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PDBsum entry 1lkd

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protein ligands metals links
Oxidoreductase PDB id
1lkd
Jmol
Contents
Protein chain
287 a.a. *
Ligands
BP6 ×2
P6G
Metals
FE2 ×2
Waters ×326
* Residue conservation analysis
PDB id:
1lkd
Name: Oxidoreductase
Title: Crystal structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase ( complexed with 2',6'-dicl dihydroxybiphenyl (dhb)
Structure: Biphenyl-2,3-diol 1,2-dioxygenase. Chain: a. Synonym: 23ohbp oxygenase, 2,3-dihydroxybiphenyl dioxygenas engineered: yes
Source: Burkholderia xenovorans. Organism_taxid: 266265. Strain: lb400. Expressed in: pseudomonas putida. Expression_system_taxid: 303. Other_details: burkholderia sp. Strain lb400 has been recla prior publications may refer to this organism as pseudomona strain lb400 or burkholderia cepacia strain lb400. See m.G. J.D.Haddock, current microbiol. (2001) 42:269-73
Biol. unit: Octamer (from PDB file)
Resolution:
1.70Å     R-factor:   0.203     R-free:   0.220
Authors: S.Dai,J.T.Bolin
Key ref:
S.Dai et al. (2002). Identification and analysis of a bottleneck in PCB biodegradation. Nat Struct Biol, 9, 934-939. PubMed id: 12415290 DOI: 10.1038/nsb866
Date:
24-Apr-02     Release date:   27-Nov-02    
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.
287 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
Bound ligand (Het Group name = BP6)
matches with 87.50% 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  

 

 
    reference    
 
 
DOI no: 10.1038/nsb866 Nat Struct Biol 9:934-939 (2002)
PubMed id: 12415290  
 
 
Identification and analysis of a bottleneck in PCB biodegradation.
S.Dai, F.H.Vaillancourt, H.Maaroufi, N.M.Drouin, D.B.Neau, V.Snieckus, J.T.Bolin, L.D.Eltis.
 
  ABSTRACT  
 
The microbial degradation of polychlorinated biphenyls (PCBs) provides the potential to destroy these widespread, toxic and persistent environmental pollutants. For example, the four-step upper bph pathway transforms some of the more than 100 different PCBs found in commercial mixtures and is being engineered for more effective PCB degradation. In the critical third step of this pathway, 2,3-dihydroxybiphenyl (DHB) 1,2-dioxygenase (DHBD; EC 1.13.11.39) catalyzes aromatic ring cleavage. Here we demonstrate that ortho-chlorinated PCB metabolites strongly inhibit DHBD, promote its suicide inactivation and interfere with the degradation of other compounds. For example, k(cat)(app) for 2',6'-diCl DHB was reduced by a factor of approximately 7,000 relative to DHB, and it bound with sufficient affinity to competitively inhibit DHB cleavage at nanomolar concentrations. Crystal structures of two complexes of DHBD with ortho-chlorinated metabolites at 1.7 A resolution reveal an explanation for these phenomena, which have important implications for bioremediation strategies.
 
  Selected figure(s)  
 
