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Oxidoreductase (oxygenase) PDB id
1han
Jmol
Contents
Protein chain
288 a.a. *
Ligands
TBU
Metals
_FE ×2
Waters ×139
* Residue conservation analysis
PDB id:
1han
Name: Oxidoreductase (oxygenase)
Title: Crystal structure of the biphenyl-cleaving extradiol dioxyge a pcb-degrading pseudomonad
Structure: 2,3-dihydroxybiphenyl 1,2-dioxygenase. Chain: a. Synonym: biphenyl-2,3-diol 1,2-dioxygenase, dhbd, bphc. Engineered: yes. Mutation: yes. Other_details: fe(ii) form under anaerobic conditions
Source: Burkholderia xenovorans. Organism_taxid: 266265. Strain: lb400. Gene: bphc. Expressed in: burkholderia cepacia. Expression_system_taxid: 292. Other_details: hyperexpressed in the parent strain
Biol. unit: Tetramer (from PQS)
Resolution:
1.90Å     R-factor:   0.162     R-free:   0.190
Authors: S.Han,J.T.Bolin
Key ref: S.Han et al. (1995). Crystal structure of the biphenyl-cleaving extradiol dioxygenase from a PCB-degrading pseudomonad. Science, 270, 976-980. PubMed id: 7481800 DOI: 10.1126/science.270.5238.976
Date:
30-Aug-95     Release date:   14-Nov-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P47228  (BPHC_BURXL) -  Biphenyl-2,3-diol 1,2-dioxygenase
Seq:
Struc: 		298 a.a.
288 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.13.11.39  - Biphenyl-2,3-diol 1,2-dioxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Biphenyl-2,3-diol + O2 = 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate
Biphenyl-2,3-diol
 + O(2)
 = 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate
      Cofactor: Manganese or iron
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   4 terms 
  Biochemical function     catalytic activity     8 terms  

 

 
    reference    
 
 
DOI no: 10.1126/science.270.5238.976 Science 270:976-980 (1995)
PubMed id: 7481800  
 
 
Crystal structure of the biphenyl-cleaving extradiol dioxygenase from a PCB-degrading pseudomonad.
S.Han, L.D.Eltis, K.N.Timmis, S.W.Muchmore, J.T.Bolin.
 
  ABSTRACT  
 
Polychlorinated biphenyls (PCBs) typify a class of stable aromatic pollutants that are targeted by bioremediation strategies. In the aerobic degradation of biphenyl by bacteria, the key step of ring cleavage is catalyzed by an Fe(II)-dependent extradiol dioxygenase. The crystal structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase from a PCB-degrading strain of Pseudomonas cepacia has been determined at 1.9 angstrom resolution. The monomer comprises amino- and carboxyl-terminal domains. Structural homology between and within the domains reveals evolutionary relationships within the extradiol dioxygenase family. The iron atom has five ligands in square pyramidal geometry: one glutamate and two histidine side chains, and two water molecules.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21153851 A.J.Fielding, E.G.Kovaleva, E.R.Farquhar, J.D.Lipscomb, and L.Que (2011).
A hyperactive cobalt-substituted extradiol-cleaving catechol dioxygenase.
  J Biol Inorg Chem, 16, 341-355.
PDB codes: 3ojj 3ojk 3ojn 3ojt
21246129 N.Anitha, and M.Palaniandavar (2011).
Mononuclear iron(III) complexes of 3N ligands in organized assemblies: spectral and redox properties and attainment of regioselective extradiol dioxygenase activity.
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20822442 M.Morar, and G.D.Wright (2010).
The genomic enzymology of antibiotic resistance.
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19566698 H.Suenaga, S.Mizuta, and K.Miyazaki (2009).
The molecular basis for adaptive evolution in novel extradiol dioxygenases retrieved from the metagenome.
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19300498 K.C.Yam, I.D'Angelo, R.Kalscheuer, H.Zhu, J.X.Wang, V.Snieckus, L.H.Ly, P.J.Converse, W.R.Jacobs, N.Strynadka, and L.D.Eltis (2009).
