PDBsum entry 1knd

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Oxidoreductase PDB id
Protein chain
288 a.a. *
TBU ×2
FE2 ×2
Waters ×121
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Crystal structure of 2,3-dihydroxybiphenyl 1,2-dioxygenasE C with catechol under anaerobic condition
Structure: 2,3-dihydroxybiphenyl 1,2-dioxygenase. Chain: a. Synonym: biphenyl-2,3-diol 1,2-dioxygenase, dhbd. Engineered: yes
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 (this or has been reclassified. Prior publications may refer to this as pseudomonas sp. Strain lb400.)
Biol. unit: Octamer (from PDB file)
1.90Å     R-factor:   0.164     R-free:   0.193
Authors: S.Han,J.T.Bolin
Key ref:
F.H.Vaillancourt et al. (1998). Molecular basis for the stabilization and inhibition of 2, 3-dihydroxybiphenyl 1,2-dioxygenase by t-butanol. J Biol Chem, 273, 34887-34895. PubMed id: 9857017 DOI: 10.1074/jbc.273.52.34887
18-Dec-01     Release date:   27-Mar-02    
Go to PROCHECK summary

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

 Enzyme reactions 
   Enzyme class: E.C.  - 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
Bound ligand (Het Group name = CAQ)
matches with 57.14% similarity
+ O(2)
= 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate
      Cofactor: Mn(2+) or Fe cation
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     7 terms  


