Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Cobyrinate a,c-diamide synthase

Gene

cbiA

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 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. Is able to use other nucleotide triphosphates as substrate, such as GTP or UTP, although less efficiently than ATP.UniRule annotation1 Publication

Catalytic activityi

2 ATP + cobyrinate + 2 L-glutamine + 2 H2O = 2 ADP + 2 phosphate + cobyrinate a,c-diamide + 2 L-glutamate.UniRule annotation1 Publication

Cofactori

Mg2+UniRule annotation

Kineticsi

kcat is 0.16 sec(-1).1 Publication

  1. KM=0.74 µM for cobyrinate1 Publication
  2. KM=2.7 µM for ATP1 Publication
  3. KM=53 µM for glutamine1 Publication
  4. KM=26200 µM for ammonia1 Publication

    pH dependencei

    The catalytic activity is essentially constant between pH 6.8 and 8.0.1 Publication

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei334 – 3341NucleophileUniRule annotation
    Sitei438 – 4381Increases nucleophilicity of active site CysUniRule annotation

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Ligase

    Keywords - Biological processi

    Cobalamin biosynthesis

    Keywords - Ligandi

    ATP-binding, Magnesium, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-13217.
    SENT99287:GCTI-2047-MONOMER.
    BRENDAi6.3.5.11. 5542.
    SABIO-RKP29946.
    UniPathwayiUPA00148; UER00231.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Cobyrinate a,c-diamide synthaseUniRule annotationCurated (EC:6.3.5.11UniRule annotation)
    Alternative name(s):
    Cobyrinic acid a,c-diamide synthetase1 PublicationUniRule annotation
    Cleaved into the following chain:
    Gene namesi
    Name:cbiA1 PublicationUniRule annotation
    Ordered Locus Names:STM2035
    OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
    Taxonomic identifieri99287 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
    ProteomesiUP000001014 Componenti: Chromosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi45 – 451D → N: Loss of amidation activity when glutamine is used as substrate, and 750-fold reduction in amidation activity whith ammonia as substrate. 1 Publication
    Mutagenesisi46 – 461Y → A: 26-fold reduction in amidation activity with glutamine as substrate. The affinity for cobyrinate is nearly not affected whereas that for the c-monoamide intermediate decreases by 27-fold. 1 Publication
    Mutagenesisi47 – 471L → A: 10-fold reduction in amidation activity with glutamine as substrate. The affinity for cobyrinate is nearly not affected whereas that for the c-monoamide intermediate decreases by 6-fold. 1 Publication
    Mutagenesisi48 – 481D → N: 500-fold reduction in amidation activity with either glutamine or ammonia as substrate. 1 Publication
    Mutagenesisi90 – 901E → Q: Loss of amidation activity with either glutamine or ammonia as substrate. 1 Publication
    Mutagenesisi97 – 971D → N: 3-fold reduction in amidation activity with glutamine as substrate. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 459459Cobyrinate a,c-diamide synthasePRO_0000141269Add
    BLAST
    Initiator methioninei1 – 11Removed; alternate1 Publication
    Chaini2 – 459458Cobyrinate a,c-diamide synthase, N-terminally processedPRO_0000430805Add
    BLAST

    Proteomic databases

    PaxDbiP29946.
    PRIDEiP29946.

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Protein-protein interaction databases

    STRINGi99287.STM2035.

    Structurei

    3D structure databases

    ProteinModelPortaliP29946.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini252 – 446195GATase cobBQ-typeUniRule annotationAdd
    BLAST

    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 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.1 PublicationUniRule annotation

    Sequence similaritiesi

    Belongs to the CobB/CbiA family.UniRule annotation
    Contains 1 GATase cobBQ-type domain.UniRule annotation

    Keywords - Domaini

    Glutamine amidotransferase

    Phylogenomic databases

    eggNOGiCOG1797.
    HOGENOMiHOG000289958.
    KOiK02224.
    OMAiCWLPGGY.
    OrthoDBiEOG6X6R8V.
    PhylomeDBiP29946.

    Family and domain databases

    Gene3Di3.40.50.300. 1 hit.
    3.40.50.880. 1 hit.
    HAMAPiMF_00027. CobB_CbiA.
    InterProiIPR004484. CbiA_synth.
    IPR029062. Class_I_gatase-like.
    IPR017929. CobB/CobQ_GATase.
    IPR002586. CobQ/CobB/MinD/ParA_Nub-bd_dom.
    IPR011698. GATase_3.
    IPR027417. P-loop_NTPase.
    [Graphical view]
    PfamiPF01656. CbiA. 1 hit.
    PF07685. GATase_3. 1 hit.
    [Graphical view]
    SUPFAMiSSF52317. SSF52317. 1 hit.
    SSF52540. SSF52540. 1 hit.
    TIGRFAMsiTIGR00379. cobB. 1 hit.
    PROSITEiPS51274. GATASE_COBBQ. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P29946-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAARHHAFIL AGTGSGCGKT TVTLGLLRLL QKRALRVQPF KVGPDYLDTG
    60 70 80 90 100
    WHTAICGVAS RNLDSFMLPP PVLNALFCEQ MRQADIAVIE GVMGLYDGYG
    110 120 130 140 150
    VDPNYCSTAA MAKQLGCPVI LLVDGKAVST SLAATVMGFQ HFDPTLNLAG
    160 170 180 190 200
    VIVNRVTSDA HYQLLKNAIE HYCSLPVLGY VPPCDGVALP ERHLGLITAR
    210 220 230 240 250
    ESLVNQQSWH DFAATLEQTV DVDALLSLSV LSALPAGMWP ERPDNTAGAG
    260 270 280 290 300
    LTLALADDEA FNFYYPDNID LLERAGVNIV RFSPLHDRAL PDCQMIWLGG
    310 320 330 340 350
    GYPELYAADL AANTVMLKHL RAAHQRGVAI YAECGGLMYL GSTLEDSGGE
    360 370 380 390 400
    IHQMANIIPG HSKMGKRLTR FGYCEAQAMQ PTLLAAPGEI VRGHEFHYSD
    410 420 430 440 450
    FIPETPAVMA CRKVRDGRVL QEWTGGWQTG NTFASYLHVH FAQRPEMLQH

