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Q05603

- COBT_SALTY

UniProt

Q05603 - COBT_SALTY

Protein

Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase

Gene

cobT

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 122 (01 Oct 2014)
      Sequence version 5 (23 Jan 2002)
      Previous versions | rss
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    Functioni

    Catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide (NAMN) and 5,6-dimethylbenzimidazole (DMB).

    Catalytic activityi

    Beta-nicotinate D-ribonucleotide + 5,6-dimethylbenzimidazole = nicotinate + alpha-ribazole 5'-phosphate.

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei317 – 3171Proton acceptor

    GO - Molecular functioni

    1. cobalamin-transporting ATPase activity Source: UniProtKB-HAMAP
    2. nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity Source: CACAO

    GO - Biological processi

    1. cobalamin biosynthetic process Source: UniProtKB-KW
    2. nucleoside biosynthetic process Source: InterPro

    Keywords - Molecular functioni

    Glycosyltransferase, Transferase

    Keywords - Biological processi

    Cobalamin biosynthesis

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-13214.
    SENT99287:GCTI-2028-MONOMER.
    UniPathwayiUPA00061; UER00516.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase (EC:2.4.2.21)
    Short name:
    NN:DBI PRT
    Alternative name(s):
    N(1)-alpha-phosphoribosyltransferase
    Gene namesi
    Name:cobT
    Ordered Locus Names:STM2016
    OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
    Taxonomic identifieri99287 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
    ProteomesiUP000001014: Chromosome

    Pathology & Biotechi

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 356356Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferasePRO_0000167069Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi160 ↔ 256

    Keywords - PTMi

    Disulfide bond

    Proteomic databases

    PaxDbiQ05603.
    PRIDEiQ05603.

    Interactioni

    Subunit structurei

    Homodimer.

    Protein-protein interaction databases

    STRINGi99287.STM2016.

    Structurei

    Secondary structure

    1
    356
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi4 – 96
    Helixi16 – 2712
    Beta strandi29 – 313
    Turni33 – 364
    Helixi37 – 4711
    Helixi50 – 523
    Beta strandi60 – 689
    Helixi71 – 755
    Helixi84 – 9310
    Helixi98 – 1069
    Beta strandi109 – 1168
    Beta strandi118 – 1203
    Beta strandi125 – 1273
    Beta strandi131 – 1344
    Turni137 – 1393
    Helixi145 – 16420
    Beta strandi167 – 1759
    Turni177 – 1793
    Helixi180 – 19112
    Helixi195 – 1984
    Turni202 – 2043
    Helixi207 – 2093
    Helixi210 – 22415
    Helixi231 – 2388
    Helixi241 – 25515
    Helixi265 – 27713
    Helixi279 – 2846
    Helixi296 – 3027
    Helixi319 – 33719
    Helixi341 – 3444

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1D0SX-ray1.90A1-356[»]
    1D0VX-ray1.90A1-356[»]
    1JH8X-ray1.80A1-356[»]
    1JHAX-ray2.00A1-356[»]
    1JHMX-ray2.20A1-356[»]
    1JHOX-ray2.00A1-356[»]
    1JHPX-ray2.20A1-356[»]
    1JHQX-ray2.00A1-356[»]
    1JHRX-ray2.00A1-356[»]
    1JHUX-ray2.00A1-356[»]
    1JHVX-ray2.00A1-356[»]
    1JHXX-ray2.00A1-356[»]
    1JHYX-ray2.00A1-356[»]
    1L4BX-ray1.70A1-356[»]
    1L4EX-ray2.00A1-356[»]
    1L4FX-ray2.10A1-356[»]
    1L4GX-ray2.10A1-356[»]
    1L4HX-ray2.10A1-356[»]
    1L4KX-ray2.20A1-356[»]
    1L4LX-ray2.00A1-356[»]
    1L4MX-ray2.00A1-356[»]
    1L4NX-ray2.00A1-356[»]
    1L5FX-ray1.90A1-356[»]
    1L5KX-ray2.00A1-356[»]
    1L5LX-ray2.00A1-356[»]
    1L5MX-ray2.00A1-356[»]
    1L5NX-ray1.90A1-356[»]
    1L5OX-ray1.60A1-356[»]
    4KQFX-ray1.90A1-356[»]
    4KQGX-ray1.90A1-356[»]
    4KQHX-ray1.90A1-356[»]
    4KQIX-ray1.40A1-356[»]
    4KQJX-ray1.95A1-356[»]
    4KQKX-ray1.47A/B1-356[»]
    ProteinModelPortaliQ05603.
    SMRiQ05603. Positions 3-350.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ05603.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the CobT family.Curated

    Phylogenomic databases

    eggNOGiCOG2038.
    HOGENOMiHOG000263499.
    KOiK00768.
    OMAiAICSVIT.
    OrthoDBiEOG6HF61K.
    PhylomeDBiQ05603.

