CBIA_SALTY
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 03-AUG-2022, entry version 133.
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, ECO:0000303|PubMed:8501034};
GN OrderedLocusNames=STM2035;
OS Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720).
OC Bacteria; Proteobacteria; 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;
CC Evidence={ECO:0000255|HAMAP-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; P29946; -.
DR EnsemblBacteria; AAL20939; AAL20939; STM2035.
DR GeneID; 1253556; -.
DR KEGG; stm:STM2035; -.
DR PATRIC; fig|99287.12.peg.2157; -.
DR HOGENOM; CLU_022752_2_0_6; -.
DR OMA; MYLTNSI; -.
DR PhylomeDB; P29946; -.
DR BioCyc; MetaCyc:MON-13217; -.
DR BioCyc; SENT99287:STM2035-MON; -.
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 Gene3D; 3.40.50.300; -; 2.
DR Gene3D; 3.40.50.880; -; 1.
DR HAMAP; MF_00027; CobB_CbiA; 1.
DR InterPro; IPR004484; CbiA_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 PANTHER; PTHR43873; PTHR43873; 1.
DR Pfam; PF01656; CbiA; 1.
DR Pfam; PF07685; GATase_3; 1.
DR SUPFAM; SSF52317; SSF52317; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR TIGRFAMs; TIGR00379; cobB; 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