    WLAAARRVL
    Length:459
    Mass (Da):50,037
    Last modified:January 23, 2002 - v3
    Checksum:iE1FEF1B5A37F5C14
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti36 – 361R → P in AAA27252 (PubMed:8501034).Curated
    Sequence conflicti111 – 1111M → I in AAA27252 (PubMed:8501034).Curated
    Sequence conflicti128 – 1281V → I in AAA27252 (PubMed:8501034).Curated
    Sequence conflicti133 – 1331A → T in AAA27252 (PubMed:8501034).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L12006 Genomic DNA. Translation: AAA27252.1.
    AE006468 Genomic DNA. Translation: AAL20939.1.
    X63012 Genomic DNA. Translation: CAA44740.1.
    PIRiS20553.
    RefSeqiNP_460980.1. NC_003197.1.
    WP_000741259.1. NC_003197.1.

    Genome annotation databases

    EnsemblBacteriaiAAL20939; AAL20939; STM2035.
    GeneIDi1253556.
    KEGGistm:STM2035.
    PATRICi32382653. VBISalEnt20916_2157.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L12006 Genomic DNA. Translation: AAA27252.1.
    AE006468 Genomic DNA. Translation: AAL20939.1.
    X63012 Genomic DNA. Translation: CAA44740.1.
    PIRiS20553.
    RefSeqiNP_460980.1. NC_003197.1.
    WP_000741259.1. NC_003197.1.

    3D structure databases

    ProteinModelPortaliP29946.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi99287.STM2035.

    Proteomic databases

    PaxDbiP29946.
    PRIDEiP29946.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAL20939; AAL20939; STM2035.
    GeneIDi1253556.
    KEGGistm:STM2035.
    PATRICi32382653. VBISalEnt20916_2157.

    Phylogenomic databases

    eggNOGiCOG1797.
    HOGENOMiHOG000289958.
    KOiK02224.
    OMAiCWLPGGY.
    OrthoDBiEOG6X6R8V.
    PhylomeDBiP29946.

    Enzyme and pathway databases

    UniPathwayiUPA00148; UER00231.
    BioCyciMetaCyc:MONOMER-13217.
    SENT99287:GCTI-2047-MONOMER.
    BRENDAi6.3.5.11. 5542.
    SABIO-RKP29946.

    Family and domain databases

    Gene3Di3.40.50.300. 1 hit.
    3.40.50.880. 1 hit.
    HAMAPiMF_00027. CobB_CbiA.
    InterProiIPR004484. CbiA_synth.
    IPR029062. Class_I_gatase-like.
    IPR017929. CobB/CobQ_GATase.
    IPR002586. CobQ/CobB/MinD/ParA_Nub-bd_dom.
    IPR011698. GATase_3.
    IPR027417. P-loop_NTPase.
    [Graphical view]
    PfamiPF01656. CbiA. 1 hit.
    PF07685. GATase_3. 1 hit.
    [Graphical view]
    SUPFAMiSSF52317. SSF52317. 1 hit.
    SSF52540. SSF52540. 1 hit.
    TIGRFAMsiTIGR00379. cobB. 1 hit.
    PROSITEiPS51274. GATASE_COBBQ. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    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. "Cobalamin (vitamin B12) repression of the Cob operon in Salmonella typhimurium requires sequences within the leader and the first translated open reading frame."
      Richter-Dahlfors A.A., Andersson D.I.
      Mol. Microbiol. 6:743-749(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-106.
      Strain: LT2.
    4. "Mechanism of cobyrinic acid a,c-diamide synthetase from Salmonella typhimurium LT2."
      Fresquet V., Williams L., Raushel F.M.
      Biochemistry 43:10619-10627(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-7, FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, DOMAIN, REACTION MECHANISM, MUTAGENESIS OF ASP-45; TYR-46; LEU-47; ASP-48; GLU-90 AND ASP-97.
      Strain: LT2 / SGSC1412 / ATCC 700720.

    Entry informationi

    Entry nameiCBIA_SALTY
    AccessioniPrimary (citable) accession number: P29946
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 1, 1993
    Last sequence update: January 23, 2002
    Last modified: May 27, 2015
    This is version 110 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The a and c carboxylates of cobyrinate 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 annotation1 Publication

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, Reference proteome

    Documents

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

    External Data

    Dasty 3

    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 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.