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P0A110

- NDOB_PSEPU

UniProt

P0A110 - NDOB_PSEPU

Protein

Naphthalene 1,2-dioxygenase subunit alpha

Gene

ndoB

Organism
Pseudomonas putida (Arthrobacter siderocapsulatus)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 63 (01 Oct 2014)
      Sequence version 1 (01 Mar 2005)
      Previous versions | rss
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    Functioni

    Component of the naphthalene dioxygenase (NDO) multicomponent enzyme system which catalyzes the incorporation of both atoms of molecular oxygen into naphthalene to form cis-naphthalene dihydrodiol.

    Catalytic activityi

    Naphthalene + NADH + O2 = (1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD+.

    Cofactori

    Binds 1 2Fe-2S cluster.Curated
    Binds 1 iron ion.Curated

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi81 – 811Iron-sulfur (2Fe-2S)
    Metal bindingi83 – 831Iron-sulfur (2Fe-2S); via pros nitrogen
    Metal bindingi101 – 1011Iron-sulfur (2Fe-2S)
    Metal bindingi104 – 1041Iron-sulfur (2Fe-2S); via pros nitrogen
    Metal bindingi208 – 2081Iron
    Metal bindingi213 – 2131Iron
    Metal bindingi362 – 3621Iron

    GO - Molecular functioni

    1. 2 iron, 2 sulfur cluster binding Source: UniProtKB-KW
    2. iron ion binding Source: InterPro
    3. naphthalene 1,2-dioxygenase activity Source: UniProtKB-EC
    4. protein binding Source: IntAct

    GO - Biological processi

    1. aromatic compound catabolic process Source: UniProtKB-KW

    Keywords - Molecular functioni

    Dioxygenase, Oxidoreductase

    Keywords - Biological processi

    Aromatic hydrocarbons catabolism

    Keywords - Ligandi

    2Fe-2S, Iron, Iron-sulfur, Metal-binding, NAD

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-12802.
    UniPathwayiUPA00082.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Naphthalene 1,2-dioxygenase subunit alpha (EC:1.14.12.12)
    Alternative name(s):
    Naphthalene 1,2-dioxygenase ISP alpha
    Gene namesi
    Name:ndoB
    Synonyms:nahA3, nahAC, ndoC2
    Encoded oniPlasmid pDTG11 Publication
    Plasmid NAH71 Publication
    Plasmid NPL11 Publication
    OrganismiPseudomonas putida (Arthrobacter siderocapsulatus)
    Taxonomic identifieri303 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 449449Naphthalene 1,2-dioxygenase subunit alphaPRO_0000085053Add
    BLAST

    Interactioni

    Subunit structurei

    Naphthalene dioxygenase (NDO) multicomponent enzyme system is composed of an electron transfer component and an iron sulfur protein (ISP). The electron transfer component is composed of ferredoxin reductase (NdoR) and ferredoxin (NdoA), and ISP is composed of a large alpha subunit (NdoB) and a small beta subunit (NdoC).

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    ndoCP0A1127EBI-1029015,EBI-1029028

    Protein-protein interaction databases

    IntActiP0A110. 1 interaction.
    MINTiMINT-257428.

    Structurei

    Secondary structure

    1
    449
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Turni3 – 53
    Helixi11 – 133
    Beta strandi15 – 173
    Helixi18 – 214
    Helixi24 – 3310
    Turni34 – 374
    Beta strandi40 – 445
    Helixi45 – 473
    Beta strandi53 – 597
    Beta strandi62 – 687
    Beta strandi74 – 807
    Turni82 – 843
    Beta strandi91 – 955
    Beta strandi97 – 1004
    Turni102 – 1043
    Beta strandi107 – 1093
    Beta strandi114 – 1163
    Helixi120 – 1234
    Turni124 – 1263
    Helixi130 – 1323
    Beta strandi139 – 1446
    Beta strandi147 – 1526
    Helixi159 – 1635
    Helixi166 – 1749
    Turni175 – 1773
    Beta strandi180 – 19314
    Helixi196 – 2049
    Helixi209 – 2124
    Helixi214 – 2207
    Helixi225 – 2306
    Beta strandi238 – 2436
    Beta strandi249 – 2535
    Turni257 – 2604
    Turni263 – 2653
    Helixi266 – 28419
    Helixi286 – 2927
    Beta strandi294 – 3007
    Turni301 – 3033
    Beta strandi304 – 3074
    Turni308 – 3114
    Beta strandi312 – 3209
    Beta strandi323 – 33311
    Helixi338 – 35215
    Helixi357 – 37216
    Turni376 – 3805
    Beta strandi382 – 3843
    Turni387 – 3904
    Beta strandi393 – 3953
    Beta strandi397 – 3993
    Beta strandi401 – 4088
    Helixi411 – 42414
    Helixi429 – 4357
    Turni436 – 4383
    Helixi439 – 4446

