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PDBsum entry 1ndo

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protein ligands metals Protein-protein interface(s) links
Non-heme iron dioxygenase PDB id
1ndo
Jmol
Contents
Protein chains
447 a.a. *
193 a.a. *
Ligands
FES ×3
Metals
_FE ×3
Waters ×1061
* Residue conservation analysis
PDB id:
1ndo
Name: Non-heme iron dioxygenase
Title: Napthalene 1,2-dioxygenase
Structure: Napthalene 1,2-dioxygenase. Chain: a, c, e. Engineered: yes. Other_details: chain a,c,e and b,d,f are the large and the small subunits respectively. Napthalene 1,2-dioxygenase. Chain: b, d, f. Engineered: yes. Other_details: chain a,c,e and b,d,f are the large and the
Source: Pseudomonas putida. Organism_taxid: 303. Collection: ncib 9816. Gene: nahacad. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: de3.
Biol. unit: Hexamer (from PQS)
Resolution:
2.25Å     R-factor:   0.220     R-free:   0.240
Authors: S.Ramaswamy,B.Kauppi,E.Carredano
Key ref:
B.Kauppi et al. (1998). Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase. Structure, 6, 571-586. PubMed id: 9634695 DOI: 10.1016/S0969-2126(98)00059-8
Date:
11-Jan-98     Release date:   23-Mar-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A110  (NDOB_PSEPU) -  Naphthalene 1,2-dioxygenase subunit alpha
Seq:
Struc:
449 a.a.
447 a.a.
Protein chains
Pfam   ArchSchema ?
P0A112  (NDOC_PSEPU) -  Naphthalene 1,2-dioxygenase subunit beta
Seq:
Struc:
194 a.a.
193 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F: E.C.1.14.12.12  - Naphthalene 1,2-dioxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Aromatic 1,2-Dioxygenases
      Reaction: Naphthalene + NADH + O2 = (1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD+
Naphthalene
+ NADH
+ O(2)
= (1R,2S)-1,2-dihydronaphthalene-1,2-diol
+ NAD(+)
      Cofactor: 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   3 terms 
  Biochemical function     catalytic activity     11 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(98)00059-8 Structure 6:571-586 (1998)
PubMed id: 9634695  
 
 
Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase.
B.Kauppi, K.Lee, E.Carredano, R.E.Parales, D.T.Gibson, H.Eklund, S.Ramaswamy.
 
  ABSTRACT  
 
BACKGROUND: Pseudomonas sp. NCIB 9816-4 utilizes a multicomponent enzyme system to oxidize naphthalene to (+)-cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene. The enzyme component catalyzing this reaction, naphthalene 1,2-dioxygenase (NDO), belongs to a family of aromatic-ring-hydroxylating dioxygenases that oxidize aromatic hydrocarbons and related compounds to cis-arene diols. These enzymes utilize a mononuclear non-heme iron center to catalyze the addition of dioxygen to their respective substrates. The present study was conducted to provide essential structural information necessary for elucidating the mechanism of action of NDO. RESULTS: The three-dimensional structure of NDO has been determined at 2.25 A resolution. The molecule is an alpha 3 beta 3 hexamer. The center and a catalytic domain that has a novel fold dominated by an antiparallel nine-stranded beta-pleated sheet against which helices pack. The active site contains a non-heme ferrous ion coordinated by His208, His213, Asp362 (bidentate) and a water molecule. Asn201 is positioned further away, 3.75 A, at center, one iron is coordinated by Cys81 and Cys101 and the other by His83 and His104. CONCLUSIONS: The domain structure and iron coordination of the Rieske domain is very similar to that of the cytochrome bc1 domain. The active-site iron center of one of the alpha subunits is directly connected by hydrogen bonds through a center in a neighboring alpha subunit. This is likely to be the main route for electron transfer.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Stereo omit F[o] -F[c] electron-density map at 2.25 resolution of crystal form II (3 rms). The map is for the region around the catalytic iron center with the ligands His208, His213 and Asp362. The iron ion was not present in the preceding refinement (close to the final stages of refinement) and the ligands were refined as alanine residues.
 
  The above figure is reprinted by permission from Cell Press: Structure (1998, 6, 571-586) copyright 1998.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

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19278452 C.G.Flocco, N.C.Gomes, W.Mac Cormack, and K.Smalla (2009).
Occurrence and diversity of naphthalene dioxygenase genes in soil microbial communities from the Maritime Antarctic.
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18813921 E.L.Ang, J.P.Obbard, and H.Zhao (2009).
Directed evolution of aniline dioxygenase for enhanced bioremediation of aromatic amines.
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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.
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PDB code: 2zyl
19172265 L.Schuler, Y.Jouanneau, S.M.Chadhain, C.Meyer, M.Pouli, G.J.Zylstra, P.Hols, and S.N.Agathos (2009).
Characterization of a ring-hydroxylating dioxygenase from phenanthrene-degrading Sphingomonas sp. strain LH128 able to oxidize benz[a]anthracene.
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19464996 M.Tarasev, S.Pullela, and D.P.Ballou (2009).
Distal end of 105-125 loop--a putative reductase binding domain of phthalate dioxygenase.
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19081995 Y.Feng, C.Y.Ke, G.Xue, and L.Que (2009).