Studies of a ring-cleaving dioxygenase illuminate the role of cholesterol metabolism in the pathogenesis of Mycobacterium tuberculosis.
  PLoS Pathog, 5, e1000344.
PDB codes: 2zi8 2zyq
19300822 M.Brivio, J.Schlosrich, M.Ahmad, C.Tolond, and T.D.Bugg (2009).
Investigation of acid-base catalysis in the extradiol and intradiol catechol dioxygenase reactions using a broad specificity mutant enzyme and model chemistry.
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18277980 E.G.Kovaleva, and J.D.Lipscomb (2008).
Versatility of biological non-heme Fe(II) centers in oxygen activation reactions.
  Nat Chem Biol, 4, 186-193.  
18826259 E.G.Kovaleva, and J.D.Lipscomb (2008).
Intermediate in the O-O bond cleavage reaction of an extradiol dioxygenase.
  Biochemistry, 47, 11168-11170.
PDB codes: 3ecj 3eck
  18496607 J.A.Conrad, and G.R.Moran (2008).
The Interaction of Hydroxymandelate Synthase with the 4-Hydroxyphenylpyruvate Dioxygenase Inhibitor: NTBC.
  Inorganica Chim Acta, 361, 1197-1201.  
19007887 J.D.Lipscomb (2008).
Mechanism of extradiol aromatic ring-cleaving dioxygenases.
  Curr Opin Struct Biol, 18, 644-649.  
18492808 J.P.Emerson, E.G.Kovaleva, E.R.Farquhar, J.D.Lipscomb, and L.Que (2008).
Swapping metals in Fe- and Mn-dependent dioxygenases: evidence for oxygen activation without a change in metal redox state.
  Proc Natl Acad Sci U S A, 105, 7347-7352.
PDB code: 3bza
18558332 K.Furukawa, and H.Fujihara (2008).
Microbial degradation of polychlorinated biphenyls: biochemical and molecular features.
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19050788 K.Sundaravel, T.Dhanalakshmi, E.Suresh, and M.Palaniandavar (2008).
Synthesis, structure, spectra and reactivity of iron(III) complexes of facially coordinating and sterically hindering 3N ligands as models for catechol dioxygenases.
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17446402 E.G.Kovaleva, and J.D.Lipscomb (2007).
Crystal structures of Fe2+ dioxygenase superoxo, alkylperoxo, and bound product intermediates.
  Science, 316, 453-457.
PDB codes: 2ig9 2iga
17567087 E.G.Kovaleva, M.B.Neibergall, S.Chakrabarty, and J.D.Lipscomb (2007).
Finding intermediates in the O2 activation pathways of non-heme iron oxygenases.
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16477023 H.Sugimoto, S.Oda, T.Otsuki, T.Hino, T.Yoshida, and Y.Shiro (2006).
Crystal structure of human indoleamine 2,3-dioxygenase: catalytic mechanism of O2 incorporation by a heme-containing dioxygenase.
  Proc Natl Acad Sci U S A, 103, 2611-2616.
PDB codes: 2d0t 2d0u
  16511281 K.Sugimoto, K.Matsufuzi, H.Ohnuma, M.Senda, M.Fukuda, and T.Senda (2006).
Crystallization and preliminary crystallographic analysis of the catechol 2,3-dioxygenase PheB from Bacillus stearothermophilus BR219.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 125-127.  
16217642 J.P.Emerson, M.L.Wagner, M.F.Reynolds, L.Que, M.J.Sadowsky, and L.P.Wackett (2005).
The role of histidine 200 in MndD, the Mn(II)-dependent 3,4-dihydroxyphenylacetate 2,3-dioxygenase from Arthrobacter globiformis CM-2, a site-directed mutagenesis study.
  J Biol Inorg Chem, 10, 751-760.  
