PDBsum entry 1ndo

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Non-heme iron dioxygenase PDB id
Protein chains
447 a.a. *
193 a.a. *
FES ×3
_FE ×3
Waters ×1061
* Residue conservation analysis
PDB id:
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)
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
11-Jan-98     Release date:   23-Mar-99    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P0A110  (NDOB_PSEPU) -  Naphthalene 1,2-dioxygenase subunit alpha
449 a.a.
447 a.a.
Protein chains
Pfam   ArchSchema ?
P0A112  (NDOC_PSEPU) -  Naphthalene 1,2-dioxygenase subunit beta
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.  - Naphthalene 1,2-dioxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Aromatic 1,2-Dioxygenases
      Reaction: Naphthalene + NADH + O2 = (1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD+
+ 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  


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.
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).
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PDB code: 2zyl
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19464996 M.Tarasev, S.Pullela, and D.P.Ballou (2009).
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PDB code: 3d89
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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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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.
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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.
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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.
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PDB codes: 2gbw 2gbx 2i7f
17704278 E.Borodina, T.Nichol, M.G.Dumont, T.J.Smith, and J.C.Murrell (2007).
Mutagenesis of the "leucine gate" to explore the basis of catalytic versatility in soluble methane monooxygenase.
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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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17269935 E.L.Ang, J.P.Obbard, and H.Zhao (2007).
Probing the molecular determinants of aniline dioxygenase substrate specificity by saturation mutagenesis.
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17451434 J.Jakoncic, Y.Jouanneau, C.Meyer, and V.Stojanoff (2007).
The crystal structure of the ring-hydroxylating dioxygenase from Sphingomonas CHY-1.
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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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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.
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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.
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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.
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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.
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16217654 H.Suenaga, M.Goto, and K.Furukawa (2006).
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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.
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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.
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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.
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16517627 K.S.Ju, and R.E.Parales (2006).
Control of substrate specificity by active-site residues in nitrobenzene dioxygenase.
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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.
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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.
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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.
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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.  
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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.
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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.
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12586937 A.Karlsson, J.V.Parales, R.E.Parales, D.T.Gibson, H.Eklund, and S.Ramaswamy (2003).
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PDB codes: 1o7g 1o7h 1o7m 1o7n 1o7p 1o7w
12829283 B.Brezna, A.A.Khan, and C.E.Cerniglia (2003).
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The crystal structure of a cyanobacterial water-soluble carotenoid binding protein.
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PDB code: 1m98
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13129960 H.K.Chang, P.Mohseni, and G.J.Zylstra (2003).
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Hydrogen peroxide-coupled cis-diol formation catalyzed by naphthalene 1,2-dioxygenase.
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Pinpointing biphenyl dioxygenase residues that are crucial for substrate interaction.
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Molecular characterization and substrate preference of a polycyclic aromatic hydrocarbon dioxygenase from Cycloclasticus sp. strain A5.
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14622009 Z.M.Beharry, D.M.Eby, E.D.Coulter, R.Viswanathan, E.L.Neidle, R.S.Phillips, and D.M.Kurtz (2003).
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Sequence and structural differences between enzyme and nonenzyme homologs.
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Analysis of the prodiginine biosynthesis gene cluster of Streptomyces coelicolor A3(2): new mechanisms for chain initiation and termination in modular multienzymes.
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Crystal structure of the 100 kDa arsenite oxidase from Alcaligenes faecalis in two crystal forms at 1.64 A and 2.03 A.
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PDB codes: 1g8j 1g8k
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Oxygenases: mechanisms and structural motifs for O(2) activation.
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A novel phenanthrene dioxygenase from Nocardioides sp. Strain KP7: expression in Escherichia coli.
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Substrate range and genetic analysis of Acinetobacter vanillate demethylase.
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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
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Engineering dioxygenases for efficient degradation of environmental pollutants.
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Environmental biotechnology.
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Advances in multiple wavelength anomalous diffraction crystallography.
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Selenium-based MAD phasing: setting the sites on larger structures.
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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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A novel aromatic-ring-hydroxylating dioxygenase from the diterpenoid-degrading bacterium Pseudomonas abietaniphila BKME-9.
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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
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Microbial desulfonation.
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Oxygen activating nonheme iron enzymes.
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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.