ID   CBIA_SALTY              Reviewed;         459 AA.
AC   P29946;
DT   01-APR-1993, integrated into UniProtKB/Swiss-Prot.
DT   23-JAN-2002, sequence version 3.
DT   27-MAR-2024, entry version 141.
DE   RecName: Full=Cobyrinate a,c-diamide synthase {ECO:0000255|HAMAP-Rule:MF_00027, ECO:0000305};
DE            EC=6.3.5.11 {ECO:0000255|HAMAP-Rule:MF_00027};
DE   AltName: Full=Cobyrinic acid a,c-diamide synthetase {ECO:0000255|HAMAP-Rule:MF_00027, ECO:0000303|PubMed:15311923};
DE   Contains:
DE     RecName: Full=Cobyrinate a,c-diamide synthase, N-terminally processed {ECO:0000305};
DE   Flags: Precursor;
GN   Name=cbiA {ECO:0000255|HAMAP-Rule:MF_00027,
GN   ECO:0000303|PubMed:8501034}; OrderedLocusNames=STM2035;
OS   Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720).
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Salmonella.
OX   NCBI_TaxID=99287;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=LT2;
RX   PubMed=8501034; DOI=10.1128/jb.175.11.3303-3316.1993;
RA   Roth J.R., Lawrence J.G., Rubenfield M., Kieffer-Higgins S., Church G.M.;
RT   "Characterization of the cobalamin (vitamin B12) biosynthetic genes of
RT   Salmonella typhimurium.";
RL   J. Bacteriol. 175:3303-3316(1993).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX   PubMed=11677609; DOI=10.1038/35101614;
RA   McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P.,
RA   Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D.,
RA   Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E.,
RA   Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R.,
RA   Wilson R.K.;
RT   "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.";
RL   Nature 413:852-856(2001).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-106.
RC   STRAIN=LT2;
RX   PubMed=1374146; DOI=10.1111/j.1365-2958.1992.tb01524.x;
RA   Richter-Dahlfors A.A., Andersson D.I.;
RT   "Cobalamin (vitamin B12) repression of the Cob operon in Salmonella
RT   typhimurium requires sequences within the leader and the first translated
RT   open reading frame.";
RL   Mol. Microbiol. 6:743-749(1992).
RN   [4]
RP   PROTEIN SEQUENCE OF 2-7, FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE
RP   SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, DOMAIN, REACTION
RP   MECHANISM, AND MUTAGENESIS OF ASP-45; TYR-46; LEU-47; ASP-48; GLU-90 AND
RP   ASP-97.
RC   STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX   PubMed=15311923; DOI=10.1021/bi048972x;
RA   Fresquet V., Williams L., Raushel F.M.;
RT   "Mechanism of cobyrinic acid a,c-diamide synthetase from Salmonella
RT   typhimurium LT2.";
RL   Biochemistry 43:10619-10627(2004).
CC   -!- FUNCTION: Catalyzes the ATP-dependent amidation of the two carboxylate
CC       groups at positions a and c of cobyrinate, using either L-glutamine or
CC       ammonia as the nitrogen source. Is able to use other nucleotide
CC       triphosphates as substrate, such as GTP or UTP, although less
CC       efficiently than ATP. {ECO:0000255|HAMAP-Rule:MF_00027,
CC       ECO:0000269|PubMed:15311923}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=2 ATP + cob(II)yrinate + 2 H2O + 2 L-glutamine = 2 ADP +
CC         cob(II)yrinate a,c diamide + 2 H(+) + 2 L-glutamate + 2 phosphate;
CC         Xref=Rhea:RHEA:26289, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC         ChEBI:CHEBI:29985, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474,
CC         ChEBI:CHEBI:58359, ChEBI:CHEBI:58537, ChEBI:CHEBI:58894,
CC         ChEBI:CHEBI:456216; EC=6.3.5.11; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_00027, ECO:0000269|PubMed:15311923};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_00027};
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=0.74 uM for cobyrinate {ECO:0000269|PubMed:15311923};
CC         KM=2.7 uM for ATP {ECO:0000269|PubMed:15311923};
CC         KM=53 uM for glutamine {ECO:0000269|PubMed:15311923};
CC         KM=26200 uM for ammonia {ECO:0000269|PubMed:15311923};
CC         Note=kcat is 0.16 sec(-1). {ECO:0000269|PubMed:15311923};
CC       pH dependence:
CC         The catalytic activity is essentially constant between pH 6.8 and
CC         8.0. {ECO:0000269|PubMed:15311923};
CC   -!- PATHWAY: Cofactor biosynthesis; adenosylcobalamin biosynthesis;
CC       cob(II)yrinate a,c-diamide from sirohydrochlorin (anaerobic route):
CC       step 10/10. {ECO:0000255|HAMAP-Rule:MF_00027,
CC       ECO:0000303|PubMed:15311923}.