Bio-inspired arene cis-dihydroxylation by a non-haem iron catalyst modeling the action of naphthalene dioxygenase.
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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.
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18703841 E.J.Levin, N.L.Elsen, K.D.Seder, J.G.McCoy, B.G.Fox, and G.N.Phillips (2008).
X-ray structure of a soluble Rieske-type ferredoxin from Mus musculus.
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PDB code: 3d89
18719951 E.N.Brown, R.Friemann, A.Karlsson, J.V.Parales, M.M.Couture, L.D.Eltis, and S.Ramaswamy (2008).
Determining Rieske cluster reduction potentials.
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PDB code: 2qpz
19060398 H.Uchimura, T.Horisaki, T.Umeda, H.Noguchi, Y.Usami, L.Li, T.Terada, S.Nakamura, K.Shimizu, T.Takemura, H.Habe, K.Furihata, T.Omori, H.Yamane, and H.Nojiri (2008).
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17562190 J.Xiao, and J.M.Vanbriesen (2008).
Expanded thermodynamic true yield prediction model: adjustments and limitations.
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18558332 K.Furukawa, and H.Fujihara (2008).
Microbial degradation of polychlorinated biphenyls: biochemical and molecular features.
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18366740 M.Lozada, J.P.Riva Mercadal, L.D.Guerrero, W.D.Di Marzio, M.A.Ferrero, and H.M.Dionisi (2008).
Novel aromatic ring-hydroxylating dioxygenase genes from coastal marine sediments of Patagonia.
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19020684 P.C.Bruijnincx, G.van Koten, and R.J.Klein Gebbink (2008).
Mononuclear non-heme iron enzymes with the 2-His-1-carboxylate facial triad: recent developments in enzymology and modeling studies.
  Chem Soc Rev, 37, 2716-2744.  
18189388 T.Ohta, S.Chakrabarty, J.D.Lipscomb, and E.I.Solomon (2008).
Near-IR MCD of the nonheme ferrous active site in naphthalene 1,2-dioxygenase: correlation to crystallography and structural insight into the mechanism of Rieske dioxygenases.
  J Am Chem Soc, 130, 1601-1610.  
17096121 A.Ono, R.Miyazaki, M.Sota, Y.Ohtsubo, Y.Nagata, and M.Tsuda (2007).
Isolation and characterization of naphthalene-catabolic genes and plasmids from oil-contaminated soil by using two cultivation-independent approaches.
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17349044 D.J.Ferraro, E.N.Brown, C.L.Yu, R.E.Parales, D.T.Gibson, and S.Ramaswamy (2007).
Structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1.
  BMC Struct Biol, 7, 10.
PDB codes: 2gbw 2gbx 2i7f
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17567087 E.G.Kovaleva, M.B.Neibergall, S.Chakrabarty, and J.D.Lipscomb (2007).
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  Acc Chem Res, 40, 475-483.  
17269935 E.L.Ang, J.P.Obbard, and H.Zhao (2007).
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  FEBS J, 274, 928-939.  
17451434 J.Jakoncic, Y.Jouanneau, C.Meyer, and V.Stojanoff (2007).
The crystal structure of the ring-hydroxylating dioxygenase from Sphingomonas CHY-1.
  FEBS J, 274, 2470-2481.  
17157819 J.Jakoncic, Y.Jouanneau, C.Meyer, and V.Stojanoff (2007).
The catalytic pocket of the ring-hydroxylating dioxygenase from Sphingomonas CHY-1.
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PDB code: 2ckf
17570147 M.A.Marti-Renom, A.Rossi, F.Al-Shahrour, F.P.Davis, U.Pieper, J.Dopazo, and A.Sali (2007).
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17567152 M.B.Neibergall, A.Stubna, Y.Mekmouche, E.Münck, and J.D.Lipscomb (2007).
Hydrogen peroxide dependent cis-dihydroxylation of benzoate by fully oxidized benzoate 1,2-dioxygenase.
  Biochemistry, 46, 8004-8016.  
17764654 M.Tarasev, C.S.Kaddis, S.Yin, J.A.Loo, J.Burgner, and D.P.Ballou (2007).
Similar enzymes, different structures: phthalate dioxygenase is an alpha3alpha3 stacked hexamer, not an alpha3beta3 trimer like "normal" Rieske oxygenases.
  Arch Biochem Biophys, 466, 31-39.  
17647036 S.M.Chadhain, E.M.Moritz, E.Kim, and G.J.Zylstra (2007).
Identification, cloning, and characterization of a multicomponent biphenyl dioxygenase from Sphingobium yanoikuyae B1.
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16611640 C.R.Simmons, Q.Liu, Q.Huang, Q.Hao, T.P.Begley, P.A.Karplus, and M.H.Stipanuk (2006).
Crystal structure of mammalian cysteine dioxygenase. A novel mononuclear iron center for cysteine thiol oxidation.
  J Biol Chem, 281, 18723-18733.
PDB codes: 2b5h 2gh2
16980501 D.J.Ferraro, A.L.Okerlund, J.C.Mowers, and S.Ramaswamy (2006).
Structural basis for regioselectivity and stereoselectivity of product formation by naphthalene 1,2-dioxygenase.
  J Bacteriol, 188, 6986-6994.