15715866 J.Wesche, E.Hammer, D.Becher, G.Burchhardt, and F.Schauer (2005).
The bphC gene-encoded 2,3-dihydroxybiphenyl-1,2-dioxygenase is involved in complete degradation of dibenzofuran by the biphenyl-degrading bacterium Ralstonia sp. SBUG 290.
  J Appl Microbiol, 98, 635-645.  
16317455 M.L.Neidig, and E.I.Solomon (2005).
Structure-function correlations in oxygen activating non-heme iron enzymes.
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15629912 P.D.Fortin, A.T.Lo, M.A.Haro, S.R.Kaschabek, W.Reineke, and L.D.Eltis (2005).
Evolutionarily divergent extradiol dioxygenases possess higher specificities for polychlorinated biphenyl metabolites.
  J Bacteriol, 187, 415-421.  
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15487948 C.K.Brown, M.W.Vetting, C.A.Earhart, and D.H.Ohlendorf (2004).
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PDB codes: 2bum 2buq 2bur 2but 2buv
15583384 K.Iwata, H.Noguchi, Y.Usami, J.W.Nam, Z.Fujimoto, H.Mizuno, H.Habe, H.Yamane, T.Omori, and H.Nojiri (2004).
Crystallization and preliminary crystallographic analysis of the 2'-aminobiphenyl-2,3-diol 1,2-dioxygenase from the carbazole-degrader Pseudomonas resinovorans strain CA10.
  Acta Crystallogr D Biol Crystallogr, 60, 2340-2342.  
15028678 M.W.Vetting, L.P.Wackett, L.Que, J.D.Lipscomb, and D.H.Ohlendorf (2004).
Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenases.
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PDB codes: 1f1r 1f1u 1f1v 1f1x 1q0c 1q0o
12598659 E.I.Solomon, A.Decker, and N.Lehnert (2003).
Non-heme iron enzymes: contrasts to heme catalysis.
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12562795 F.H.Vaillancourt, M.A.Haro, N.M.Drouin, Z.Karim, H.Maaroufi, and L.D.Eltis (2003).
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Expression, purification, and characterization of 2'-aminobiphenyl-2,3-diol 1,2-dioxygenase from carbazole-degrader Pseudomonas resinovorans strain CA10.
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PDB code: 1k4n
  12377129 A.E.Todd, C.A.Orengo, and J.M.Thornton (2002).
Sequence and structural differences between enzyme and nonenzyme homologs.
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12047377 L.Hörnsten, C.Su, A.E.Osbourn, U.Hellman, and E.H.Oliw (2002).
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  Nat Struct Biol, 9, 934-939.
PDB codes: 1lgt 1lkd
  12121648 T.W.Martin, Z.Dauter, Y.Devedjiev, P.Sheffield, F.Jelen, M.He, D.H.Sherman, J.Otlewski, Z.S.Derewenda, and U.Derewenda (2002).
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  Structure, 10, 933-942.
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12107126 Y.Ge, F.H.Vaillancourt, N.Y.Agar, and L.D.Eltis (2002).
Reactivity of toluate dioxygenase with substituted benzoates and dioxygen.
  J Bacteriol, 184, 4096-4103.  
  11470438 A.A.McCarthy, H.M.Baker, S.C.Shewry, M.L.Patchett, and E.N.Baker (2001).
Crystal structure of methylmalonyl-coenzyme A epimerase from P. shermanii: a novel enzymatic function on an ancient metal binding scaffold.
  Structure, 9, 637-646.
PDB codes: 1jc4 1jc5
11395407 J.A.Gerlt, and P.C.Babbitt (2001).
Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies.
  Annu Rev Biochem, 70, 209-246.  
  11578928 T.D.Bugg (2001).
Oxygenases: mechanisms and structural motifs for O(2) activation.
  Curr Opin Chem Biol, 5, 550-555.  
11244073 U.Riegert, S.Bürger, and A.Stolz (2001).
Altering catalytic properties of 3-chlorocatechol-oxidizing extradiol dioxygenase from Sphingomonas xenophaga BN6 by random mutagenesis.