CC   -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:15311923}.
CC   -!- DOMAIN: Comprises of two domains. The C-terminal domain contains the
CC       binding site for glutamine and catalyzes the hydrolysis of this
CC       substrate to glutamate and ammonia. The N-terminal domain is
CC       anticipated to bind ATP and cobyrinate and catalyzes the ultimate
CC       synthesis of the diamide product. The ammonia produced via the
CC       glutaminase domain is probably translocated to the adjacent domain via
CC       a molecular tunnel, where it reacts with an activated intermediate.
CC       {ECO:0000255|HAMAP-Rule:MF_00027, ECO:0000303|PubMed:15311923}.
CC   -!- MISCELLANEOUS: The a and c carboxylates of cobyrinate are activated for
CC       nucleophilic attack via formation of a phosphorylated intermediate by
CC       ATP. CbiA catalyzes first the amidation of the c-carboxylate, and then
CC       that of the a-carboxylate. {ECO:0000255|HAMAP-Rule:MF_00027,
CC       ECO:0000269|PubMed:15311923}.
CC   -!- SIMILARITY: Belongs to the CobB/CbiA family. {ECO:0000255|HAMAP-
CC       Rule:MF_00027}.
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DR   EMBL; L12006; AAA27252.1; -; Genomic_DNA.
DR   EMBL; AE006468; AAL20939.1; -; Genomic_DNA.
DR   EMBL; X63012; CAA44740.1; -; Genomic_DNA.
DR   PIR; S20553; S20553.
DR   RefSeq; NP_460980.1; NC_003197.2.
DR   RefSeq; WP_000741259.1; NC_003197.2.
DR   AlphaFoldDB; P29946; -.
DR   SMR; P29946; -.
DR   STRING; 99287.STM2035; -.
DR   PaxDb; 99287-STM2035; -.
DR   GeneID; 1253556; -.
DR   KEGG; stm:STM2035; -.
DR   PATRIC; fig|99287.12.peg.2157; -.
DR   HOGENOM; CLU_022752_2_0_6; -.
DR   OMA; CDGVYLP; -.
DR   PhylomeDB; P29946; -.
DR   BioCyc; MetaCyc:MONOMER-13217; -.
DR   BioCyc; SENT99287:STM2035-MONOMER; -.
DR   BRENDA; 6.3.5.11; 5542.
DR   SABIO-RK; P29946; -.
DR   UniPathway; UPA00148; UER00231.
DR   Proteomes; UP000001014; Chromosome.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0042242; F:cobyrinic acid a,c-diamide synthase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0009236; P:cobalamin biosynthetic process; IEA:UniProtKB-UniRule.
DR   GO; GO:0006541; P:glutamine metabolic process; IEA:UniProtKB-KW.
DR   CDD; cd05388; CobB_N; 1.
DR   CDD; cd03130; GATase1_CobB; 1.
DR   Gene3D; 3.40.50.880; -; 1.
DR   Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 2.
DR   HAMAP; MF_00027; CobB_CbiA; 1.
DR   InterPro; IPR004484; CbiA/CobB_synth.
DR   InterPro; IPR029062; Class_I_gatase-like.
DR   InterPro; IPR002586; CobQ/CobB/MinD/ParA_Nub-bd_dom.
DR   InterPro; IPR011698; GATase_3.
DR   InterPro; IPR027417; P-loop_NTPase.
DR   NCBIfam; TIGR00379; cobB; 1.
DR   PANTHER; PTHR43873; COBYRINATE A,C-DIAMIDE SYNTHASE; 1.
DR   PANTHER; PTHR43873:SF1; COBYRINATE A,C-DIAMIDE SYNTHASE; 1.
DR   Pfam; PF01656; CbiA; 1.