PDB codes: 2hmj 2hmk 2hml 2hmm 2hmn 2hmo
16391757 D.R.Boyd, and T.D.Bugg (2006).
Arene cis-dihydrodiol formation: from biology to application.
  Org Biomol Chem, 4, 181-192.  
16217654 H.Suenaga, M.Goto, and K.Furukawa (2006).
Active-site engineering of biphenyl dioxygenase: effect of substituted amino acids on substrate specificity and regiospecificity.
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16923069 H.W.Zhou, C.L.Guo, Y.S.Wong, and N.F.Tam (2006).
Genetic diversity of dioxygenase genes in polycyclic aromatic hydrocarbon-degrading bacteria isolated from mangrove sediments.
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16923884 J.K.Lee, E.L.Ang, and H.Zhao (2006).
Probing the substrate specificity of aminopyrrolnitrin oxygenase (PrnD) by mutational analysis.
  J Bacteriol, 188, 6179-6183.  
16342311 J.Lee, and H.Zhao (2006).
Mechanistic studies on the conversion of arylamines into arylnitro compounds by aminopyrrolnitrin oxygenase: identification of intermediates and kinetic studies.
  Angew Chem Int Ed Engl, 45, 622-625.  
17031039 K.Furukawa (2006).
Oxygenases and dehalogenases: molecular approaches to efficient degradation of chlorinated environmental pollutants.
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16448512 K.Lee (2006).
p-hydroxylation reactions catalyzed by naphthalene dioxygenase.
  FEMS Microbiol Lett, 255, 316-320.  
16517627 K.S.Ju, and R.E.Parales (2006).
Control of substrate specificity by active-site residues in nitrobenzene dioxygenase.
  Appl Environ Microbiol, 72, 1817-1824.  
16627939 L.A.Moe, C.A.Bingman, G.E.Wesenberg, G.N.Phillips, and B.G.Fox (2006).
Structure of T4moC, the Rieske-type ferredoxin component of toluene 4-monooxygenase.
  Acta Crystallogr D Biol Crystallogr, 62, 476-482.
PDB code: 1vm9
16637091 M.R.Bukowski, P.Comba, A.Lienke, C.Limberg, C.Lopez de Laorden, R.Mas-Ballesté, M.Merz, and L.Que (2006).
Catalytic epoxidation and 1,2-dihydroxylation of olefins with bispidine-iron(II)/H2O2 systems.
  Angew Chem Int Ed Engl, 45, 3446-3449.  
16517628 M.Sasoh, E.Masai, S.Ishibashi, H.Hara, N.Kamimura, K.Miyauchi, and M.Fukuda (2006).
Characterization of the terephthalate degradation genes of Comamonas sp. strain E6.
  Appl Environ Microbiol, 72, 1825-1832.  
16922496 M.Tarasev, A.Pinto, D.Kim, S.J.Elliott, and D.P.Ballou (2006).
The "bridging" aspartate 178 in phthalate dioxygenase facilitates interactions between the Rieske center and the iron(II)--mononuclear center.
  Biochemistry, 45, 10208-10216.  
16517671 M.Zielinski, S.Kahl, C.Standfuss-Gabisch, B.Cámara, M.Seeger, and B.Hofer (2006).
Generation of novel-substrate-accepting biphenyl dioxygenases through segmental random mutagenesis and identification of residues involved in enzyme specificity.
  Appl Environ Microbiol, 72, 2191-2199.  
16871511 R.Mas-Ballesté, M.Costas, T.van den Berg, and L.Que (2006).
Ligand topology effects on olefin oxidations by bio-inspired [FeII(N2Py2)] catalysts.
  Chemistry, 12, 7489-7500.  
15983802 S.Hirano, M.Haruki, K.Takano, T.Imanaka, M.Morikawa, and S.Kanaya (2006).
Gene cloning and in vivo characterization of a dibenzothiophene dioxygenase from Xanthobacter polyaromaticivorans.
  Appl Microbiol Biotechnol, 69, 672-681.  
  17012793 T.Iwasaki, A.Kounosu, D.Ohmori, and T.Kumasaka (2006).
Crystallization and preliminary X-ray diffraction studies of a hyperthermophilic Rieske protein variant (SDX-triple) with an engineered rubredoxin-like mononuclear iron site.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 993-995.  
16315327 T.Leungsakul, B.G.Keenan, M.A.Mori, M.D.Morton, J.D.Stuart, B.F.Smets, and T.K.Wood (2006).
Oxidation of aminonitrotoluenes by 2,4-DNT dioxygenase of Burkholderia sp. strain DNT.
  Biotechnol Bioeng, 93, 231-237.  
17087501 Y.Chang, and B.G.Fox (2006).
Identification of Rv3230c as the NADPH oxidoreductase of a two-protein DesA3 acyl-CoA desaturase in Mycobacterium tuberculosis H37Rv.
  Biochemistry, 45, 13476-13486.  
17041157 Y.Liang, D.R.Gardner, C.D.Miller, D.Chen, A.J.Anderson, B.C.Weimer, and R.C.Sims (2006).
Study of biochemical pathways and enzymes involved in pyrene degradation by Mycobacterium sp. strain KMS.
  Appl Environ Microbiol, 72, 7821-7828.  