  J Bacteriol, 183, 2322-2330.  
  11188691 C.L.Colbert, M.M.Couture, L.D.Eltis, and J.T.Bolin (2000).
A cluster exposed: structure of the Rieske ferredoxin from biphenyl dioxygenase and the redox properties of Rieske Fe-S proteins.
  Structure, 8, 1267-1278.
PDB code: 1fqt
10633115 E.Andújar, M.J.Hernáez, S.R.Kaschabek, W.Reineke, and E.Santero (2000).
Identification of an extradiol dioxygenase involved in tetralin biodegradation: gene sequence analysis and purification and characterization of the gene product.
  J Bacteriol, 182, 789-795.  
12483570 K.Furukawa (2000).
Biochemical and genetic bases of microbial degradation of polychlorinated biphenyls (PCBs).
  J Gen Appl Microbiol, 46, 283-296.  
10913283 M.M.He, S.L.Clugston, J.F.Honek, and B.W.Matthews (2000).
Determination of the structure of Escherichia coli glyoxalase I suggests a structural basis for differential metal activation.
  Biochemistry, 39, 8719-8727.
PDB codes: 1f9z 1fa5 1fa6 1fa7 1fa8
10891075 M.W.Vetting, D.A.D'Argenio, L.N.Ornston, and D.H.Ohlendorf (2000).
Structure of Acinetobacter strain ADP1 protocatechuate 3, 4-dioxygenase at 2.2 A resolution: implications for the mechanism of an intradiol dioxygenase.
  Biochemistry, 39, 7943-7955.
PDB codes: 1eo2 1eo9 1eoa 1eob 1eoc
  10801478 M.W.Vetting, and D.H.Ohlendorf (2000).
The 1.8 A crystal structure of catechol 1,2-dioxygenase reveals a novel hydrophobic helical zipper as a subunit linker.
  Structure, 8, 429-440.
PDB codes: 1dlm 1dlq 1dlt 1dmh
11076500 R.N.Armstrong (2000).
Mechanistic diversity in a metalloenzyme superfamily.
  Biochemistry, 39, 13625-13632.  
  9973359 A.E.Mars, J.Kingma, S.R.Kaschabek, W.Reineke, and D.B.Janssen (1999).
Conversion of 3-chlorocatechol by various catechol 2,3-dioxygenases and sequence analysis of the chlorocatechol dioxygenase region of Pseudomonas putida GJ31.
  J Bacteriol, 181, 1309-1318.  
  10368270 A.Kita, S.Kita, I.Fujisawa, K.Inaka, T.Ishida, K.Horiike, M.Nozaki, and K.Miki (1999).
An archetypical extradiol-cleaving catecholic dioxygenase: the crystal structure of catechol 2,3-dioxygenase (metapyrocatechase) from Ppseudomonas putida mt-2.
  Structure, 7, 25-34.
PDB code: 1mpy
10393920 A.M.Rocklin, D.L.Tierney, V.Kofman, N.M.Brunhuber, B.M.Hoffman, R.E.Christoffersen, N.O.Reich, J.D.Lipscomb, and L.Que (1999).
Role of the nonheme Fe(II) center in the biosynthesis of the plant hormone ethylene.
  Proc Natl Acad Sci U S A, 96, 7905-7909.  
10360943 B.A.Bernat, L.T.Laughlin, and R.N.Armstrong (1999).
Elucidation of a monovalent cation dependence and characterization of the divalent cation binding site of the fosfomycin resistance protein (FosA).
  Biochemistry, 38, 7462-7469.  
  9922262 B.E.Haigler, G.R.Johnson, W.C.Suen, and J.C.Spain (1999).
Biochemical and genetic evidence for meta-ring cleavage of 2,4, 5-trihydroxytoluene in Burkholderia sp. strain DNT.
  J Bacteriol, 181, 965-972.  