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1EG9X-ray1.60A1-449[»]
    1NDOX-ray2.25A/C/E1-449[»]
    1O7GX-ray1.70A1-449[»]
    1O7HX-ray2.20A1-449[»]
    1O7MX-ray1.75A1-449[»]
    1O7NX-ray1.40A1-449[»]
    1O7PX-ray1.95A1-449[»]
    1O7WX-ray1.90A1-449[»]
    1UUVX-ray1.65A1-449[»]
    1UUWX-ray2.30A1-449[»]
    ProteinModelPortaliP0A110.
    SMRiP0A110. Positions 1-447.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0A110.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini39 – 13799RieskePROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Contains 1 Rieske domain.PROSITE-ProRule annotation

    Family and domain databases

    Gene3Di2.102.10.10. 1 hit.
    3.90.380.10. 1 hit.
    InterProiIPR017941. Rieske_2Fe-2S.
    IPR015881. Ring-hydroxy_dOase_2Fe2S_BS.
    IPR015879. Ring_hydroxy_dOase_asu_C_dom.
    IPR001663. Rng_hydr_dOase-A.
    [Graphical view]
    PfamiPF00355. Rieske. 1 hit.
    PF00848. Ring_hydroxyl_A. 1 hit.
    [Graphical view]
    PRINTSiPR00090. RNGDIOXGNASE.
    SUPFAMiSSF50022. SSF50022. 1 hit.
    PROSITEiPS51296. RIESKE. 1 hit.
    PS00570. RING_HYDROXYL_ALPHA. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P0A110-1 [UniParc]FASTAAdd to Basket

    « Hide

    MNYNNKILVS ESGLSQKHLI HGDEELFQHE LKTIFARNWL FLTHDSLIPA    50
    PGDYVTAKMG IDEVIVSRQN DGSIRAFLNV CRHRGKTLVS VEAGNAKGFV 100
    CSYHGWGFGS NGELQSVPFE KDLYGESLNK KCLGLKEVAR VESFHGFIYG 150
    CFDQEAPPLM DYLGDAAWYL EPMFKHSGGL ELVGPPGKVV IKANWKAPAE 200
    NFVGDAYHVG WTHASSLRSG ESIFSSLAGN AALPPEGAGL QMTSKYGSGM 250
    GVLWDGYSGV HSADLVPELM AFGGAKQERL NKEIGDVRAR IYRSHLNCTV 300
    FPNNSMLTCS GVFKVWNPID ANTTEVWTYA IVEKDMPEDL KRRLADSVQR 350
    TFGPAGFWES DDNDNMETAS QNGKKYQSRD SDLLSNLGFG EDVYGDAVYP 400
    GVVGKSAIGE TSYRGFYRAY QAHVSSSNWA EFEHASSTWH TELTKTTDR 449
    Length:449
    Mass (Da):49,608
    Last modified:March 1, 2005 - v1
    Checksum:i1FD2F42296B4F7A8
    GO

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti4 – 41N → K in strain: G7.
    Natural varianti12 – 121S → F in strain: ATCC 17484.
    Natural varianti15 – 151S → T in strain: G7.
    Natural varianti32 – 321K → R in strain: G7.
    Natural varianti50 – 501A → S in strain: G7.
    Natural varianti70 – 701N → S in strain: G7.
    Natural varianti90 – 912SV → NA in strain: G7.
    Natural varianti122 – 1221D → E in strain: G7.
    Natural varianti173 – 1731M → I in strain: G7.
    Natural varianti225 – 2251S → A in strain: G7.
    Natural varianti225 – 2251S → C in strain: BS202.
    Natural varianti232 – 2321A → V in strain: G7.
    Natural varianti275 – 2751A → S in strain: G7.
    Natural varianti391 – 3911E → K in strain: G7.
    Natural varianti421 – 4211Q → R in strain: ATCC 17484.
    Natural varianti434 – 4341H → D in strain: G7.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M23914 Genomic DNA. Translation: AAB47591.1.
    U49496 Genomic DNA. Translation: AAA92141.1.
    M83949 Genomic DNA. Translation: AAA25902.1.
    AF010471 Genomic DNA. Translation: AAB62707.1.
    AF004284 Genomic DNA. Translation: AAB61373.1.
    PIRiJN0644.
    JS0071.
    RefSeqiNP_863072.1. NC_004999.1.
    YP_534822.1. NC_007926.1.