15942729 A.Karlsson, J.V.Parales, R.E.Parales, D.T.Gibson, H.Eklund, and S.Ramaswamy (2005).
NO binding to naphthalene dioxygenase.
  J Biol Inorg Chem, 10, 483-489.
PDB codes: 1uuv 1uuw
15893671 B.M.Martins, T.Svetlitchnaia, and H.Dobbek (2005).
2-Oxoquinoline 8-monooxygenase oxygenase component: active site modulation by Rieske-[2Fe-2S] center oxidation/reduction.
  Structure, 13, 817-824.
PDB codes: 1z01 1z02 1z03
15746362 C.Bagnéris, R.Cammack, and J.R.Mason (2005).
Subtle difference between benzene and toluene dioxygenases of Pseudomonas putida.
  Appl Environ Microbiol, 71, 1570-1580.  
15614564 D.H.Pieper (2005).
Aerobic degradation of polychlorinated biphenyls.
  Appl Microbiol Biotechnol, 67, 170-191.  
15893657 J.D.Lipscomb, and B.M.Hoffman (2005).
Allosteric control of O2 reactivity in Rieske oxygenases.
  Structure, 13, 684-685.  
16150698 J.Lee, M.Simurdiak, and H.Zhao (2005).
Reconstitution and characterization of aminopyrrolnitrin oxygenase, a Rieske N-oxygenase that catalyzes unusual arylamine oxidation.
  J Biol Chem, 280, 36719-36727.  
15645447 J.W.Nam, H.Noguchi, Z.Fujimoto, H.Mizuno, Y.Ashikawa, M.Abo, S.Fushinobu, N.Kobashi, T.Wakagi, K.Iwata, T.Yoshida, H.Habe, H.Yamane, T.Omori, and H.Nojiri (2005).
Crystal structure of the ferredoxin component of carbazole 1,9a-dioxygenase of Pseudomonas resinovorans strain CA10, a novel Rieske non-heme iron oxygenase system.
  Proteins, 58, 779-789.
PDB code: 1vck
15739104 K.D.Koehntop, J.P.Emerson, and L.Que (2005).
The 2-His-1-carboxylate facial triad: a versatile platform for dioxygen activation by mononuclear non-heme iron(II) enzymes.
  J Biol Inorg Chem, 10, 87-93.  
  16511124 K.Lee, R.Friemann, J.V.Parales, D.T.Gibson, and S.Ramaswamy (2005).
Purification, crystallization and preliminary X-ray diffraction studies of the three components of the toluene 2,3-dioxygenase enzyme system.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 669-672.  
16175409 K.S.Lee, J.V.Parales, R.Friemann, and R.E.Parales (2005).
Active site residues controlling substrate specificity in 2-nitrotoluene dioxygenase from Acidovorax sp. strain JS42.
  J Ind Microbiol Biotechnol, 32, 465-473.  
16237006 L.Gakhar, Z.A.Malik, C.C.Allen, D.A.Lipscomb, M.J.Larkin, and S.Ramaswamy (2005).
Structure and increased thermostability of Rhodococcus sp. naphthalene 1,2-dioxygenase.
  J Bacteriol, 187, 7222-7231.
PDB codes: 2b1x 2b24
16317455 M.L.Neidig, and E.I.Solomon (2005).
Structure-function correlations in oxygen activating non-heme iron enzymes.
  Chem Commun (Camb), (), 5843-5863.  
15855162 P.L.Herman, M.Behrens, S.Chakraborty, B.M.Chrastil, J.Barycki, and D.P.Weeks (2005).
A three-component dicamba O-demethylase from Pseudomonas maltophilia, strain DI-6: gene isolation, characterization, and heterologous expression.
  J Biol Chem, 280, 24759-24767.  
16000792 R.E.Parales, R.Huang, C.L.Yu, J.V.Parales, F.K.Lee, D.J.Lessner, M.M.Ivkovic-Jensen, W.Liu, R.Friemann, S.Ramaswamy, and D.T.Gibson (2005).
Purification, characterization, and crystallization of the components of the nitrobenzene and 2-nitrotoluene dioxygenase enzyme systems.
  Appl Environ Microbiol, 71, 3806-3814.  
16028295 T.Leungsakul, B.G.Keenan, H.Yin, B.F.Smets, and T.K.Wood (2005).
Saturation mutagenesis of 2,4-DNT dioxygenase of Burkholderia sp. strain DNT for enhanced dinitrotoluene degradation.
  Biotechnol Bioeng, 92, 416-426.  
15774891 X.Dong, S.Fushinobu, E.Fukuda, T.Terada, S.Nakamura, K.Shimizu, H.Nojiri, T.Omori, H.Shoun, and T.Wakagi (2005).
Crystal structure of the terminal oxygenase component of cumene dioxygenase from Pseudomonas fluorescens IP01.
  J Bacteriol, 187, 2483-2490.
PDB code: 1wql
14726526 A.Kounosu, Z.Li, N.J.Cosper, J.E.Shokes, R.A.Scott, T.Imai, A.Urushiyama, and T.Iwasaki (2004).
Engineering a three-cysteine, one-histidine ligand environment into a new hyperthermophilic archaeal Rieske-type [2Fe-2S] ferredoxin from Sulfolobus solfataricus.