10607676 C.J.Schofield, and Z.Zhang (1999).
Structural and mechanistic studies on 2-oxoglutarate-dependent oxygenases and related enzymes.
  Curr Opin Struct Biol, 9, 722-731.  
10600135 E.L.Hegg, A.K.Whiting, R.E.Saari, J.McCracken, R.P.Hausinger, and L.Que (1999).
Herbicide-degrading alpha-keto acid-dependent enzyme TfdA: metal coordination environment and mechanistic insights.
  Biochemistry, 38, 16714-16726.  
  10224022 J.Wiegel, X.Zhang, and Q.Wu (1999).
Anaerobic dehalogenation of hydroxylated polychlorinated biphenyls by Desulfitobacterium dehalogenans.
  Appl Environ Microbiol, 65, 2217-2221.  
  10542173 K.Miyauchi, Y.Adachi, Y.Nagata, and M.Takagi (1999).
Cloning and sequencing of a novel meta-cleavage dioxygenase gene whose product is involved in degradation of gamma-hexachlorocyclohexane in Sphingomonas paucimobilis.
  J Bacteriol, 181, 6712-6719.  
  10467151 K.Sugimoto, T.Senda, H.Aoshima, E.Masai, M.Fukuda, and Y.Mitsui (1999).
Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions.
  Structure, 7, 953-965.
PDB codes: 1b4u 1bou
  10467142 L.Serre, A.Sailland, D.Sy, P.Boudec, A.Rolland, E.Pebay-Peyroula, and C.Cohen-Addad (1999).
Crystal structure of Pseudomonas fluorescens 4-hydroxyphenylpyruvate dioxygenase: an enzyme involved in the tyrosine degradation pathway.
  Structure, 7, 977-988.
PDB code: 1cjx
  10427057 M.Seeger, M.Zielinski, K.N.Timmis, and B.Hofer (1999).
Regiospecificity of dioxygenation of di- to pentachlorobiphenyls and their degradation to chlorobenzoates by the bph-encoded catabolic pathway of Burkholderia sp. strain LB400.
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  9864349 S.Beil, K.N.Timmis, and D.H.Pieper (1999).
Genetic and biochemical analyses of the tec operon suggest a route for evolution of chlorobenzene degradation genes.
  J Bacteriol, 181, 341-346.  
  10438749 U.Riegert, G.Heiss, A.E.Kuhm, C.Müller, M.Contzen, H.J.Knackmuss, and A.Stolz (1999).
Catalytic properties of the 3-chlorocatechol-oxidizing 2, 3-dihydroxybiphenyl 1,2-dioxygenase from Sphingomonas sp. strain BN6.
  J Bacteriol, 181, 4812-4817.  
9671502 A.P.Saint-Jean, K.R.Phillips, D.J.Creighton, and M.J.Stone (1998).
Active monomeric and dimeric forms of Pseudomonas putida glyoxalase I: evidence for 3D domain swapping.
  Biochemistry, 37, 10345-10353.  
  9634695 B.Kauppi, K.Lee, E.Carredano, R.E.Parales, D.T.Gibson, H.Eklund, and S.Ramaswamy (1998).
Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase.
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PDB code: 1ndo
9561730 F.M.Duffner, and R.Müller (1998).
A novel phenol hydroxylase and catechol 2,3-dioxygenase from the thermophilic Bacillus thermoleovorans strain A2: nucleotide sequence and analysis of the genes.
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  9818186 J.A.Gerlt, and P.C.Babbitt (1998).
Mechanistically diverse enzyme superfamilies: the importance of chemistry in the evolution of catalysis.
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9626667 J.Haavik, and K.Toska (1998).
Tyrosine hydroxylase and Parkinson's disease.
  Mol Neurobiol, 16, 285-309.  
  10082363 M.Bergdoll, L.D.Eltis, A.D.Cameron, P.Dumas, and J.T.Bolin (1998).
All in the family: structural and evolutionary relationships among three modular proteins with diverse functions and variable assembly.
