIRAS method. The protein model consists of two homodimers. The subunit consists of three domains, the first of which contains a beta sheet that binds FAD with a typical beta alpha beta nucleotide-binding motif and also a fingerprint motif for NADPH binding. The active site is located at the interface between the first and second domains; the second domain also binds the phenolic substrate. The third domain contains a thioredoxin-like fold and is involved in dimer contacts. The subunits within the dimer show substantial differences in structure and in FAD conformation. This conformational flexibility allows the substrate to gain access to the active site and excludes solvent during the hydroxylation reaction. CONCLUSIONS: Two of the domains of phenol hydroxylase are similar in structure to p-hydroxybenzoate hydroxylase. Thus, phenol hydroxylase is a member of a family of flavin-containing aromatic hydroxylases that share the same overall fold, in spite of large differences in amino acid sequences and chain length. The structure of phenol hydroxylase is consistent with a hydroxyl transfer mechanism via a peroxo-FAD intermediate. We propose that a movement of FAD takes place in concert with a large conformational change of residues 170-210 during catalysis.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Schematic drawing of the FAD-binding site of phenol hydroxylase in (a) the `in' conformation and (b) the `out' conformation. The two conformations are stabilised by hydrogen bonds, but the bonding pattern is significantly different in the two states. Most notable are the hydrogen bonds from the isoalloxazine ring to the mainchain nitrogen atoms of residues Gly55, Gly369, Met370 and Asn371, which are all broken and in some cases exchanged to hydrogen bonds to water molecules in the out conformation. Residue His 189 (in (a)), depicted with an asterisk, is located in the flexible segment of the polypeptide chain and consequently does not make contacts to FAD in the out conformation, where the loop is in the open conformation. In addition, residues 43-52 move slightly between the two conformations, in concert with the movement of the isoalloxazine ring. Most notable here is Gln52, which works as a hinge for this stretch of residues. In the in case Gln52 is hydrogen bonded to an oxygen atom of the ribityl chain; in the out case Gln52 has moved its sidechain to lie parallel to the isoalloxazine ring. A new hydrogen bond is formed from the same oxygen, but this time to Gln117. Most of the hydrogen bonds to FAD are conserved for this class of aromatic hydroxylases.
 
  The above figure is reprinted by permission from Cell Press: Structure (1998, 6, 605-617) copyright 1998.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21290541 K.Groom, A.Bhattacharya, and D.L.Zechel (2011).
Rebeccamycin and Staurosporine Biosynthesis: Insight into the Mechanisms of the Flavin-Dependent Monooxygenases RebC and StaC.
  Chembiochem, 12, 396-400.  
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.  
21264995 T.Awakawa, N.Fujita, M.Hayakawa, Y.Ohnishi, and S.Horinouchi (2011).
Characterization of the Biosynthesis Gene Cluster for Alkyl-O-Dihydrogeranyl-Methoxyhydroquinones in Actinoplanes missouriensis.
  Chembiochem, 12, 439-448.  
20066695 B.Tian, Y.Tu, A.Strid, and L.A.Eriksson (2010).
Hydroxylation and ring-opening mechanism of an unusual flavoprotein monooxygenase, 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase: a theoretical study.
  Chemistry, 16, 2557-2566.  
20055497 U.E.Ukaegbu, A.Kantz, M.Beaton, G.T.Gassner, and A.C.Rosenzweig (2010).
Structure and ligand binding properties of the epoxidase component of styrene monooxygenase .
  Biochemistry, 49, 1678-1688.
PDB code: 3ihm
19218392 J.J.Zhang, H.Liu, Y.Xiao, X.E.Zhang, and N.Y.Zhou (2009).
Identification and characterization of catabolic para-nitrophenol 4-monooxygenase and para-benzoquinone reductase from Pseudomonas sp. strain WBC-3.
  J Bacteriol, 191, 2703-2710.  
19368334 K.M.Meneely, E.W.Barr, J.M.Bollinger, and A.L.Lamb (2009).
Kinetic mechanism of ornithine hydroxylase (PvdA) from Pseudomonas aeruginosa: substrate triggering of O2 addition but not flavin reduction.
  Biochemistry, 48, 4371-4376.  
19148270 W.Tong, Y.Wei, L.F.Murga, M.J.Ondrechen, and R.J.Williams (2009).
Partial order optimum likelihood (POOL): maximum likelihood prediction of protein active site residues using 3D Structure and sequence properties.
  PLoS Comput Biol, 5, e1000266.  
17562190 J.Xiao, and J.M.Vanbriesen (2008).
Expanded thermodynamic true yield prediction model: adjustments and limitations.
  Biodegradation, 19, 99.  
18364359 M.Funabashi, N.Funa, and S.Horinouchi (2008).
Phenolic lipids synthesized by type III polyketide synthase confer penicillin resistance on Streptomyces griseus.
