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Entry version 103 (13 Nov 2019)
Sequence version 1 (13 Sep 2005)
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Protein

Cobyrinate a,c-diamide synthase

Gene

cbiA

Organism
Methanosarcina barkeri (strain Fusaro / DSM 804)
Status
Reviewed-Annotation score:

Annotation score:4 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 the ATP-dependent amidation of the two carboxylate groups at positions a and c of cobyrinate, using either L-glutamine or ammonia as the nitrogen source (Potential). Involved in the biosynthesis of the unique nickel-containing tetrapyrrole coenzyme F430, the prosthetic group of methyl-coenzyme M reductase (MCR), which plays a key role in methanogenesis and anaerobic methane oxidation (PubMed:28225763). Catalyzes the ATP-dependent amidation of the two carboxylate groups at positions a and c of Ni-sirohydrochlorin, using L-glutamine or ammonia as the nitrogen source (PubMed:28225763). Also able to use sirohydrochlorin as substrate, but only produces a monoamide species in a much slower reaction (PubMed:28225763). Unable to use other metallosirohydrochlorins such as sirohaem and Co-sirohydrochlorin (PubMed:28225763).UniRule annotation1 Publication

Miscellaneous

The a and c carboxylates of cobyrinate and Ni-sirohydrochlorin are activated for nucleophilic attack via formation of a phosphorylated intermediate by ATP. CbiA catalyzes first the amidation of the c-carboxylate, and then that of the a-carboxylate.UniRule annotation

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">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 provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Mg2+UniRule annotation1 Publication

<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 1.03 min(-1) for ATP as substrate. Kcat is 0.78 min(-1) for L-glutamine as substrate.1 Publication
  1. KM=46 µM for L-glutamine1 Publication
  2. KM=28 µM for ATP1 Publication

    <p>This subsection of the <a href="http://www.uniprot.org/help/function_section">'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 10 of the subpathway that synthesizes cob(II)yrinate a,c-diamide from sirohydrochlorin (anaerobic route).UniRule annotation
    Proteins known to be involved in the 10 steps of the subpathway in this organism are:
    1. Sirohydrochlorin cobaltochelatase (cbiX), Sirohydrochlorin cobaltochelatase (cbiX)
    2. no protein annotated in this organism
    3. no protein annotated in this organism
    4. no protein annotated in this organism
    5. no protein annotated in this organism
    6. Cobalt-precorrin-5B C(1)-methyltransferase (cbiD)
    7. no protein annotated in this organism
    8. Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) (cbiT)
    9. no protein annotated in this organism
    10. Cobyrinate a,c-diamide synthase (cbiA), Cobyrinate a,c-diamide synthase (cbiA), Cobyrinate a,c-diamide synthase (cbiA)
    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 cob(II)yrinate a,c-diamide from sirohydrochlorin (anaerobic route), 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_section">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 sitei352NucleophileUniRule annotation1
    <p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections (‘Function’, ‘PTM / Processing’, ‘Pathology and Biotech’) according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei467Increases nucleophilicity of active site CysUniRule annotation1

    <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 functionLigase
    Biological processCobalamin biosynthesis, Methanogenesis
    LigandATP-binding, Magnesium, Nucleotide-binding

    Enzyme and pathway databases

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

    More...
    UniPathwayi
    UPA00148;UER00231

    <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_and_taxonomy_section">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:
    Cobyrinate a,c-diamide synthaseUniRule annotation (EC:6.3.5.11UniRule annotation)
    Alternative name(s):
    Cobyrinic acid a,c-diamide synthetaseUniRule annotation
    Ni-sirohydrochlorin a,c-diamide synthase1 PublicationUniRule annotation (EC:6.3.5.12UniRule annotation1 Publication)
    Ni-sirohydrochlorin a,c-diamide synthetase1 PublicationUniRule annotation
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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:cbiAUniRule annotation
    Synonyms:cfbB1 PublicationUniRule annotation
    Ordered Locus Names:Mbar_A0348Imported
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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>OrganismiMethanosarcina barkeri (strain Fusaro / DSM 804)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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 identifieri269797 [NCBI]
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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 lineageiArchaeaEuryarchaeotaStenosarchaea groupMethanomicrobiaMethanosarcinalesMethanosarcinaceaeMethanosarcina
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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
    • UP000008156 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">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 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.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00004424591 – 494Cobyrinate a,c-diamide synthaseAdd BLAST494

    <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

    Protein-protein interaction databases

    STRING: functional protein association networks

    More...
    STRINGi
    269797.Mbar_A0348

    <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

    3D structure databases

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

    More...
    SMRi
    Q46FL0

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    <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

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini270 – 475GATase cobBQ-typeUniRule annotationAdd BLAST206

    <p>This subsection of the ‘Family and domains’ section provides general information on the biological role of a domain. The term ‘domain’ is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

    Comprises of two domains. The C-terminal domain contains the binding site for glutamine and catalyzes the hydrolysis of this substrate to glutamate and ammonia. The N-terminal domain is anticipated to bind ATP, and cobyrinate or Ni-sirohydrochlorin, and catalyzes the ultimate synthesis of the diamide product. The ammonia produced via the glutaminase domain is probably translocated to the adjacent domain via a molecular tunnel, where it reacts with an activated intermediate.UniRule annotation

