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Protein

Cobyrinate a,c-diamide synthase

Gene

cbiA

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed-Annotation score: -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

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

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: adenosylcobalamin biosynthesis

    This protein is involved in step 10 of the subpathway that synthesizes cob(II)yrinate a,c-diamide from sirohydrochlorin (anaerobic route).1 PublicationUniRule annotation
    Proteins known to be involved in the 10 steps of the subpathway in this organism are:
    1. Sirohydrochlorin cobaltochelatase (cbiK)
    2. Cobalt-precorrin-2 C(20)-methyltransferase (cbiL)
    3. Probable cobalt-factor III C(17)-methyltransferase (cbiH)
    4. Cobalt-precorrin-4 C(11)-methyltransferase (cbiF)
    5. Cobalt-precorrin-5A hydrolase (cbiG)
    6. Cobalt-precorrin-5B C(1)-methyltransferase (cbiD)
    7. Cobalt-precorrin-6A reductase (cbiJ)
    8. Cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) (cbiT), Cobalt-precorrin-7 C(5)-methyltransferase (cbiE)
    9. Cobalt-precorrin-8 methylmutase (cbiC)
    10. 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
    Active sitei334NucleophileUniRule annotation1
    Sitei438Increases nucleophilicity of active site CysUniRule annotation1

    GO - Molecular functioni

    GO - Biological processi

    Keywordsi

    Molecular functionLigase
    Biological processCobalamin biosynthesis
    LigandATP-binding, Magnesium, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-13217
    SENT99287:G1FZD-2054-MONOMER
    BRENDAi6.3.5.11 5542
    SABIO-RKiP29946
    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
    Proteomesi
    • UP000001014 Componenti: Chromosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi45D → N: Loss of amidation activity when glutamine is used as substrate, and 750-fold reduction in amidation activity whith ammonia as substrate. 1 Publication1
    Mutagenesisi46Y → 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 Publication1
    Mutagenesisi47L → 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 Publication1
    Mutagenesisi48D → N: 500-fold reduction in amidation activity with either glutamine or ammonia as substrate. 1 Publication1
    Mutagenesisi90E → Q: Loss of amidation activity with either glutamine or ammonia as substrate. 1 Publication1
    Mutagenesisi97D → N: 3-fold reduction in amidation activity with glutamine as substrate. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001412691 – 459Cobyrinate a,c-diamide synthaseAdd BLAST459
    Initiator methionineiRemoved; alternate1 Publication
    ChainiPRO_00004308052 – 459Cobyrinate a,c-diamide synthase, N-terminally processedAdd BLAST458

    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)DescriptionActionsGraphical viewLength
    Domaini252 – 446GATase cobBQ-typeUniRule annotationAdd BLAST195

    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

    Keywords - Domaini

    Glutamine amidotransferase

    Phylogenomic databases

    eggNOGiENOG4105C0Y Bacteria
    COG1797 LUCA
    HOGENOMiHOG000289958
    KOiK02224
    OMAiMYLTNSI
    PhylomeDBiP29946

    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
    IPR002586 CobQ/CobB/MinD/ParA_Nub-bd_dom
    IPR011698 GATase_3
    IPR027417 P-loop_NTPase
    PANTHERiPTHR43873 PTHR43873, 1 hit
    PfamiView protein in Pfam
    PF01656 CbiA, 1 hit
    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

    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)DescriptionActionsGraphical viewLength
    Sequence conflicti36R → P in AAA27252 (PubMed:8501034).Curated1
    Sequence conflicti111M → I in AAA27252 (PubMed:8501034).Curated1
    Sequence conflicti128V → I in AAA27252 (PubMed:8501034).Curated1
    Sequence conflicti133A → T in AAA27252 (PubMed:8501034).Curated1

    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_003197.2
    WP_000741259.1, NC_003197.2

    Genome annotation databases

    EnsemblBacteriaiAAL20939; AAL20939; STM2035
    GeneIDi1253556
    KEGGistm:STM2035
    PATRICifig|99287.12.peg.2157

    Similar proteinsi

    Entry informationi

    Entry nameiCBIA_SALTY
    AccessioniPrimary (citable) accession number: P29946
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 1, 1993
    Last sequence update: January 23, 2002
    Last modified: March 28, 2018
    This is version 119 of the entry and version 3 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, Reference proteome
    UniProt is an ELIXIR core data resource
    Main funding by: National Institutes of Health