    Family and domain databases

    Gene3Di1.10.1610.10. 1 hit.
    HAMAPiMF_00230. CobT.
    InterProiIPR003200. Nict_dMeBzImd_PRibTrfase-like.
    IPR023195. Nict_dMeBzImd_PRibTrfase_N.
    IPR017846. Nict_dMeBzImd_PRibTrfase_pro.
    [Graphical view]
    PfamiPF02277. DBI_PRT. 1 hit.
    [Graphical view]
    SUPFAMiSSF52733. SSF52733. 1 hit.
    TIGRFAMsiTIGR03160. cobT_DBIPRT. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q05603-1 [UniParc]FASTAAdd to Basket

    « Hide

    MQTLHALLRD IPAPDAEAMA RAQQHIDGLL KPPGSLGRLE TLAVQLAGMP    50
    GLNGTPQVGE KAVLVMCADH GVWDEGVAVS PKIVTAIQAA NMTRGTTGVC 100
    VLAAQAGAKV HVIDVGIDAE PIPGVVNMRV ARGCGNIAVG PAMSRLQAEA 150
    LLLEVSRYTC DLAQRGVTLF GVGELGMANT TPAAAMVSVF TGSDAKEVVG 200
    IGANLPPSRI DNKVDVVRRA IAINQPNPRD GIDVLSKVGG FDLVGMTGVM 250
    LGAARCGLPV LLDGFLSYSA ALAACQIAPA VRPYLIPSHF SAEKGARIAL 300
    AHLSMEPYLH MAMRLGEGSG AALAMPIVEA ACAMFHNMGE LAASNIVLPE 350
    GNANAT 356
    Length:356
    Mass (Da):36,613
    Last modified:January 23, 2002 - v5
    Checksum:i3665FD3BB1B8A44C
    GO

    Sequence cautioni

    The sequence AAA27271.1 differs from that shown. Reason: Erroneous initiation.
    The sequence AAA69297.1 differs from that shown. Reason: Erroneous initiation.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti22 – 221A → T(PubMed:7883701)Curated
    Sequence conflicti22 – 221A → T(PubMed:8501034)Curated
    Sequence conflicti158 – 1592YT → CA(PubMed:7883701)Curated
    Sequence conflicti158 – 1592YT → CA(PubMed:8501034)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L35477 Genomic DNA. Translation: AAA69297.1. Different initiation.
    AE006468 Genomic DNA. Translation: AAL20920.1.
    L12006 Genomic DNA. Translation: AAA27271.1. Different initiation.
    RefSeqiNP_460961.1. NC_003197.1.

