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Q89MB9

- NRDJ_BRADU

UniProt

Q89MB9 - NRDJ_BRADU

Protein

Vitamin B12-dependent ribonucleotide reductase

Gene

nrdJ

Organism
Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 78 (01 Oct 2014)
      Sequence version 1 (01 Jun 2003)
      Previous versions | rss
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    Functioni

    Catalyzes the reduction of ribonucleotides to deoxyribonucleotides. May function to provide a pool of deoxyribonucleotide precursors for DNA repair during oxygen limitation and/or for immediate growth after restoration of oxygen By similarity.By similarity

    Catalytic activityi

    2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin.

    Cofactori

    5'-deoxyadenosylcobalamine (coenzyme B12).By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei153 – 1531SubstrateBy similarity
    Binding sitei230 – 2301Substrate; via amide nitrogenBy similarity
    Active sitei474 – 4741Proton acceptorBy similarity
    Active sitei476 – 4761Cysteine radical intermediateBy similarity
    Active sitei478 – 4781Proton acceptorBy similarity

    GO - Molecular functioni

    1. cobalamin binding Source: UniProtKB-KW
    2. cobalt ion binding Source: InterPro
    3. nucleotide binding Source: UniProtKB-KW
    4. ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Source: UniProtKB-EC

    GO - Biological processi

    1. DNA replication Source: UniProtKB-KW

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    DNA synthesis

    Keywords - Ligandi

    Cobalamin, Cobalt, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciBJAP224911:GJEJ-4300-MONOMER.
    RETL1328306-WGS:GSTH-1794-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Vitamin B12-dependent ribonucleotide reductase (EC:1.17.4.1)
    Alternative name(s):
    Ribonucleoside-diphosphate reductase NrdJ
    Gene namesi
    Name:nrdJ
    Ordered Locus Names:bll4274
    OrganismiBradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
    Taxonomic identifieri224911 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeBradyrhizobium
    ProteomesiUP000002526: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 12541254Vitamin B12-dependent ribonucleotide reductasePRO_0000231658Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi199 ↔ 487Redox-activeBy similarity

    Keywords - PTMi

    Disulfide bond

    Interactioni

    Protein-protein interaction databases

    STRINGi224911.bll4274.

    Structurei

    3D structure databases

    ProteinModelPortaliQ89MB9.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni198 – 1992Substrate bindingBy similarity
    Regioni474 – 4785Substrate bindingBy similarity
    Regioni675 – 6795Substrate bindingBy similarity

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0209.
    HOGENOMiHOG000021770.
    KOiK00525.
    OrthoDBiEOG6H4K5F.
    PhylomeDBiQ89MB9.

    Family and domain databases

    InterProiIPR013678. RNR_2_N.
    IPR000788. RNR_lg_C.
    IPR013344. RNR_NrdJ/NrdZ.
    IPR024434. TSCPD_dom.
    IPR029072. YebC-like.
    [Graphical view]
    PfamiPF08471. Ribonuc_red_2_N. 1 hit.
    PF02867. Ribonuc_red_lgC. 2 hits.
    PF12637. TSCPD. 1 hit.
    [Graphical view]
    PRINTSiPR01183. RIBORDTASEM1.
    SUPFAMiSSF75625. SSF75625. 1 hit.
    TIGRFAMsiTIGR02504. NrdJ_Z. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q89MB9-1 [UniParc]FASTAAdd to Basket

