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PDBsum entry 1g8k

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1g8k
Jmol
Contents
Protein chains
822 a.a. *
133 a.a. *
Ligands
MGD ×8
__O ×4
F3S ×4
EDO ×9
FES ×4
Metals
_HG ×12
_CA ×8
4MO ×4
Waters ×4087
* Residue conservation analysis
PDB id:
1g8k
Name: Oxidoreductase
Title: Crystal structure analysis of arsenite oxidase from alcalige faecalis
Structure: Arsenite oxidase. Chain: a, c, e, g. Arsenite oxidase. Chain: b, d, f, h
Source: Alcaligenes faecalis. Organism_taxid: 511. Strain: ncib 8687. Strain: ncib 8687
Biol. unit: Dimer (from PQS)
Resolution:
1.64Å     R-factor:   0.154     R-free:   0.179
Authors: P.J.Ellis,T.Conrads,R.Hille,P.Kuhn
Key ref:
P.J.Ellis et al. (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. PubMed id: 11250197 DOI: 10.1016/S0969-2126(01)00566-4
Date:
17-Nov-00     Release date:   13-Dec-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q7SIF4  (AIOA_ALCFA) -  Arsenite oxidase subunit AioA
Seq:
Struc:
 
Seq:
Struc:
826 a.a.
822 a.a.*
Protein chains
Pfam   ArchSchema ?
Q7SIF3  (AIOB_ALCFA) -  Arsenite oxidase subunit AioB
Seq:
Struc:
175 a.a.
133 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 22 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F, G, H: E.C.1.20.9.1  - Arsenate reductase (azurin).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Arsenite + H2O + 2 oxidized azurin = arsenate + 2 reduced azurin + 2 H+
Arsenite
+ H(2)O
+ 2 × oxidized azurin
= arsenate
+ 2 × reduced azurin
+ 2 × H(+)
      Cofactor: Iron-sulfur; Mo cation; Molybdopterin
Iron-sulfur
Mo cation
Molybdopterin
Bound ligand (Het Group name = MGD) matches with 51.06% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   1 term 
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     oxidoreductase activity     8 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(01)00566-4 Structure 9:125-132 (2001)
PubMed id: 11250197  
 
 
Crystal structure of the 100 kDa arsenite oxidase from Alcaligenes faecalis in two crystal forms at 1.64 A and 2.03 A.
P.J.Ellis, T.Conrads, R.Hille, P.Kuhn.
 
  ABSTRACT  
 
BACKGROUND: Arsenite oxidase from Alcaligenes faecalis NCIB 8687 is a molybdenum/iron protein involved in the detoxification of arsenic. It is induced by the presence of AsO(2-) (arsenite) and functions to oxidize As(III)O(2-), which binds to essential sulfhydryl groups of proteins and dithiols, to the relatively less toxic As(V)O(4)(3-) (arsenate) prior to methylation. RESULTS: Using a combination of multiple isomorphous replacement with anomalous scattering (MIRAS) and multiple-wavelength anomalous dispersion (MAD) methods, the crystal structure of arsenite oxidase was determined to 2.03 A in a P2(1) crystal form with two molecules in the asymmetric unit and to 1.64 A in a P1 crystal form with four molecules in the asymmetric unit. Arsenite oxidase consists of a large subunit of 825 residues and a small subunit of approximately 134 residues. The large subunit contains a Mo site, consisting of a Mo atom cluster. The small subunit site. CONCLUSIONS: The large subunit of arsenite oxidase is similar to other members of the dimethylsulfoxide (DMSO) reductase family of molybdenum enzymes, particularly the dissimilatory periplasmic nitrate reductase from Desulfovibrio desulfuricans, but is unique in having no covalent bond between the polypeptide and the Mo atom. The small subunit has no counterpart among known Mo protein structures but is homologous to the Rieske protein domain of the cytochrome bc(1) and cytochrome b(6)f complexes and to the Rieske domain of naphthalene 1,2-dioxygenase.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Schematic Representation of the Proposed Reaction Mechanism for the Oxidation of Arsenite by Arsenite OxidaseThe oxygen atom transferred from water to arsenite during the catalytic cycle is highlighted in red