 
  The above figure is reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2002, 9, 934-939) copyright 2002.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21358756 K.C.Yam, S.Okamoto, J.N.Roberts, and L.D.Eltis (2011).
Adventures in Rhodococcus - from steroids to explosives.
  Can J Microbiol, 57, 155-168.  
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
19360792 L.F.Pacios, V.M.Campos, I.Merino, and L.Gómez (2009).
Structures and thermodynamics of biphenyl dihydrodiol stereoisomers and their metabolites in the enzymatic degradation of arene xenobiotics.
  J Comput Chem, 30, 2420-2432.  
18558332 K.Furukawa, and H.Fujihara (2008).
Microbial degradation of polychlorinated biphenyls: biochemical and molecular features.
  J Biosci Bioeng, 105, 433-449.  
18248454 S.A.Adebusoye, F.W.Picardal, M.O.Ilori, and O.O.Amund (2008).
Evidence of aerobic utilization of di-ortho-substituted trichlorobiphenyls as growth substrates by Pseudomonas sp. SA-6 and Ralstonia sp. SA-4.
  Environ Microbiol, 10, 1165-1174.  
17047953 S.A.Adebusoye, F.W.Picardal, M.O.Ilori, O.O.Amund, C.Fuqua, and N.Grindle (2007).
Growth on dichlorobiphenyls with chlorine substitution on each ring by bacteria isolated from contaminated African soils.
  Appl Microbiol Biotechnol, 74, 484-492.  
17932031 S.Bhowmik, G.P.Horsman, J.T.Bolin, and L.D.Eltis (2007).
The molecular basis for inhibition of BphD, a C-C bond hydrolase involved in polychlorinated biphenyls degradation: large 3-substituents prevent tautomerization.
  J Biol Chem, 282, 36377-36385.
PDB codes: 2rht 2rhw
16791559 J.Feliciano, S.Xu, X.Guan, H.J.Lehmler, L.G.Bachas, and S.Daunert (2006).
ClcR-based biosensing system in the detection of cis-dihydroxylated (chloro-)biphenyls.
  Anal Bioanal Chem, 385, 807-813.  
16740949 P.D.Fortin, G.P.Horsman, H.M.Yang, and L.D.Eltis (2006).
A glutathione S-transferase catalyzes the dehalogenation of inhibitory metabolites of polychlorinated biphenyls.
  J Bacteriol, 188, 4424-4430.  
16391095 V.J.Denef, J.A.Klappenbach, M.A.Patrauchan, C.Florizone, J.L.Rodrigues, T.V.Tsoi, W.Verstraete, L.D.Eltis, and J.M.Tiedje (2006).
Genetic and genomic insights into the role of benzoate-catabolic pathway redundancy in Burkholderia xenovorans LB400.
  Appl Environ Microbiol, 72, 585-595.  
15614564 D.H.Pieper (2005).
Aerobic degradation of polychlorinated biphenyls.
  Appl Microbiol Biotechnol, 67, 170-191.  
15880452 J.L.Pellequer, S.W.Chen, Y.S.Keum, A.E.Karu, Q.X.Li, and V.A.Roberts (2005).
Structural basis for preferential binding of non-ortho-substituted polychlorinated biphenyls by the monoclonal antibody S2B1.
  J Mol Recognit, 18, 282-294.  
16317455 M.L.Neidig, and E.I.Solomon (2005).
Structure-function correlations in oxygen activating non-heme iron enzymes.
  Chem Commun (Camb), (), 5843-5863.  
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.  
16227200 P.D.Fortin, I.MacPherson, D.B.Neau, J.T.Bolin, and L.D.Eltis (2005).
Directed evolution of a ring-cleaving dioxygenase for polychlorinated biphenyl degradation.
  J Biol Chem, 280, 42307-42314.  
16329907 S.Tillmann, C.Strömpl, K.N.Timmis, and W.R.Abraham (2005).
Stable isotope probing reveals the dominant role of Burkholderia species in aerobic degradation of PCBs.
  FEMS Microbiol Ecol, 52, 207-217.  
16291673 V.J.Denef, M.A.Patrauchan, C.Florizone, J.Park, T.V.Tsoi, W.Verstraete, J.M.Tiedje, and L.D.Eltis (2005).
Growth substrate- and phase-specific expression of biphenyl, benzoate, and C1 metabolic pathways in Burkholderia xenovorans LB400.
  J Bacteriol, 187, 7996-8005.  
15294836 V.J.Denef, J.Park, T.V.Tsoi, J.M.Rouillard, H.Zhang, J.A.Wibbenmeyer, W.Verstraete, E.Gulari, S.A.Hashsham, and J.M.Tiedje (2004).
Biphenyl and benzoate metabolism in a genomic context: outlining genome-wide metabolic networks in Burkholderia xenovorans LB400.
  Appl Environ Microbiol, 70, 4961-4970.  
12700274 D.B.McKay, M.Prucha, W.Reineke, K.N.Timmis, and D.H.Pieper (2003).
Substrate specificity and expression of three 2,3-dihydroxybiphenyl 1,2-dioxygenases from Rhodococcus globerulus strain P6.
  J Bacteriol, 185, 2944-2951.  
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.  
12727376 K.Furukawa (2003).
'Super bugs' for bioremediation.
  Trends Biotechnol, 21, 187-190.  
  12770715 N.Gilmartin, D.Ryan, O.Sherlock, and D.Dowling (2003).
BphK shows dechlorination activity against 4-chlorobenzoate, an end product of bph-promoted degradation of PCBs.
  FEMS Microbiol Lett, 222, 251-255.  
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.