DOI no: 10.1074/jbc.273.52.34887 J Biol Chem 273:34887-34895 (1998)
PubMed id: 9857017  
Molecular basis for the stabilization and inhibition of 2, 3-dihydroxybiphenyl 1,2-dioxygenase by t-butanol.
F.H.Vaillancourt, S.Han, P.D.Fortin, J.T.Bolin, L.D.Eltis.
The steady-state cleavage of catechols by 2,3-dihydroxybiphenyl 1, 2-dioxygenase (DHBD), the extradiol dioxygenase of the biphenyl biodegradation pathway, was investigated using a highly active, anaerobically purified preparation of enzyme. The kinetic data obtained using 2,3-dihydroxybiphenyl (DHB) fit a compulsory order ternary complex mechanism in which substrate inhibition occurs. The Km for dioxygen was 1280 +/- 70 microM, which is at least 2 orders of magnitude higher than that reported for catechol 2,3-dioxygenases. Km and Kd for DHB were 22 +/- 2 and 8 +/- 1 microM, respectively. DHBD was subject to reversible substrate inhibition and mechanism-based inactivation. In air-saturated buffer, the partition ratios of catecholic substrates substituted at C-3 were inversely related to their apparent specificity constants. Small organic molecules that stabilized DHBD most effectively also inhibited the cleavage reaction most strongly. The steady-state kinetic data and crystallographic results suggest that the stabilization and inhibition are due to specific interactions between the organic molecule and the active site of the enzyme. t-Butanol stabilized the enzyme and inhibited the cleavage of DHB in a mixed fashion, consistent with the distinct binding sites occupied by t-butanol in the crystal structures of the substrate-free form of the enzyme and the enzyme-DHB complex. In contrast, crystal structures of complexes with catechol and 3-methylcatechol revealed relationships between the binding of these smaller substrates and t-butanol that are consistent with the observed competitive inhibition.
  Selected figure(s)  
Figure 3.
Fig. 3. Relationship of the two t-butanol-binding sites to groups at the active site. A, in the free enzyme, t-butanol occupies the distal portion of the substrate-binding site. B, in the enzyme-substrate complexes, t-butanol occupies an auxiliary site adjacent to the distal portion of the substrate-binding site, further removed from the iron.
Figure 4.
Fig. 4. Electron density maps and models illustrating the structure of the DHBD:3-methylcatechol-bound and substrate-free forms of DHBD. Each part is a (divergent) stereo drawing prepared with the program MolView (42). The identical observed structure factors were used in all maps, which demonstrates the presence of both forms of the enzyme in the same crystal. All maps are at 1.9-Å resolution and are contoured at two standard deviations above the mean of the map. In the models, the carbon atoms are more darkly shaded than the nitrogen and oxygen atoms. A, F[o] F[c] electron density representing the iron, 3-methylcatechol, and two water ligands. The F[c] 's and phases are from the structure of the substrate-free enzyme (3). The model is the initial fit to this density. B, residual F[o] F[c] electron density following refinement of a model that included the iron, 3-methylcatechol, two water ligands, and a t-butanol bound in the auxiliary site, as shown. The F[c] 's and phases are from this model. The density features arise from the fraction of the crystal that is in the substrate free-form, as demonstrated by C, which shows the refined model of this form (3) in conjunction with the same density. Note that the t-butanol binds in the substrate-binding site in this form of the enzyme.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1998, 273, 34887-34895) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19234303 J.K.Capyk, I.D'Angelo, N.C.Strynadka, and L.D.Eltis (2009).
Characterization of 3-ketosteroid 9{alpha}-hydroxylase, a Rieske oxygenase in the cholesterol degradation pathway of Mycobacterium tuberculosis.
  J Biol Chem, 284, 9937-9946.
PDB code: 2zyl
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
19494914 L.Gu, B.Wang, A.Kulkarni, T.W.Geders, R.V.Grindberg, L.Gerwick, K.Håkansson, P.Wipf, J.L.Smith, W.H.Gerwick, and D.H.Sherman (2009).
Metamorphic enzyme assembly in polyketide diversification.
  Nature, 459, 731-735.  
17526697 L.Gómez-Gil, P.Kumar, D.Barriault, J.T.Bolin, M.Sylvestre, and L.D.Eltis (2007).
Characterization of biphenyl dioxygenase of Pandoraea pnomenusa B-356 as a potent polychlorinated biphenyl-degrading enzyme.
  J Bacteriol, 189, 5705-5715.  
17021212 J.J.Parnell, J.Park, V.Denef, T.Tsoi, S.Hashsham, J.Quensen, and J.M.Tiedje (2006).
Coping with polychlorinated biphenyl (PCB) toxicity: Physiological and genome-wide responses of Burkholderia xenovorans LB400 to PCB-mediated stress.
  Appl Environ Microbiol, 72, 6607-6614.  
16359327 M.C.Anderton, S.Bhakta, G.S.Besra, P.Jeavons, L.D.Eltis, and E.Sim (2006).
Characterization of the putative operon containing arylamine N-acetyltransferase (nat) in Mycobacterium bovis BCG.
  Mol Microbiol, 59, 181-192.  
16121186 F.H.Vaillancourt, E.Yeh, D.A.Vosburg, S.E.O'Connor, and C.T.Walsh (2005).
Cryptic chlorination by a non-haem iron enzyme during cyclopropyl amino acid biosynthesis.
  Nature, 436, 1191-1194.  
16002467 F.H.Vaillancourt, J.Yin, and C.T.Walsh (2005).
SyrB2 in syringomycin E biosynthesis is a nonheme FeII alpha-ketoglutarate- and O2-dependent halogenase.
  Proc Natl Acad Sci U S A, 102, 10111-10116.  
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.  
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.  
15006807 A.Okuta, K.Ohnishi, and S.Harayama (2004).
Construction of chimeric catechol 2,3-dioxygenase exhibiting improved activity against the suicide inhibitor 4-methylcatechol.
  Appl Environ Microbiol, 70, 1804-1810.  
12562795 F.H.Vaillancourt, M.A.Haro, N.M.Drouin, Z.Karim, H.Maaroufi, and L.D.Eltis (2003).
Characterization of extradiol dioxygenases from a polychlorinated biphenyl-degrading strain that possess higher specificities for chlorinated metabolites.
  J Bacteriol, 185, 1253-1260.  
12949084 Y.Ge, and L.D.Eltis (2003).
Characterization of hybrid toluate and benzoate dioxygenases.
  J Bacteriol, 185, 5333-5341.  
12415290 S.Dai, F.H.Vaillancourt, H.Maaroufi, N.M.Drouin, D.B.Neau, V.Snieckus, J.T.Bolin, and L.D.Eltis (2002).
Identification and analysis of a bottleneck in PCB biodegradation.
  Nat Struct Biol, 9, 934-939.
PDB codes: 1lgt 1lkd
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.  
11160080 S.Y.Seah, G.Labbé, S.R.Kaschabek, F.Reifenrath, W.Reineke, and L.D.Eltis (2001).
Comparative specificities of two evolutionarily divergent hydrolases involved in microbial degradation of polychlorinated biphenyls.
  J Bacteriol, 183, 1511-1516.  
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
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.  
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.