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    MRIERRHTTT GQSPYAGIDF RLTTSEIRNP DGSVVFKLDN VEVPTEWSQV     50
    ASDVLAQKYF RKAGVAARLK KVEEESVPSF LWRSVPDTEA LSQLPEKERY 100
    VSELSAKQVF DRLAGCWTYW GWKGGYFTND EDAQAFYDEL RYMLAMQMVA 150
    PNSPQWFNTG LHWAYGIDGP GQGHYYVDPF TGKLTKSKSA YEHPQPHACF 200
    IQGVGDDLVN EGGIMDLWVR EARLFKYGSG TGSNFSRLRG EGEKLSGGGR 250
    SSGLMSFLKI GDRAAGAIKS GGTTRRAAKM VVVDVDHPDI ETYIDWKVKE 300
    EQKVAALVTG SKINQKHLKA VLKACVNCEG SGDDCFDPEK NPALRREIKL 350
    ARRSLVPDNY IKRVIQFAKQ GYKDIQFDVY DTDWDSEAYL TVSGQNSNNS 400
    VSLKDDFLRA VETDGDWNLN ARTSKKVTKT LKARDLWEKI GYAAWASADP 450
    GLHFNTTMND WHTCKASGDI RASNPCSEYM FLDDTACNLA SANLLTFYNV 500
    ATKHFDVEGY EHLCRLWTVV LEISVMMAQF PSKAIAELSY EFRTLGLGYA 550
    NIGGLLMTMG LPYDSKEGRA LCGALTAVMT GITYKTSAEI AAELGTFPGY 600
    KKNAAHMLRV IRNHRRAAHG QSNGYEALSV NPVPLDLVSC PQADLVSHAQ 650
    AAWDAALELG EKHGYRNAQT TVIAPTGTIG LVMDCDTTGI EPDFALVKFK 700
    KLAGGGYFKI INRAVPAALR ALGYRESEIA EIEAYAVGHG SLSNAPGINA 750
    STLKAKGFTD EAIAKVEKAL PTAFDIKFAF NKWTFGEDFI RDQLGIGAEA 800
    IAAPGFDLLQ AVGFTKREIE AANVHICGAM TVEGAPHLKA EHYPVFDCAN 850
    PCGKIGKRYL SVESHIRMMA AAQPFISGAI SKTINMPNDA TVEDCKSAYM 900
    LSWKLALKAN ALYRDGSKLS QPLNSQLIAD DEDEDDAVES LYEKPMAART 950
    AQVSEKIVEK LVERIIVMRE REKMPDRRKG YTQKAVVGGH KVYLRTGEYD 1000
    DGRLGEIFID MHKEGAALRS FINNFAIAVS LGLQYGVPLD EYVDAFTFTR 1050
    FEPAGPVQGN DSIKYATSIL DYVFRELAVS YMSRFDLAHV DPTESNFDAL 1100
    GKGVEEGKEP DEGHHASKLV SRGLTRSRTD NLVVMRGGST AVAQGNDSAP 1150
    SGGSKVTALA SHGASARVGD VLEGAVALKQ EVSHDLSPTE KLEALQWSKS 1200
    GTAQTLVPSK AERRAEAKAK GYEGEMCSEC GNFTLVRNGT CMKCDTCGST 1250
    TGCS 1254
    Length:1,254
    Mass (Da):137,465
    Last modified:June 1, 2003 - v1
    Checksum:iFF888DB9EE21A33B
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BA000040 Genomic DNA. Translation: BAC49539.1.
    RefSeqiNP_770914.1. NC_004463.1.

    Genome annotation databases

    EnsemblBacteriaiBAC49539; BAC49539; BAC49539.
    GeneIDi1053203.
    KEGGibja:bll4274.
    PATRICi21192088. VBIBraJap65052_4300.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BA000040 Genomic DNA. Translation: BAC49539.1 .
    RefSeqi NP_770914.1. NC_004463.1.

    3D structure databases

    ProteinModelPortali Q89MB9.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 224911.bll4274.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAC49539 ; BAC49539 ; BAC49539 .
    GeneIDi 1053203.
    KEGGi bja:bll4274.
    PATRICi 21192088. VBIBraJap65052_4300.

    Phylogenomic databases

    eggNOGi COG0209.
    HOGENOMi HOG000021770.
    KOi K00525.
    OrthoDBi EOG6H4K5F.
    PhylomeDBi Q89MB9.

    Enzyme and pathway databases

    BioCyci BJAP224911:GJEJ-4300-MONOMER.
    RETL1328306-WGS:GSTH-1794-MONOMER.

    Family and domain databases

    InterProi IPR013678. RNR_2_N.
    IPR000788. RNR_lg_C.
    IPR013344. RNR_NrdJ/NrdZ.
    IPR024434. TSCPD_dom.
    IPR029072. YebC-like.
    [Graphical view ]
    Pfami PF08471. Ribonuc_red_2_N. 1 hit.
    PF02867. Ribonuc_red_lgC. 2 hits.
    PF12637. TSCPD. 1 hit.
    [Graphical view ]
    PRINTSi PR01183. RIBORDTASEM1.
    SUPFAMi SSF75625. SSF75625. 1 hit.
    TIGRFAMsi TIGR02504. NrdJ_Z. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110.

    Entry informationi

    Entry nameiNRDJ_BRADU
    AccessioniPrimary (citable) accession number: Q89MB9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 4, 2006
    Last sequence update: June 1, 2003
    Last modified: October 1, 2014
    This is version 78 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

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3