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Entry version 136 (22 Apr 2020)
Sequence version 2 (01 Oct 1996)
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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

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

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

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the 'Function' section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>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

    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>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. Corrinoid adenosyltransferase (pduO), Corrinoid 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)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei47GMP-histidine intermediate1 Publication1
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei59GTP1
    Binding sitei81GTP; via carbonyl oxygen1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi7 – 14GTP8
    Nucleotide bindingi31 – 33GTP3
    Nucleotide bindingi48 – 51GTP4

    <p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

    GO - Biological processi

    <p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

    Molecular functionKinase, Transferase
    Biological processCobalamin biosynthesis
    LigandATP-binding, GTP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    MetaCyc:MONOMER-13215
    SENT99287:STM2018-MONOMER

    UniPathway: a resource for the exploration and annotation of metabolic pathways

    More...
    UniPathwayi
    UPA00148;UER00236
    UPA00148;UER00237

    <p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>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)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
    Name:cobU
    Ordered Locus Names:STM2018
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri99287 [NCBI]
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
    • UP000001014 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome

    <p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi46H → A: 3-5 fold reduction in activity. 1 Publication1
    Mutagenesisi46H → A: No activity; when associated with Ala-47. 1 Publication1
    Mutagenesisi47H → A: Almost no residual activity. 1 Publication1
    Mutagenesisi47H → A: No activity; when associated with Ala-46. 1 Publication1
    Mutagenesisi47H → N: Very little residual activity. 1 Publication1

    Chemistry databases

    Drug and drug target database

    More...
    DrugBanki
    DB00115 Cyanocobalamin
    DB01972 Guanosine-5'-Monophosphate

    <p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000899981 – 181Bifunctional adenosylcobalamin biosynthesis protein CobUAdd BLAST181

    Proteomic databases

    PaxDb, a database of protein abundance averages across all three domains of life

    More...
    PaxDbi
    Q05599

    PRoteomics IDEntifications database

    More...
    PRIDEi
    Q05599

    <p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

    <p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

    Homotrimer.

    2 Publications

    <p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

    Secondary structure

    1181
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    SWISS-MODEL Repository - a database of annotated 3D protein structure models

    More...
    SMRi
    Q05599

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    Protein Data Bank in Europe - Knowledge Base

    More...
    PDBe-KBi
    Search...

    Miscellaneous databases

    Relative evolutionary importance of amino acids within a protein sequence

    More...
    EvolutionaryTracei
    Q05599

    <p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

    <p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

    Belongs to the CobU/CobP family.Curated

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    ENOG4108YZT Bacteria
    COG2087 LUCA

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    CLU_094161_0_2_6

    KEGG Orthology (KO)

    More...
    KOi
    K02231

    Identification of Orthologs from Complete Genome Data

    More...
    OMAi
    DCLTVWL

    Database for complete collections of gene phylogenies

    More...
    PhylomeDBi
    Q05599

    Family and domain databases

    Conserved Domains Database

    More...
    CDDi
    cd00544 CobU, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR003203 Cobinamide_kinase/P_G-Trfase
    IPR027417 P-loop_NTPase

    The PANTHER Classification System

    More...
    PANTHERi
    PTHR34848 PTHR34848, 1 hit

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF02283 CobU, 1 hit

    PIRSF; a whole-protein classification database

    More...
    PIRSFi
    PIRSF006135 CobU, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF52540 SSF52540, 1 hit

    <p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

    <p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
    <p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iF6F89892C6BEE091
    GO

    <p>This subsection of the 'Sequence' section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

    The sequence AAA27269 differs from that shown. Reason: Erroneous initiation. Truncated N-terminus.Curated

    Sequence databases

    Select the link destinations:

    EMBL nucleotide sequence database

    More...
    EMBLi

    GenBank nucleotide sequence database

    More...
    GenBanki

    DNA Data Bank of Japan; a nucleotide sequence database

    More...
    DDBJi
    Links Updated
    L12006 Genomic DNA Translation: AAA27269.1 Different initiation.
    AE006468 Genomic DNA Translation: AAL20922.1

    NCBI Reference Sequences

    More...
    RefSeqi
    NP_460963.1, NC_003197.2
    WP_000973145.1, NC_003197.2

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    AAL20922; AAL20922; STM2018

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    1253539

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    stm:STM2018

    Pathosystems Resource Integration Center (PATRIC)

    More...
    PATRICi
    fig|99287.12.peg.2140

    <p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

    <p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>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_003197.2
    WP_000973145.1, NC_003197.2

    3D structure databases

    Select the link destinations:

    Protein Data Bank Europe

    More...
    PDBei

    Protein Data Bank RCSB

    More...
    RCSB PDBi

    Protein Data Bank Japan

    More...
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1C9KX-ray2.20A/B/C2-181[»]
    1CBUX-ray2.30A/B/C2-181[»]
    SMRiQ05599
    ModBaseiSearch...
    PDBe-KBiSearch...

    Chemistry databases

    DrugBankiDB00115 Cyanocobalamin
    DB01972 Guanosine-5'-Monophosphate

    Proteomic databases

    PaxDbiQ05599
    PRIDEiQ05599

    Genome annotation databases

    EnsemblBacteriaiAAL20922; AAL20922; STM2018
    GeneIDi1253539
    KEGGistm:STM2018
    PATRICifig|99287.12.peg.2140

    Phylogenomic databases

    eggNOGiENOG4108YZT Bacteria
    COG2087 LUCA
    HOGENOMiCLU_094161_0_2_6
    KOiK02231
    OMAiDCLTVWL
    PhylomeDBiQ05599

    Enzyme and pathway databases

    UniPathwayiUPA00148;UER00236
    UPA00148;UER00237
    BioCyciMetaCyc:MONOMER-13215
    SENT99287:STM2018-MONOMER

    Miscellaneous databases

    EvolutionaryTraceiQ05599

    Family and domain databases

    CDDicd00544 CobU, 1 hit
    InterProiView protein in InterPro
    IPR003203 Cobinamide_kinase/P_G-Trfase
    IPR027417 P-loop_NTPase
    PANTHERiPTHR34848 PTHR34848, 1 hit
    PfamiView protein in Pfam
    PF02283 CobU, 1 hit
    PIRSFiPIRSF006135 CobU, 1 hit
    SUPFAMiSSF52540 SSF52540, 1 hit

    ProtoNet; Automatic hierarchical classification of proteins

    More...
    ProtoNeti
    Search...

    MobiDB: a database of protein disorder and mobility annotations

    More...
    MobiDBi
    Search...

    <p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

    <p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiCOBU_SALTY
    <p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q05599
    <p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 1, 1994
    Last sequence update: October 1, 1996
    Last modified: April 22, 2020
    This is version 136 of the entry and version 2 of the sequence. See complete history.
    <p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    <p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

    Keywords - Technical termi

    3D-structure, 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
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