    Genome annotation databases

    GeneIDi1343187.
    3974209.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M23914 Genomic DNA. Translation: AAB47591.1 .
    U49496 Genomic DNA. Translation: AAA92141.1 .
    M83949 Genomic DNA. Translation: AAA25902.1 .
    AF010471 Genomic DNA. Translation: AAB62707.1 .
    AF004284 Genomic DNA. Translation: AAB61373.1 .
    PIRi JN0644.
    JS0071.
    RefSeqi NP_863072.1. NC_004999.1.
    YP_534822.1. NC_007926.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1EG9 X-ray 1.60 A 1-449 [» ]
    1NDO X-ray 2.25 A/C/E 1-449 [» ]
    1O7G X-ray 1.70 A 1-449 [» ]
    1O7H X-ray 2.20 A 1-449 [» ]
    1O7M X-ray 1.75 A 1-449 [» ]
    1O7N X-ray 1.40 A 1-449 [» ]
    1O7P X-ray 1.95 A 1-449 [» ]
    1O7W X-ray 1.90 A 1-449 [» ]
    1UUV X-ray 1.65 A 1-449 [» ]
    1UUW X-ray 2.30 A 1-449 [» ]
    ProteinModelPortali P0A110.
    SMRi P0A110. Positions 1-447.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi P0A110. 1 interaction.
    MINTi MINT-257428.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 1343187.
    3974209.

    Enzyme and pathway databases

    UniPathwayi UPA00082 .
    BioCyci MetaCyc:MONOMER-12802.

    Miscellaneous databases

    EvolutionaryTracei P0A110.

    Family and domain databases

    Gene3Di 2.102.10.10. 1 hit.
    3.90.380.10. 1 hit.
    InterProi IPR017941. Rieske_2Fe-2S.
    IPR015881. Ring-hydroxy_dOase_2Fe2S_BS.
    IPR015879. Ring_hydroxy_dOase_asu_C_dom.
    IPR001663. Rng_hydr_dOase-A.
    [Graphical view ]
    Pfami PF00355. Rieske. 1 hit.
    PF00848. Ring_hydroxyl_A. 1 hit.
    [Graphical view ]
    PRINTSi PR00090. RNGDIOXGNASE.
    SUPFAMi SSF50022. SSF50022. 1 hit.
    PROSITEi PS51296. RIESKE. 1 hit.
    PS00570. RING_HYDROXYL_ALPHA. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Cloning, nucleotide sequence and characterization of genes encoding naphthalene dioxygenase of Pseudomonas putida strain NCIB9816."
      Kurkela S., Lehvaeslaiho H., Palva E.T., Teeri T.H.
      Gene 73:355-362(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: DSM 8368 / NCIMB 9816.
    2. "Cloning and sequencing of the genes encoding 2-nitrotoluene dioxygenase from Pseudomonas sp. JS42."
      Parales J.V., Kumar A., Parales R.E., Gibson D.T.
      Gene 181:57-61(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: NCIMB 9816-4.
      Plasmid: pDTG1
    3. "Sequences of genes encoding naphthalene dioxygenase in Pseudomonas putida strains G7 and NCIB 9816-4."
      Simon M.J., Osslund T.D., Saunders R., Ensley B.D., Suggs S., Harcourt A.A., Suen W.-C., Cruden D.L., Gibson D.T., Zylstra G.J.
      Gene 127:31-37(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 17485 / DSM 50208 / JCM 6158 / NCIMB 12092 / Stanier 111 / Biotype A.
      Plasmid: NAH7
    4. "Nucleotide sequences of genes encoding an upper pathway of naphthalene metabolism of NPL1 plasmid from Pseudomonas putida strain BS202."
      Bezborodnikov S.G., Boronin A.M., Tiedje J.M.
      Submitted (JUL-1997) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: BS202.
      Plasmid: NPL1
    5. "Naphthalene dioxygenase genes from Pseudomonas putida."
      Hamann C.
      Submitted (JUN-1997) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 17484 / DSM 50222 / NCIMB 10535 / Stanier 110 / Biotype B.
    6. "Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase."
      Kauppi B., Lee K., Carredano E., Parales R.E., Gibson D.T., Eklund H., Ramaswamy S.
      Structure 6:571-586(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS).
      Strain: NCIMB 9816-4.

    Entry informationi

    Entry nameiNDOB_PSEPU
    AccessioniPrimary (citable) accession number: P0A110
    Secondary accession number(s): O07830
    , O33461, P23094, Q52124
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 1, 2005
    Last sequence update: March 1, 2005
    Last modified: October 1, 2014
    This is version 63 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Plasmid

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3