  J Biol Chem, 279, 12519-12528.  
15071504 A.Sultana, P.Kallio, A.Jansson, J.S.Wang, J.Niemi, P.Mäntsälä, and G.Schneider (2004).
Structure of the polyketide cyclase SnoaL reveals a novel mechanism for enzymatic aldol condensation.
  EMBO J, 23, 1911-1921.
PDB code: 1sjw
15184115 B.G.Keenan, T.Leungsakul, B.F.Smets, and T.K.Wood (2004).
Saturation mutagenesis of Burkholderia cepacia R34 2,4-dinitrotoluene dioxygenase at DntAc valine 350 for synthesizing nitrohydroquinone, methylhydroquinone, and methoxyhydroquinone.
  Appl Environ Microbiol, 70, 3222-3231.  
16233711 H.Habe, M.Kanemitsu, M.Nomura, T.Takemura, K.Iwata, H.Nojiri, H.Yamane, and T.Omori (2004).
Isolation and characterization of an alkaliphilic bacterium utilizing pyrene as a carbon source.
  J Biosci Bioeng, 98, 306-308.  
15240274 H.M.Dionisi, C.S.Chewning, K.H.Morgan, F.M.Menn, J.P.Easter, and G.S.Sayler (2004).
Abundance of dioxygenase genes similar to Ralstonia sp. strain U2 nagAc is correlated with naphthalene concentrations in coal tar-contaminated freshwater sediments.
  Appl Environ Microbiol, 70, 3988-3995.  
15292119 K.Furukawa, H.Suenaga, and M.Goto (2004).
Biphenyl dioxygenases: functional versatilities and directed evolution.
  J Bacteriol, 186, 5189-5196.  
15452777 L.Skjeldal, F.C.Peterson, J.F.Doreleijers, L.A.Moe, J.D.Pikus, W.M.Westler, J.L.Markley, B.F.Volkman, and B.G.Fox (2004).
Solution structure of T4moC, the Rieske ferredoxin component of the toluene 4-monooxygenase complex.
  J Biol Inorg Chem, 9, 945-953.
PDB code: 1sjg
15358414 O.Pinyakong, H.Habe, A.Kouzuma, H.Nojiri, H.Yamane, and T.Omori (2004).
Isolation and characterization of genes encoding polycyclic aromatic hydrocarbon dioxygenase from acenaphthene and acenaphthylene degrading Sphingomonas sp. strain A4.
  FEMS Microbiol Lett, 238, 297-305.  
15560776 P.Hlavica (2004).
Models and mechanisms of O-O bond activation by cytochrome P450. A critical assessment of the potential role of multiple active intermediates in oxidative catalysis.
  Eur J Biochem, 271, 4335-4360.  
15272185 T.Uchiyama, A.Kounosu, T.Sato, N.Tanaka, T.Iwasaki, and T.Kumasaka (2004).
Crystallization and preliminary X-ray diffraction studies of the hyperthermophilic archaeal sulredoxin having the unique Rieske [2Fe-2S] cluster environment.
  Acta Crystallogr D Biol Crystallogr, 60, 1487-1489.  
12586937 A.Karlsson, J.V.Parales, R.E.Parales, D.T.Gibson, H.Eklund, and S.Ramaswamy (2003).
Crystal structure of naphthalene dioxygenase: side-on binding of dioxygen to iron.
  Science, 299, 1039-1042.
PDB codes: 1o7g 1o7h 1o7m 1o7n 1o7p 1o7w
12829283 B.Brezna, A.A.Khan, and C.E.Cerniglia (2003).
Molecular characterization of dioxygenases from polycyclic aromatic hydrocarbon-degrading Mycobacterium spp.
  FEMS Microbiol Lett, 223, 177-183.  
12517340 C.A.Kerfeld, M.R.Sawaya, V.Brahmandam, D.Cascio, K.K.Ho, C.C.Trevithick-Sutton, D.W.Krogmann, and T.O.Yeates (2003).
The crystal structure of a cyanobacterial water-soluble carotenoid binding protein.
  Structure, 11, 55-65.
PDB code: 1m98
12728980 H.Habe, and T.Omori (2003).
Genetics of polycyclic aromatic hydrocarbon metabolism in diverse aerobic bacteria.
  Biosci Biotechnol Biochem, 67, 225-243.  
13129960 H.K.Chang, P.Mohseni, and G.J.Zylstra (2003).
Characterization and regulation of the genes for a novel anthranilate 1,2-dioxygenase from Burkholderia cepacia DBO1.
  J Bacteriol, 185, 5871-5881.  
12773375 M.Arand, B.M.Hallberg, J.Zou, T.Bergfors, F.Oesch, M.J.van der Werf, J.A.de Bont, T.A.Jones, and S.L.Mowbray (2003).
Structure of Rhodococcus erythropolis limonene-1,2-epoxide hydrolase reveals a novel active site.
  EMBO J, 22, 2583-2592.
PDB codes: 1nu3 1nww
12403773 M.D.Wolfe, and J.D.Lipscomb (2003).
Hydrogen peroxide-coupled cis-diol formation catalyzed by naphthalene 1,2-dioxygenase.
  J Biol Chem, 278, 829-835.  