 
  The above figure is reprinted by permission from Cell Press: Structure (2001, 9, 125-132) copyright 2001.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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21246143 H.Sugimoto, H.Tano, H.Miyake, and S.Itoh (2011).
Generation of bis(dithiolene)dioxomolybdenum(vi) complexes from bis(dithiolene)monooxomolybdenum(iv) complexes by proton-coupled electron transfer in aqueous media.
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Temporal transcriptomic response during arsenic stress in Herminiimonas arsenicoxydans.
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20167112 S.Koechler, J.Cleiss-Arnold, C.Proux, O.Sismeiro, M.A.Dillies, F.Goulhen-Chollet, F.Hommais, D.Lièvremont, F.Arsène-Ploetze, J.Y.Coppée, and P.N.Bertin (2010).
Multiple controls affect arsenite oxidase gene expression in Herminiimonas arsenicoxydans.
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19549320 C.G.Bryan, M.Marchal, F.Battaglia-Brunet, V.Kugler, C.Lemaitre-Guillier, D.Lièvremont, P.N.Bertin, and F.Arsène-Ploetze (2009).
Carbon and arsenic metabolism in Thiomonas strains: differences revealed diverse adaptation processes.
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Arsenic resistant bacteria isolated from arsenic contaminated river in the Atacama Desert (Chile).
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18642094 I.H.Yoon, J.S.Chang, J.H.Lee, and K.W.Kim (2009).
Arsenite oxidation by Alcaligenes sp. strain RS-19 isolated from arsenic-contaminated mines in the Republic of Korea.
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19214757 K.S.Prasad, V.Subramanian, and J.Paul (2009).
Purification and characterization of arsenite oxidase from Arthrobacter sp.
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19283378 L.Cai, C.Rensing, X.Li, and G.Wang (2009).
Novel gene clusters involved in arsenite oxidation and resistance in two arsenite oxidizers: Achromobacter sp. SY8 and Pseudomonas sp. TS44.
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19196273 N.Hamamura, R.E.Macur, S.Korf, G.Ackerman, W.P.Taylor, M.Kozubal, A.L.Reysenbach, and W.P.Inskeep (2009).
Linking microbial oxidation of arsenic with detection and phylogenetic analysis of arsenite oxidase genes in diverse geothermal environments.
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19525272 R.Branco, R.Francisco, A.P.Chung, and P.V.Morais (2009).
Identification of an aox system that requires cytochrome c in the highly arsenic-resistant bacterium Ochrobactrum tritici SCII24.
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19880307 S.L.Tsai, S.Singh, and W.Chen (2009).
Arsenic metabolism by microbes in nature and the impact on arsenic remediation.
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19479286 U.Ryde, C.Schulzke, and K.Starke (2009).
Which functional groups of the molybdopterin ligand should be considered when modeling the active sites of the molybdenum and tungsten cofactors? A density functional theory study.
  J Biol Inorg Chem, 14, 1053-1064.  
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.
  J Biol Inorg Chem, 13, 1301-1313.
PDB code: 2qpz
18502920 M.Quéméneur, A.Heinrich-Salmeron, D.Muller, D.Lièvremont, M.Jauzein, P.N.Bertin, F.Garrido, and C.Joulian (2008).
Diversity surveys and evolutionary relationships of aoxB genes in aerobic arsenite-oxidizing bacteria.
  Appl Environ Microbiol, 74, 4567-4573.  
18631373 S.Duval, A.L.Ducluzeau, W.Nitschke, and B.Schoepp-Cothenet (2008).
Enzyme phylogenies as markers for the oxidation state of the environment: the case of respiratory arsenate reductase and related enzymes.
  BMC Evol Biol, 8, 206.  
17846760 C.Michel, M.Jean, S.Coulon, M.C.Dictor, F.Delorme, D.Morin, and F.Garrido (2007).
Biofilms of As(III)-oxidising bacteria: formation and activity studies for bioremediation process development.
  Appl Microbiol Biotechnol, 77, 457-467.  
17426855 K.Ray, T.Petrenko, K.Wieghardt, and F.Neese (2007).
Joint spectroscopic and theoretical investigations of transition metal complexes involving non-innocent ligands.
  Dalton Trans, (), 1552-1566.  
17827309 S.D'Imperio, C.R.Lehr, M.Breary, and T.R.McDermott (2007).
Autecology of an arsenite chemolithotroph: sulfide constraints on function and distribution in a geothermal spring.
  Appl Environ Microbiol, 73, 7067-7074.  
17359265 W.P.Inskeep, R.E.Macur, N.Hamamura, T.P.Warelow, S.A.Ward, and J.M.Santini (2007).
Detection, diversity and expression of aerobic bacterial arsenite oxidase genes.
