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Protein

Bifunctional adenosylcobalamin biosynthesis protein CobU

Gene

cobU

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes ATP-dependent phosphorylation of adenosylcobinamide and addition of GMP to adenosylcobinamide phosphate.1 Publication

Catalytic activityi

ATP or GTP + adenosylcobinamide = adenosylcobinamide phosphate + ADP or GDP.2 Publications
GTP + adenosylcobinamide phosphate = diphosphate + adenosylcobinamide-GDP.2 Publications

Kineticsi

kcat is 15.1 min(-1) for adenosylcobinamide kinase activity. kcat is 5.6 min(-1) for guanylyltransferase activity.

  1. KM=66 µM for adenosylcobinamide1 Publication
  2. KM=206 µM for ATP1 Publication
  3. KM=102 µM for adenosylcobinamide phosphate1 Publication
  4. KM=21.3 µM for GTP1 Publication

    pH dependencei

    Optimum pH is 8.8-9.0.1 Publication

    Temperature dependencei

    Optimum temperature is 37 degrees Celsius.1 Publication

    Pathwayi: adenosylcobalamin biosynthesis

    This protein is involved in step 5 and 6 of the subpathway that synthesizes adenosylcobalamin from cob(II)yrinate a,c-diamide.
    Proteins known to be involved in the 7 steps of the subpathway in this organism are:
    1. no protein annotated in this organism
    2. Cob(I)yrinic acid a,c-diamide adenosyltransferase (btuR)
    3. no protein annotated in this organism
    4. Cobalamin biosynthesis protein CbiB (cbiB)
    5. Bifunctional adenosylcobalamin biosynthesis protein CobU (cobU)
    6. Bifunctional adenosylcobalamin biosynthesis protein CobU (cobU)
    7. Adenosylcobinamide-GDP ribazoletransferase (cobS)
    This subpathway is part of the pathway adenosylcobalamin biosynthesis, which is itself part of Cofactor biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes adenosylcobalamin from cob(II)yrinate a,c-diamide, the pathway adenosylcobalamin biosynthesis and in Cofactor biosynthesis.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei47 – 471GMP-histidine intermediate1 Publication
    Binding sitei59 – 591GTP
    Binding sitei81 – 811GTP; via carbonyl oxygen

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi7 – 148GTP
    Nucleotide bindingi31 – 333GTP
    Nucleotide bindingi48 – 514GTP

    GO - Molecular functioni

    GO - Biological processi

    Keywords - Molecular functioni

    Kinase, Transferase

    Keywords - Biological processi

    Cobalamin biosynthesis

    Keywords - Ligandi

    ATP-binding, GTP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-13215.
    SENT99287:GCTI-2030-MONOMER.
    UniPathwayiUPA00148; UER00236.
    UPA00148; UER00237.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Bifunctional adenosylcobalamin biosynthesis protein CobU
    Alternative name(s):
    Adenosylcobinamide kinase (EC:2.7.1.1562 Publications)
    Adenosylcobinamide-phosphate guanylyltransferase (EC:2.7.7.622 Publications)
    Gene namesi
    Name:cobU
    Ordered Locus Names:STM2018
    OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
    Taxonomic identifieri99287 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
    Proteomesi
    • UP000001014 Componenti: Chromosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi46 – 461H → A: 3-5 fold reduction in activity. 1 Publication
    Mutagenesisi46 – 461H → A: No activity; when associated with Ala-47. 1 Publication
    Mutagenesisi47 – 471H → A: Almost no residual activity. 1 Publication
    Mutagenesisi47 – 471H → A: No activity; when associated with Ala-46. 1 Publication
    Mutagenesisi47 – 471H → N: Very little residual activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 181181Bifunctional adenosylcobalamin biosynthesis protein CobUPRO_0000089998Add
    BLAST

    Proteomic databases

    PaxDbiQ05599.
    PRIDEiQ05599.

    Interactioni

    Subunit structurei

    Homotrimer.2 Publications

    Protein-protein interaction databases

    STRINGi99287.STM2018.

    Structurei

    Secondary structure

    1
    181
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 75Combined sources
    Helixi13 – 219Combined sources
    Beta strandi25 – 317Combined sources
    Helixi38 – 414Combined sources
    Helixi43 – 497Combined sources
    Beta strandi55 – 584Combined sources
    Helixi64 – 663Combined sources
    Beta strandi77 – 815Combined sources
    Helixi83 – 9311Combined sources
    Helixi100 – 1023Combined sources
    Helixi105 – 12521Combined sources
    Beta strandi128 – 1336Combined sources
    Helixi146 – 16520Combined sources
    Beta strandi167 – 1737Combined sources
    Beta strandi176 – 1794Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1C9KX-ray2.20A/B/C2-181[»]
    1CBUX-ray2.30A/B/C2-181[»]
    ProteinModelPortaliQ05599.
    SMRiQ05599. Positions 2-181.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ05599.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the CobU/CobP family.Curated

    Phylogenomic databases

    eggNOGiENOG4108YZT. Bacteria.
    COG2087. LUCA.
    HOGENOMiHOG000286613.
    KOiK02231.
    OMAiLWLTNHL.
    OrthoDBiEOG6Z0QGH.
    PhylomeDBiQ05599.