12676698 M.S.Wilson, J.B.Herrick, C.O.Jeon, D.E.Hinman, and E.L.Madsen (2003).
Horizontal transfer of phnAc dioxygenase genes within one of two phenotypically and genotypically distinctive naphthalene-degrading guilds from adjacent soil environments.
  Appl Environ Microbiol, 69, 2172-2181.  
14617661 M.Zielinski, S.Kahl, H.J.Hecht, and B.Hofer (2003).
Pinpointing biphenyl dioxygenase residues that are crucial for substrate interaction.
  J Bacteriol, 185, 6976-6980.  
12670689 T.Shigematsu, K.Yumihara, Y.Ueda, S.Morimura, and K.Kida (2003).
Purification and gene cloning of the oxygenase component of the terephthalate 1,2-dioxygenase system from Delftia tsuruhatensis strain T7.
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12949084 Y.Ge, and L.D.Eltis (2003).
Characterization of hybrid toluate and benzoate dioxygenases.
  J Bacteriol, 185, 5333-5341.  
14602629 Y.Kasai, K.Shindo, S.Harayama, and N.Misawa (2003).
Molecular characterization and substrate preference of a polycyclic aromatic hydrocarbon dioxygenase from Cycloclasticus sp. strain A5.
  Appl Environ Microbiol, 69, 6688-6697.  
14622009 Z.M.Beharry, D.M.Eby, E.D.Coulter, R.Viswanathan, E.L.Neidle, R.S.Phillips, and D.M.Kurtz (2003).
Histidine ligand protonation and redox potential in the rieske dioxygenases: role of a conserved aspartate in anthranilate 1,2-dioxygenase.
  Biochemistry, 42, 13625-13636.  
12377129 A.E.Todd, C.A.Orengo, and J.M.Thornton (2002).
Sequence and structural differences between enzyme and nonenzyme homologs.
  Structure, 10, 1435-1451.  
12324375 B.Morasch, H.H.Richnow, B.Schink, A.Vieth, and R.U.Meckenstock (2002).
Carbon and hydrogen stable isotope fractionation during aerobic bacterial degradation of aromatic hydrocarbons.
  Appl Environ Microbiol, 68, 5191-5194.  
12081948 D.Barriault, M.M.Plante, and M.Sylvestre (2002).
Family shuffling of a targeted bphA region to engineer biphenyl dioxygenase.
  J Bacteriol, 184, 3794-3800.  
11823201 D.J.Lessner, G.R.Johnson, R.E.Parales, J.C.Spain, and D.T.Gibson (2002).
Molecular characterization and substrate specificity of nitrobenzene dioxygenase from Comamonas sp. strain JS765.
  Appl Environ Microbiol, 68, 634-641.  
12450109 H.Nojiri, and T.Omori (2002).
Molecular bases of aerobic bacterial degradation of dioxins: involvement of angular dioxygenation.
  Biosci Biotechnol Biochem, 66, 2001-2016.  
12057964 H.Suenaga, T.Watanabe, M.Sato, Ngadiman, and K.Furukawa (2002).
Alteration of regiospecificity in biphenyl dioxygenase by active-site engineering.
  J Bacteriol, 184, 3682-3688.  
12450807 J.W.Nam, H.Nojiri, H.Noguchi, H.Uchimura, T.Yoshida, H.Habe, H.Yamane, and T.Omori (2002).
Purification and characterization of carbazole 1,9a-dioxygenase, a three-component dioxygenase system of Pseudomonas resinovorans strain CA10.
  Appl Environ Microbiol, 68, 5882-5890.  
12136152 J.W.Nam, Z.Fujimoto, H.Mizuno, H.Yamane, T.Yoshida, H.Habe, H.Nojiri, and T.Omori (2002).
Crystallization and preliminary crystallographic analysis of the terminal oxygenase component of carbazole 1,9a-dioxygenase of Pseudomonas resinovorans strain CA10.
  Acta Crystallogr D Biol Crystallogr, 58, 1350-1352.  
11823244 M.Ferrero, E.Llobet-Brossa, J.Lalucat, E.García-Valdés, R.Rosselló-Mora, and R.Bosch (2002).
Coexistence of two distinct copies of naphthalene degradation genes in Pseudomonas strains isolated from the western Mediterranean region.
  Appl Environ Microbiol, 68, 957-962.  
12441394 N.J.Cosper, D.M.Eby, A.Kounosu, N.Kurosawa, E.L.Neidle, D.M.Kurtz, T.Iwasaki, and R.A.Scott (2002).
Redox-dependent structural changes in archaeal and bacterial Rieske-type [2Fe-2S] clusters.
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11872705 N.Y.Zhou, J.Al-Dulayymi, M.S.Baird, and P.A.Williams (2002).
Salicylate 5-hydroxylase from Ralstonia sp. strain U2: a monooxygenase with close relationships to and shared electron transport proteins with naphthalene dioxygenase.
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12038995 P.C.Cirino, and F.H.Arnold (2002).
Protein engineering of oxygenases for biocatalysis.
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12423753 P.M.Taylor, J.M.Medd, L.Schoenborn, B.Hodgson, and P.H.Janssen (2002).
Detection of known and novel genes encoding aromatic ring-hydroxylating dioxygenases in soils and in aromatic hydrocarbon-degrading bacteria.