    Genome annotation databases

    EnsemblBacteriaiAAL20920; AAL20920; STM2016.
    GeneIDi1253537.
    KEGGistm:STM2016.
    PATRICi32382615. VBISalEnt20916_2138.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L35477 Genomic DNA. Translation: AAA69297.1 . Different initiation.
    AE006468 Genomic DNA. Translation: AAL20920.1 .
    L12006 Genomic DNA. Translation: AAA27271.1 . Different initiation.
    RefSeqi NP_460961.1. NC_003197.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1D0S X-ray 1.90 A 1-356 [» ]
    1D0V X-ray 1.90 A 1-356 [» ]
    1JH8 X-ray 1.80 A 1-356 [» ]
    1JHA X-ray 2.00 A 1-356 [» ]
    1JHM X-ray 2.20 A 1-356 [» ]
    1JHO X-ray 2.00 A 1-356 [» ]
    1JHP X-ray 2.20 A 1-356 [» ]
    1JHQ X-ray 2.00 A 1-356 [» ]
    1JHR X-ray 2.00 A 1-356 [» ]
    1JHU X-ray 2.00 A 1-356 [» ]
    1JHV X-ray 2.00 A 1-356 [» ]
    1JHX X-ray 2.00 A 1-356 [» ]
    1JHY X-ray 2.00 A 1-356 [» ]
    1L4B X-ray 1.70 A 1-356 [» ]
    1L4E X-ray 2.00 A 1-356 [» ]
    1L4F X-ray 2.10 A 1-356 [» ]
    1L4G X-ray 2.10 A 1-356 [» ]
    1L4H X-ray 2.10 A 1-356 [» ]
    1L4K X-ray 2.20 A 1-356 [» ]
    1L4L X-ray 2.00 A 1-356 [» ]
    1L4M X-ray 2.00 A 1-356 [» ]
    1L4N X-ray 2.00 A 1-356 [» ]
    1L5F X-ray 1.90 A 1-356 [» ]
    1L5K X-ray 2.00 A 1-356 [» ]
    1L5L X-ray 2.00 A 1-356 [» ]
    1L5M X-ray 2.00 A 1-356 [» ]
    1L5N X-ray 1.90 A 1-356 [» ]
    1L5O X-ray 1.60 A 1-356 [» ]
    4KQF X-ray 1.90 A 1-356 [» ]
    4KQG X-ray 1.90 A 1-356 [» ]
    4KQH X-ray 1.90 A 1-356 [» ]
    4KQI X-ray 1.40 A 1-356 [» ]
    4KQJ X-ray 1.95 A 1-356 [» ]
    4KQK X-ray 1.47 A/B 1-356 [» ]
    ProteinModelPortali Q05603.
    SMRi Q05603. Positions 3-350.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 99287.STM2016.

    Chemistry

    DrugBanki DB00173. Adenine.

    Proteomic databases

    PaxDbi Q05603.
    PRIDEi Q05603.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAL20920 ; AAL20920 ; STM2016 .
    GeneIDi 1253537.
    KEGGi stm:STM2016.
    PATRICi 32382615. VBISalEnt20916_2138.

    Phylogenomic databases

    eggNOGi COG2038.
    HOGENOMi HOG000263499.
    KOi K00768.
    OMAi AICSVIT.
    OrthoDBi EOG6HF61K.
    PhylomeDBi Q05603.

    Enzyme and pathway databases

    UniPathwayi UPA00061 ; UER00516 .
    BioCyci MetaCyc:MONOMER-13214.
    SENT99287:GCTI-2028-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q05603.

    Family and domain databases

    Gene3Di 1.10.1610.10. 1 hit.
    HAMAPi MF_00230. CobT.
    InterProi IPR003200. Nict_dMeBzImd_PRibTrfase-like.
    IPR023195. Nict_dMeBzImd_PRibTrfase_N.
    IPR017846. Nict_dMeBzImd_PRibTrfase_pro.
    [Graphical view ]
    Pfami PF02277. DBI_PRT. 1 hit.
    [Graphical view ]
    SUPFAMi SSF52733. SSF52733. 1 hit.
    TIGRFAMsi TIGR03160. cobT_DBIPRT. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "The end of the cob operon: evidence that the last gene (cobT) catalyzes synthesis of the lower ligand of vitamin B12, dimethylbenzimidazole."
      Chen P., Ailion M., Weyand N., Roth J.R.
      J. Bacteriol. 177:1461-1469(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: LT2.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: LT2 / SGSC1412 / ATCC 700720.
    3. "Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium."
      Roth J.R., Lawrence J.G., Rubenfield M., Kieffer-Higgins S., Church G.M.
      J. Bacteriol. 175:3303-3316(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-242.
      Strain: LT2.
    4. "The three-dimensional structures of nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) from Salmonella typhimurium complexed with 5,6-dimethybenzimidazole and its reaction products determined to 1.9-A resolution."
      Cheong C.-G., Escalante-Semerena J.C., Rayment I.
      Biochemistry 38:16125-16135(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS), SEQUENCE REVISION TO 158.

    Entry informationi

    Entry nameiCOBT_SALTY
    AccessioniPrimary (citable) accession number: Q05603
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 1, 1994
    Last sequence update: January 23, 2002
    Last modified: October 1, 2014
    This is version 122 of the entry and version 5 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    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