DR   Pfam; PF07685; GATase_3; 1.
DR   SUPFAM; SSF52317; Class I glutamine amidotransferase-like; 1.
DR   SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 1.
DR   PROSITE; PS51274; GATASE_COBBQ; 1.
PE   1: Evidence at protein level;
KW   ATP-binding; Cobalamin biosynthesis; Direct protein sequencing;
KW   Glutamine amidotransferase; Ligase; Magnesium; Nucleotide-binding;
KW   Reference proteome.
FT   CHAIN           1..459
FT                   /note="Cobyrinate a,c-diamide synthase"
FT                   /id="PRO_0000141269"
FT   INIT_MET        1
FT                   /note="Removed; alternate"
FT                   /evidence="ECO:0000269|PubMed:15311923"
FT   CHAIN           2..459
FT                   /note="Cobyrinate a,c-diamide synthase, N-terminally
FT                   processed"
FT                   /id="PRO_0000430805"
FT   DOMAIN          252..446
FT                   /note="GATase cobBQ-type"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00027"
FT   ACT_SITE        334
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00027"
FT   SITE            438
FT                   /note="Increases nucleophilicity of active site Cys"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00027"
FT   MUTAGEN         45
FT                   /note="D->N: Loss of amidation activity when glutamine is
FT                   used as substrate, and 750-fold reduction in amidation
FT                   activity with ammonia as substrate."
FT                   /evidence="ECO:0000269|PubMed:15311923"
FT   MUTAGEN         46
FT                   /note="Y->A: 26-fold reduction in amidation activity with
FT                   glutamine as substrate. The affinity for cobyrinate is
FT                   nearly not affected whereas that for the c-monoamide
FT                   intermediate decreases by 27-fold."
FT                   /evidence="ECO:0000269|PubMed:15311923"
FT   MUTAGEN         47
FT                   /note="L->A: 10-fold reduction in amidation activity with
FT                   glutamine as substrate. The affinity for cobyrinate is
FT                   nearly not affected whereas that for the c-monoamide
FT                   intermediate decreases by 6-fold."
FT                   /evidence="ECO:0000269|PubMed:15311923"
FT   MUTAGEN         48
FT                   /note="D->N: 500-fold reduction in amidation activity with
FT                   either glutamine or ammonia as substrate."
FT                   /evidence="ECO:0000269|PubMed:15311923"
FT   MUTAGEN         90
FT                   /note="E->Q: Loss of amidation activity with either
FT                   glutamine or ammonia as substrate."
FT                   /evidence="ECO:0000269|PubMed:15311923"
FT   MUTAGEN         97
FT                   /note="D->N: 3-fold reduction in amidation activity with
FT                   glutamine as substrate."
FT                   /evidence="ECO:0000269|PubMed:15311923"
FT   CONFLICT        36
FT                   /note="R -> P (in Ref. 1; AAA27252)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        111
FT                   /note="M -> I (in Ref. 1; AAA27252)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        128
FT                   /note="V -> I (in Ref. 1; AAA27252)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        133
FT                   /note="A -> T (in Ref. 1; AAA27252)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   459 AA;  50037 MW;  E1FEF1B5A37F5C14 CRC64;
     MAARHHAFIL AGTGSGCGKT TVTLGLLRLL QKRALRVQPF KVGPDYLDTG WHTAICGVAS
     RNLDSFMLPP PVLNALFCEQ MRQADIAVIE GVMGLYDGYG VDPNYCSTAA MAKQLGCPVI
     LLVDGKAVST SLAATVMGFQ HFDPTLNLAG VIVNRVTSDA HYQLLKNAIE HYCSLPVLGY
     VPPCDGVALP ERHLGLITAR ESLVNQQSWH DFAATLEQTV DVDALLSLSV LSALPAGMWP
     ERPDNTAGAG LTLALADDEA FNFYYPDNID LLERAGVNIV RFSPLHDRAL PDCQMIWLGG
     GYPELYAADL AANTVMLKHL RAAHQRGVAI YAECGGLMYL GSTLEDSGGE IHQMANIIPG
     HSKMGKRLTR FGYCEAQAMQ PTLLAAPGEI VRGHEFHYSD FIPETPAVMA CRKVRDGRVL
     QEWTGGWQTG NTFASYLHVH FAQRPEMLQH WLAAARRVL
//