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12324310 R.E.Parales, N.C.Bruce, A.Schmid, and L.P.Wackett (2002).
Biodegradation, biotransformation, and biocatalysis (b3).
  Appl Environ Microbiol, 68, 4699-4709.  
12107126 Y.Ge, F.H.Vaillancourt, N.Y.Agar, and L.D.Eltis (2002).
Reactivity of toluate dioxygenase with substituted benzoates and dioxygen.
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12454491 Z.A.Malik, C.C.Allen, L.Gakhar, D.A.Lipscomb, M.J.Larkin, and S.Ramaswamy (2002).
Crystallization and preliminary X-ray diffraction analysis of naphthalene dioxygenase from Rhodococcus sp. strain NCIMB 12038.
  Acta Crystallogr D Biol Crystallogr, 58, 2173-2174.  
11472934 A.A.Khan, R.F.Wang, W.W.Cao, D.R.Doerge, D.Wennerstrom, and C.E.Cerniglia (2001).
Molecular cloning, nucleotide sequence, and expression of genes encoding a polycyclic aromatic ring dioxygenase from Mycobacterium sp. strain PYR-1.
  Appl Environ Microbiol, 67, 3577-3585.  
11514230 A.M.Cerdeño, M.J.Bibb, and G.L.Challis (2001).
Analysis of the prodiginine biosynthesis gene cluster of Streptomyces coelicolor A3(2): new mechanisms for chain initiation and termination in modular multienzymes.
  Chem Biol, 8, 817-829.  
11114907 D.M.Eby, Z.M.Beharry, E.D.Coulter, D.M.Kurtz, and E.L.Neidle (2001).
Characterization and evolution of anthranilate 1,2-dioxygenase from Acinetobacter sp. strain ADP1.
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11849939 D.R.Boyd, N.D.Sharma, and C.C.Allen (2001).
Aromatic dioxygenases: molecular biocatalysis and applications.
  Curr Opin Biotechnol, 12, 564-573.  
11729263 E.Díaz, A.Ferrández, M.A.Prieto, and J.L.García (2001).
Biodegradation of aromatic compounds by Escherichia coli.
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12483604 H.Nojiri, H.Habe, and T.Omori (2001).
Bacterial degradation of aromatic compounds via angular dioxygenation.
  J Gen Appl Microbiol, 47, 279-305.  
11371531 H.Nojiri, H.Sekiguchi, K.Maeda, M.Urata, S.Nakai, T.Yoshida, H.Habe, and T.Omori (2001).
Genetic characterization and evolutionary implications of a car gene cluster in the carbazole degrader Pseudomonas sp. strain CA10.
  J Bacteriol, 183, 3663-3679.  
11514531 H.Suenaga, M.Mitsuoka, Y.Ura, T.Watanabe, and K.Furukawa (2001).
Directed evolution of biphenyl dioxygenase: emergence of enhanced degradation capacity for benzene, toluene, and alkylbenzenes.
  J Bacteriol, 183, 5441-5444.  
11589708 I.Martensen, R.Schauer, and L.Shaw (2001).
Cloning and expression of a membrane-bound CMP-N-acetylneuraminic acid hydroxylase from the starfish Asterias rubens.
  Eur J Biochem, 268, 5157-5166.  
11302156 J.W.Nam, H.Nojiri, T.Yoshida, H.Habe, H.Yamane, and T.Omori (2001).
New classification system for oxygenase components involved in ring-hydroxylating oxygenations.
  Biosci Biotechnol Biochem, 65, 254-263.  
11526005 K.Pollmann, S.Beil, and D.H.Pieper (2001).
Transformation of chlorinated benzenes and toluenes by Ralstonia sp. strain PS12 tecA (tetrachlorobenzene dioxygenase) and tecB (chlorobenzene dihydrodiol dehydrogenase) gene products.
  Appl Environ Microbiol, 67, 4057-4063.  
11141059 M.M.Couture, C.L.Colbert, E.Babini, F.I.Rosell, A.G.Mauk, J.T.Bolin, and L.D.Eltis (2001).
Characterization of BphF, a Rieske-type ferredoxin with a low reduction potential.
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11250197 P.J.Ellis, T.Conrads, R.Hille, and P.Kuhn (2001).
Crystal structure of the 100 kDa arsenite oxidase from Alcaligenes faecalis in two crystal forms at 1.64 A and 2.03 A.
  Structure, 9, 125-132.
PDB codes: 1g8j 1g8k
11578928 T.D.Bugg (2001).
Oxygenases: mechanisms and structural motifs for O(2) activation.
  Curr Opin Chem Biol, 5, 550-555.  
11746694 Y.Nagata, K.Mori, M.Takagi, A.G.Murzin, and J.Damborský (2001).
Identification of protein fold and catalytic residues of gamma-hexachlorocyclohexane dehydrochlorinase LinA.
  Proteins, 45, 471-477.  
10735855 A.Saito, T.Iwabuchi, and S.Harayama (2000).
A novel phenanthrene dioxygenase from Nocardioides sp. Strain KP7: expression in Escherichia coli.
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10671462 B.Morawski, A.Segura, and L.N.Ornston (2000).
Substrate range and genetic analysis of Acinetobacter vanillate demethylase.
  J Bacteriol, 182, 1383-1389.  
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.