    <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 CobB/CbiA family.UniRule annotation

    Keywords - Domaini

    Glutamine amidotransferase

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    arCOG00106 Archaea
    COG1797 LUCA

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    HOG000289958

    KEGG Orthology (KO)

    More...
    KOi
    K22012

    Identification of Orthologs from Complete Genome Data

    More...
    OMAi
    MYLTNSI

    Database of Orthologous Groups

    More...
    OrthoDBi
    14023at2157

    Family and domain databases

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    3.40.50.880, 1 hit

    HAMAP database of protein families

    More...
    HAMAPi
    MF_00027 CobB_CbiA, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR004484 CbiA_synth
    IPR029062 Class_I_gatase-like
    IPR017929 CobB/CobQ_GATase
    IPR011698 GATase_3
    IPR027417 P-loop_NTPase

    The PANTHER Classification System

    More...
    PANTHERi
    PTHR43873 PTHR43873, 1 hit

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF07685 GATase_3, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF52317 SSF52317, 1 hit
    SSF52540 SSF52540, 1 hit

    TIGRFAMs; a protein family database

    More...
    TIGRFAMsi
    TIGR00379 cobB, 1 hit

    PROSITE; a protein domain and family database

    More...
    PROSITEi
    View protein in PROSITE
    PS51274 GATASE_COBBQ, 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_length">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_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">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.

    Q46FL0-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MLNDKQSVEN IPRILISADR SSSGKTTISM GLMAALVSRG YKVQPFKVAL
    60 70 80 90 100
    DYIDPSYHTE ITGRFCRNLD GYLMDENGIL DVYTHACEAG EKADIAIIEG
    110 120 130 140 150
    VRGLYEGFES LSDLGSTAQI AKILNCPVIF VINARSITRS SAALINGYRN
    160 170 180 190 200
    FDPDVEIAGV ILNNIGSRRH AKKAKEAIEY YTGVPVIGIV PRDPAMQISM
    210 220 230 240 250
    RHLGLMPALE GRRRLGDGGF EARLRGIEEI INKGIDVDRF MEIAKSAKAL
    260 270 280 290 300
    KSPENSVFSS VSDPGAPRPK IGVALDEAFN FYYRDNIDLL NLAGAEIVYF
    310 320 330 340 350
    SPVKDASLPE VDGLYIGGGY PELFAAELEA NESMRQDIKK ASAAGMPIYA
    360 370 380 390 400
    ECGGLMYLTE KISTGVPGKG TYHDASMPES TYSMVGALPG HTIMGQTRVV
    410 420 430 440 450
    SYNIGTLNKD CLLGKKYNSF KGHEFHHSEI REIPEDAEFA ITLSRGTGIK
    460 470 480 490
    NGMDGLISGN TLGSYAHLHG VAYREFASSL VEAARNFRDS RVLP
    Length:494
    Mass (Da):53,786
    Last modified:September 13, 2005 - v1
    <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:i88D530FF1A2500C4
    GO

    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
    CP000099 Genomic DNA Translation: AAZ69332.1

    NCBI Reference Sequences

    More...
    RefSeqi
    WP_011305385.1, NC_007355.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    AAZ69332; AAZ69332; Mbar_A0348

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    3626592

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    mba:Mbar_A0348

    <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
    CP000099 Genomic DNA Translation: AAZ69332.1
    RefSeqiWP_011305385.1, NC_007355.1

    3D structure databases

    SMRiQ46FL0
    ModBaseiSearch...

    Protein-protein interaction databases

    STRINGi269797.Mbar_A0348

    Genome annotation databases

    EnsemblBacteriaiAAZ69332; AAZ69332; Mbar_A0348
    GeneIDi3626592
    KEGGimba:Mbar_A0348

    Phylogenomic databases

    eggNOGiarCOG00106 Archaea
    COG1797 LUCA
    HOGENOMiHOG000289958
    KOiK22012
    OMAiMYLTNSI
    OrthoDBi14023at2157

    Enzyme and pathway databases

    UniPathwayiUPA00148;UER00231

    Family and domain databases

    Gene3Di3.40.50.880, 1 hit
    HAMAPiMF_00027 CobB_CbiA, 1 hit
    InterProiView protein in InterPro
    IPR004484 CbiA_synth
    IPR029062 Class_I_gatase-like
    IPR017929 CobB/CobQ_GATase
    IPR011698 GATase_3
    IPR027417 P-loop_NTPase
    PANTHERiPTHR43873 PTHR43873, 1 hit
    PfamiView protein in Pfam
    PF07685 GATase_3, 1 hit
    SUPFAMiSSF52317 SSF52317, 1 hit
    SSF52540 SSF52540, 1 hit
    TIGRFAMsiTIGR00379 cobB, 1 hit
    PROSITEiView protein in PROSITE
    PS51274 GATASE_COBBQ, 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 nameiCBIA_METBF
    <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: Q46FL0
    <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_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 22, 2017
    Last sequence update: September 13, 2005
    Last modified: November 13, 2019
    This is version 103 of the entry and version 1 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

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
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