  Protein Sci, 7, 1661-1670.  
9819237 S.C.Daubner, and P.F.Fitzpatrick (1998).
Mutation to phenylalanine of tyrosine 371 in tyrosine hydroxylase increases the affinity for phenylalanine.
  Biochemistry, 37, 16440-16444.  
  9667935 S.J.Lange, and L.Que (1998).
Oxygen activating nonheme iron enzymes.
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  9647824 X.Peng, T.Egashira, K.Hanashiro, E.Masai, S.Nishikawa, Y.Katayama, K.Kimbara, and M.Fukuda (1998).
Cloning of a Sphingomonas paucimobilis SYK-6 gene encoding a novel oxygenase that cleaves lignin-related biphenyl and characterization of the enzyme.
  Appl Environ Microbiol, 64, 2520-2527.  
9218781 A.D.Cameron, B.Olin, M.Ridderström, B.Mannervik, and T.A.Jones (1997).
Crystal structure of human glyoxalase I--evidence for gene duplication and 3D domain swapping.
  EMBO J, 16, 3386-3395.
PDB code: 1fro
9254600 A.M.Orville, J.D.Lipscomb, and D.H.Ohlendorf (1997).
Crystal structures of substrate and substrate analog complexes of protocatechuate 3,4-dioxygenase: endogenous Fe3+ ligand displacement in response to substrate binding.
  Biochemistry, 36, 10052-10066.
PDB codes: 3pca 3pcj 3pck 3pcl 3pcm
  8981980 A.Schmid, B.Rothe, J.Altenbuchner, W.Ludwig, and K.H.Engesser (1997).
Characterization of three distinct extradiol dioxygenases involved in mineralization of dibenzofuran by Terrabacter sp. strain DPO360.
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9115979 B.A.Bernat, L.T.Laughlin, and R.N.Armstrong (1997).
Fosfomycin resistance protein (FosA) is a manganese metalloglutathione transferase related to glyoxalase I and the extradiol dioxygenases.
  Biochemistry, 36, 3050-3055.  
9434907 C.J.Schofield, J.E.Baldwin, M.F.Byford, I.Clifton, J.Hajdu, C.Hensgens, and P.Roach (1997).
Proteins of the penicillin biosynthesis pathway.
  Curr Opin Struct Biol, 7, 857-864.  
9461283 E.L.Hegg, and L.Que (1997).
The 2-His-1-carboxylate facial triad--an emerging structural motif in mononuclear non-heme iron(II) enzymes.
  Eur J Biochem, 250, 625-629.  
9228951 K.E.Goodwill, C.Sabatier, C.Marks, R.Raag, P.F.Fitzpatrick, and R.C.Stevens (1997).
Crystal structure of tyrosine hydroxylase at 2.3 A and its implications for inherited neurodegenerative diseases.
  Nat Struct Biol, 4, 578-585.
PDB code: 1toh
  9190809 N.Kimura, A.Nishi, M.Goto, and K.Furukawa (1997).
Functional analyses of a variety of chimeric dioxygenases constructed from two biphenyl dioxygenases that are similar structurally but different functionally.
  J Bacteriol, 179, 3936-3943.  
  9244273 S.I.Sato, N.Ouchiyama, T.Kimura, H.Nojiri, H.Yamane, and T.Omori (1997).
Cloning of genes involved in carbazole degradation of Pseudomonas sp. strain CA10: nucleotide sequences of genes and characterization of meta-cleavage enzymes and hydrolase.
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The extended environment of mononuclear metal centers in protein structures.
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9069115 S.R.Schmidt, A.Gehrig, M.R.Koehler, M.Schmid, C.R.Müller, and W.Kress (1997).
Cloning of the homogentisate 1,2-dioxygenase gene, the key enzyme of alkaptonuria in mouse.
  Mamm Genome, 8, 168-171.  
  9045797 S.Vuilleumier (1997).
Bacterial glutathione S-transferases: what are they good for?
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