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PDB code: 1fqt
11214797 C.Yeates, A.J.Holmes, and M.R.Gillings (2000).
Novel forms of ring-hydroxylating dioxygenases are widespread in pristine and contaminated soils.
  Environ Microbiol, 2, 644-653.  
10851148 D.H.Pieper, and W.Reineke (2000).
Engineering bacteria for bioremediation.
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10851146 D.T.Gibson, and R.E.Parales (2000).
Aromatic hydrocarbon dioxygenases in environmental biotechnology.
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10713518 E.Carredano, B.Kauppi, D.Choudhury, and S.Ramaswamy (2000).
Pseudo-symmetry characterization and refinement of a trigonal crystal form of naphthalene 1,2-dioxygenase.
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10851151 K.Furukawa (2000).
Engineering dioxygenases for efficient degradation of environmental pollutants.
  Curr Opin Biotechnol, 11, 244-249.  
  10620687 L.A.Kulakov, C.C.Allen, D.A.Lipscomb, and M.J.Larkin (2000).
Cloning and characterization of a novel cis-naphthalene dihydrodiol dehydrogenase gene (narB) from Rhodococcus sp. NCIMB12038.
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10631776 L.P.Wackett (2000).
Environmental biotechnology.
  Trends Biotechnol, 18, 19-21.  
10939808 L.P.Wackett, and N.C.Bruce (2000).
Environmental biotechnology. Towards sustainability.
  Curr Opin Biotechnol, 11, 229-231.  
11120645 N.Zhang, B.G.Stewart, J.C.Moore, R.L.Greasham, D.K.Robinson, B.C.Buckland, and C.Lee (2000).
Directed evolution of toluene dioxygenase from Pseudomonas putida for improved selectivity toward cis-indandiol during indene bioconversion.
  Metab Eng, 2, 339-348.  
10692370 R.E.Parales, K.Lee, S.M.Resnick, H.Jiang, D.J.Lessner, and D.T.Gibson (2000).
Substrate specificity of naphthalene dioxygenase: effect of specific amino acids at the active site of the enzyme.
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10986254 R.E.Parales, S.M.Resnick, C.L.Yu, D.R.Boyd, N.D.Sharma, and D.T.Gibson (2000).
Regioselectivity and enantioselectivity of naphthalene dioxygenase during arene cis-dihydroxylation: control by phenylalanine 352 in the alpha subunit.
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10679382 R.J.Kazlauskas (2000).
Molecular modeling and biocatalysis: explanations, predictions, limitations, and opportunities.
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11006535 S.E.Ealick (2000).
Advances in multiple wavelength anomalous diffraction crystallography.
  Curr Opin Chem Biol, 4, 495-499.  
10425674 A.M.Deacon, and S.E.Ealick (1999).
Selenium-based MAD phasing: setting the sites on larger structures.
  Structure, 7, R161-R166.  
9888813 B.Xia, J.D.Pikus, W.Xia, K.McClay, R.J.Steffan, Y.K.Chae, W.M.Westler, J.L.Markley, and B.G.Fox (1999).
Detection and classification of hyperfine-shifted 1H, 2H, and 15N resonances of the Rieske ferredoxin component of toluene 4-monooxygenase.
  Biochemistry, 38, 727-739.  
10607676 C.J.Schofield, and Z.Zhang (1999).
Structural and mechanistic studies on 2-oxoglutarate-dependent oxygenases and related enzymes.
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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.
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Tuning biphenyl dioxygenase for extended substrate specificity.
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Heterologous expression and characterization of the purified oxygenase component of Rhodococcus globerulus P6 biphenyl dioxygenase and of chimeras derived from it.
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The alpha subunit of toluene dioxygenase from Pseudomonas putida F1 can accept electrons from reduced FerredoxinTOL but is catalytically inactive in the absence of the beta subunit.
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10551849 H.S.Cho, N.C.Ha, G.Choi, H.J.Kim, D.Lee, K.S.Oh, K.S.Kim, W.Lee, K.Y.Choi, and B.H.Oh (1999).
Crystal structure of delta(5)-3-ketosteroid isomerase from Pseudomonas testosteroni in complex with equilenin settles the correct hydrogen bonding scheme for transition state stabilization.
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PDB code: 1qjg
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Benzene-induced uncoupling of naphthalene dioxygenase activity and enzyme inactivation by production of hydrogen peroxide.
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Purification and characterization of a novel naphthalene dioxygenase from Rhodococcus sp. strain NCIMB12038.
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Aspartate 205 in the catalytic domain of naphthalene dioxygenase is essential for activity.
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  10217753 V.J.Martin, and W.W.Mohn (1999).
A novel aromatic-ring-hydroxylating dioxygenase from the diterpenoid-degrading bacterium Pseudomonas abietaniphila BKME-9.
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Engineering of improved microbes and enzymes for bioremediation.
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High-resolution structures of scytalone dehydratase-inhibitor complexes crystallized at physiological pH.
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PDB codes: 4std 5std 6std 7std
9990724 A.M.Cook, H.Laue, and F.Junker (1998).
Microbial desulfonation.
  FEMS Microbiol Rev, 22, 399-419.  
9667935 S.J.Lange, and L.Que (1998).
Oxygen activating nonheme iron enzymes.
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