  Environ Microbiol, 9, 934-943.  
16962969 D.P.Kloer, C.Hagel, J.Heider, and G.E.Schulz (2006).
Crystal structure of ethylbenzene dehydrogenase from Aromatoleum aromaticum.
  Structure, 14, 1377-1388.
PDB code: 2ivf
16452441 D.R.Kashyap, L.M.Botero, C.Lehr, D.J.Hassett, and T.R.McDermott (2006).
A Na+:H+ antiporter and a molybdate transporter are essential for arsenite oxidation in Agrobacterium tumefaciens.
  J Bacteriol, 188, 1577-1584.  
16428412 D.R.Kashyap, L.M.Botero, W.L.Franck, D.J.Hassett, and T.R.McDermott (2006).
Complex regulation of arsenite oxidation in Agrobacterium tumefaciens.
  J Bacteriol, 188, 1081-1088.  
16623746 E.D.Rhine, C.D.Phelps, and L.Y.Young (2006).
Anaerobic arsenite oxidation by novel denitrifying isolates.
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16704340 J.F.Stolz, P.Basu, J.M.Santini, and R.S.Oremland (2006).
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16627939 L.A.Moe, C.A.Bingman, G.E.Wesenberg, G.N.Phillips, and B.G.Fox (2006).
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15786505 A.J.Millar, C.J.Doonan, P.D.Smith, V.N.Nemykin, P.Basu, and C.G.Young (2005).
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  Chemistry, 11, 3255-3267.  
16234938 H.Sugimoto, M.Tarumizu, K.Tanaka, H.Miyake, and H.Tsukube (2005).
A new series of molybdenum-(IV), -(V), and -(VI) dithiolate compounds as active site models of molybdoenzymes: preparation, crystal structures, spectroscopic/electrochemical properties and reactivity in oxygen atom transfer.
  Dalton Trans, (), 3558-3565.  
16218872 M.Boll, B.Schink, A.Messerschmidt, and P.M.Kroneck (2005).
Novel bacterial molybdenum and tungsten enzymes: three-dimensional structure, spectroscopy, and reaction mechanism.
  Biol Chem, 386, 999.  
15948965 S.Ouchane, W.Nitschke, P.Bianco, A.Vermeglio, and C.Astier (2005).
Multiple Rieske genes in prokaryotes: exchangeable Rieske subunits in the cytochrome bc-complex of Rubrivivax gelatinosus.
  Mol Microbiol, 57, 261-275.  
16133099 S.Silver, and l.e. .T.Phung (2005).
A bacterial view of the periodic table: genes and proteins for toxic inorganic ions.
  J Ind Microbiol Biotechnol, 32, 587-605.  
14996791 J.M.Santini, and R.N.vanden Hoven (2004).
Molybdenum-containing arsenite oxidase of the chemolithoautotrophic arsenite oxidizer NT-26.
  J Bacteriol, 186, 1614-1619.  
15355966 L.Loschi, S.J.Brokx, T.L.Hills, G.Zhang, M.G.Bertero, A.L.Lovering, J.H.Weiner, and N.C.Strynadka (2004).
Structural and biochemical identification of a novel bacterial oxidoreductase.
  J Biol Chem, 279, 50391-50400.
PDB codes: 1xdq 1xdy
15568975 L.R.Croal, J.A.Gralnick, D.Malasarn, and D.K.Newman (2004).
The genetics of geochemistry.
  Annu Rev Genet, 38, 175-202.  
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
13129615 E.Afkar, J.Lisak, C.Saltikov, P.Basu, R.S.Oremland, and J.F.Stolz (2003).
The respiratory arsenate reductase from Bacillus selenitireducens strain MLS10.
  FEMS Microbiol Lett, 226, 107-112.  
12594934 F.Baymann, E.Lebrun, M.Brugna, B.Schoepp-Cothenet, M.T.Giudici-Orticoni, and W.Nitschke (2003).
The redox protein construction kit: pre-last universal common ancestor evolution of energy-conserving enzymes.
  Philos Trans R Soc Lond B Biol Sci, 358, 267-274.  
12948771 M.Jormakka, B.Byrne, and S.Iwata (2003).
Formate dehydrogenase--a versatile enzyme in changing environments.
  Curr Opin Struct Biol, 13, 418-423.  
12738852 R.S.Oremland, and J.F.Stolz (2003).
The ecology of arsenic.
  Science, 300, 939-944.  
12829274 S.Silver (2003).
Bacterial silver resistance: molecular biology and uses and misuses of silver compounds.
  FEMS Microbiol Rev, 27, 341-353.  
12067345 C.A.McDevitt, P.Hugenholtz, G.R.Hanson, and A.G.McEwan (2002).
Molecular analysis of dimethyl sulphide dehydrogenase from Rhodovulum sulfidophilum: its place in the dimethyl sulphoxide reductase family of microbial molybdopterin-containing enzymes.
  Mol Microbiol, 44, 1575-1587.  
12114025 R.Hille (2002).
Molybdenum and tungsten in biology.
  Trends Biochem Sci, 27, 360-367.  
12165430 R.Mukhopadhyay, B.P.Rosen, L.T.Phung, and S.Silver (2002).
Microbial arsenic: from geocycles to genes and enzymes.
  FEMS Microbiol Rev, 26, 311-325.  
11679756 Z.Guan, L.Hederstedt, J.Li, and X.D.Su (2001).
Preparation and crystallization of a Bacillus subtilis arsenate reductase.
  Acta Crystallogr D Biol Crystallogr, 57, 1718-1721.  
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.