  J Biol Chem, 283, 13983-13991.  
17654627 K.Palmu, K.Ishida, P.Mäntsälä, C.Hertweck, and M.Metsä-Ketelä (2007).
Artificial reconstruction of two cryptic angucycline antibiotic biosynthetic pathways.
  Chembiochem, 8, 1577-1584.  
18059531 M.Zhao, X.Jia, C.Wang, Q.Li, K.Zhou, L.Wang, H.Liu, and S.Peng (2007).
PAK: an essential motif for forming beta-turn structures and exhibiting the thrombolytic effect of P6A and its analogs.
  Biochem Cell Biol, 85, 730-740.  
17804419 S.H.Kim, T.Hisano, K.Takeda, W.Iwasaki, A.Ebihara, and K.Miki (2007).
Crystal structure of the oxygenase component (HpaB) of the 4-hydroxyphenylacetate 3-monooxygenase from Thermus thermophilus HB8.
  J Biol Chem, 282, 33107-33117.
PDB codes: 2yyg 2yyi 2yyj 2yyk 2yyl 2yym
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
16905618 K.A.Feenstra, K.Hofstetter, R.Bosch, A.Schmid, J.N.Commandeur, and N.P.Vermeulen (2006).
Enantioselective substrate binding in a monooxygenase protein model by molecular dynamics and docking.
  Biophys J, 91, 3206-3216.
PDB code: 2hd8
16275926 M.Nadella, M.A.Bianchet, S.B.Gabelli, J.Barrila, and L.M.Amzel (2005).
Structure and activity of the axon guidance protein MICAL.
  Proc Natl Acad Sci U S A, 102, 16830-16835.
PDB code: 2bra
  16511028 W.Oonanant, J.Sucharitakul, J.Yuvaniyama, and P.Chaiyen (2005).
Crystallization and preliminary X-ray crystallographic analysis of 2-methyl-3-hydroxypyridine-5-carboxylic acid (MHPC) oxygenase from Pseudomonas sp. MA-1.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 312-314.  
15066836 M.Dai, and S.D.Copley (2004).
Genome shuffling improves degradation of the anthropogenic pesticide pentachlorophenol by Sphingobium chlorophenolicum ATCC 39723.
  Appl Environ Microbiol, 70, 2391-2397.  
12657798 A.Meyer, D.Tanner, A.Schmid, D.F.Sargent, H.P.Kohler, and B.Witholt (2003).
Crystallization and preliminary X-ray analysis of native and selenomethionine 2-hydroxybiphenyl 3-monooxygenase.
  Acta Crystallogr D Biol Crystallogr, 59, 741-743.  
12925790 C.Enroth (2003).
High-resolution structure of phenol hydroxylase and correction of sequence errors.
  Acta Crystallogr D Biol Crystallogr, 59, 1597-1602.
PDB code: 1pn0
14600375 T.Nakamura, T.Motoyama, T.Hirokawa, S.Hirono, and I.Yamaguchi (2003).
Computer-aided modeling of pentachlorophenol 4-monooxygenase and site-directed mutagenesis of its active site.
  Chem Pharm Bull (Tokyo), 51, 1293-1298.  
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.  
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.  
11747900 M.D.Krasowski, K.Nishikawa, N.Nikolaeva, A.Lin, and N.L.Harrison (2001).
Methionine 286 in transmembrane domain 3 of the GABAA receptor beta subunit controls a binding cavity for propofol and other alkylphenol general anesthetics.
  Neuropharmacology, 41, 952-964.  
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.  
11514662 O.Dym, and D.Eisenberg (2001).
Sequence-structure analysis of FAD-containing proteins.
  Protein Sci, 10, 1712-1728.  
11092935 J.Beynon, E.R.Rafanan, B.Shen, and A.J.Fisher (2000).
Crystallization and preliminary X-ray analysis of tetracenomycin A2 oxygenase: a flavoprotein hydroxylase involved in polyketide biosynthesis.
  Acta Crystallogr D Biol Crystallogr, 56, 1647-1651.  
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.  
10651042 O.Vallon (2000).
New sequence motifs in flavoproteins: evidence for common ancestry and tools to predict structure.
  Proteins, 38, 95.  
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
10064136 M.Stehr, L.Smau, M.Singh, O.Seth, P.Macheroux, S.Ghisla, and H.Diekmann (1999).
Studies with lysine N6-hydroxylase. Effect of a mutation in the assumed FAD binding site on coenzyme affinities and on lysine hydroxylating activity.
  Biol Chem, 380, 47-54.  
10368302 P.Trickey, M.A.Wagner, M.S.Jorns, and F.S.Mathews (1999).
Monomeric sarcosine oxidase: structure of a covalently flavinylated amine oxidizing enzyme.
  Structure, 7, 331-345.
PDB codes: 1b3m 1l9f 2gb0
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.  
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 code is shown on the right.