    Family and domain databases

    Gene3Di3.40.50.300. 1 hit.
    InterProiIPR003203. Cobinamide_kinase/P_G-Trfase.
    IPR027417. P-loop_NTPase.
    [Graphical view]
    PfamiPF02283. CobU. 1 hit.
    [Graphical view]
    PIRSFiPIRSF006135. CobU. 1 hit.
    SUPFAMiSSF52540. SSF52540. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q05599-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MMILVTGGAR SGKSRHAEAL IGDAPQVLYI ATSQILDDEM AARIQHHKDG
    60 70 80 90 100
    RPAHWRTAEC WRHLDTLITA DLAPDDAILL ECITTMVTNL LFALGGENDP
    110 120 130 140 150
    EQWDYAAMER AIDDEIQILI AACQRCPAKV VLVTNEVGMG IVPENRLARH
    160 170 180
    FRDIAGRVNQ RLAAAADEVW LVVSGIGVKI K
    Length:181
    Mass (Da):19,902
    Last modified:October 1, 1996 - v2
    Checksum:iF6F89892C6BEE091
    GO

    Sequence cautioni

    The sequence AAA27269.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L12006 Genomic DNA. Translation: AAA27269.1. Different initiation.
    AE006468 Genomic DNA. Translation: AAL20922.1.
    RefSeqiNP_460963.1. NC_003197.1.
    WP_000973145.1. NC_003197.1.

    Genome annotation databases

    EnsemblBacteriaiAAL20922; AAL20922; STM2018.
    GeneIDi1253539.
    KEGGistm:STM2018.
    PATRICi32382619. VBISalEnt20916_2140.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L12006 Genomic DNA. Translation: AAA27269.1. Different initiation.
    AE006468 Genomic DNA. Translation: AAL20922.1.
    RefSeqiNP_460963.1. NC_003197.1.
    WP_000973145.1. NC_003197.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1C9KX-ray2.20A/B/C2-181[»]
    1CBUX-ray2.30A/B/C2-181[»]
    ProteinModelPortaliQ05599.
    SMRiQ05599. Positions 2-181.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi99287.STM2018.

    Proteomic databases

    PaxDbiQ05599.
    PRIDEiQ05599.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAL20922; AAL20922; STM2018.
    GeneIDi1253539.
    KEGGistm:STM2018.
    PATRICi32382619. VBISalEnt20916_2140.

    Phylogenomic databases

    eggNOGiENOG4108YZT. Bacteria.
    COG2087. LUCA.
    HOGENOMiHOG000286613.
    KOiK02231.
    OMAiLWLTNHL.
    OrthoDBiEOG6Z0QGH.
    PhylomeDBiQ05599.

    Enzyme and pathway databases

    UniPathwayiUPA00148; UER00236.
    UPA00148; UER00237.
    BioCyciMetaCyc:MONOMER-13215.
    SENT99287:GCTI-2030-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiQ05599.

    Family and domain databases

    Gene3Di3.40.50.300. 1 hit.
    InterProiIPR003203. Cobinamide_kinase/P_G-Trfase.
    IPR027417. P-loop_NTPase.
    [Graphical view]
    PfamiPF02283. CobU. 1 hit.
    [Graphical view]
    PIRSFiPIRSF006135. CobU. 1 hit.
    SUPFAMiSSF52540. SSF52540. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    1. "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].
      Strain: LT2.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: LT2 / SGSC1412 / ATCC 700720.
    3. "Purification and characterization of the bifunctional CobU enzyme of Salmonella typhimurium LT2. Evidence for a CobU-GMP intermediate."
      O'Toole G.A., Escalante-Semerena J.C.
      J. Biol. Chem. 270:23560-23569(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF N-TERMINUS, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY.
      Strain: LT2.
    4. "Analysis of the adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase (CobU) enzyme of Salmonella typhimurium LT2. Identification of residue His-46 as the site of guanylylation."
      Thomas M.G., Thompson T.B., Rayment I., Escalante-Semerena J.C.
      J. Biol. Chem. 275:27576-27586(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: CATALYTIC ACTIVITY, MUTAGENESIS OF HIS-46 AND HIS-47.
      Strain: LT2.
    5. "Three-dimensional structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase from Salmonella typhimurium determined to 2.3-A resolution."
      Thompson T.B., Thomas M.G., Escalante-Semerena J.C., Rayment I.
      Biochemistry 37:7686-7695(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS), SUBUNIT.
      Strain: LT2.
    6. "Three-dimensional structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase (CobU) complexed with GMP: evidence for a substrate-induced transferase active site."
      Thompson T.B., Thomas M.G., Escalante-Semerena J.C., Rayment I.
      Biochemistry 38:12995-13005(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEX WITH GMP AND PHOSPHATE, ACTIVE SITE.

    Entry informationi

    Entry nameiCOBU_SALTY
    AccessioniPrimary (citable) accession number: Q05599
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 1, 1994
    Last sequence update: October 1, 1996
    Last modified: January 20, 2016
    This is version 118 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, 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

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.