ID I3TPB7_TISMK Unreviewed; 446 AA.
AC I3TPB7;
DT 05-SEP-2012, integrated into UniProtKB/TrEMBL.
DT 05-SEP-2012, sequence version 1.
DT 27-MAR-2024, entry version 58.
DE RecName: Full=Cobyrinate a,c-diamide synthase {ECO:0000256|HAMAP-Rule:MF_00027};
DE EC=6.3.5.11 {ECO:0000256|HAMAP-Rule:MF_00027};
DE AltName: Full=Cobyrinic acid a,c-diamide synthetase {ECO:0000256|HAMAP-Rule:MF_00027};
GN Name=cobB {ECO:0000313|EMBL:AFK54605.1};
GN Synonyms=cbiA {ECO:0000256|HAMAP-Rule:MF_00027};
GN OrderedLocusNames=TMO_2767 {ECO:0000313|EMBL:AFK54605.1};
OS Tistrella mobilis (strain KA081020-065).
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Geminicoccales;
OC Geminicoccaceae; Tistrella.
OX NCBI_TaxID=1110502 {ECO:0000313|EMBL:AFK54605.1, ECO:0000313|Proteomes:UP000005258};
RN [1] {ECO:0000313|EMBL:AFK54605.1, ECO:0000313|Proteomes:UP000005258}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=KA081020-065 {ECO:0000313|EMBL:AFK54605.1,
RC ECO:0000313|Proteomes:UP000005258};
RX PubMed=22458477; DOI=10.1021/ja301735a;
RA Xu Y., Kersten R.D., Nam S.J., Lu L., Al-Suwailem A.M., Zheng H.,
RA Fenical W., Dorrestein P.C., Moore B.S., Qian P.Y.;
RT "Bacterial biosynthesis and maturation of the didemnin anti-cancer
RT agents.";
RL J. Am. Chem. Soc. 134:8625-8632(2012).
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. {ECO:0000256|HAMAP-Rule:MF_00027}.
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:0000256|HAMAP-
CC Rule:MF_00027};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|ARBA:ARBA00001946,
CC ECO:0000256|HAMAP-Rule:MF_00027};
CC -!- PATHWAY: Cofactor biosynthesis; adenosylcobalamin biosynthesis;
CC cob(II)yrinate a,c-diamide from sirohydrochlorin (anaerobic route):
CC step 10/10. {ECO:0000256|HAMAP-Rule:MF_00027}.
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:0000256|HAMAP-Rule:MF_00027}.
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:0000256|HAMAP-Rule:MF_00027}.
CC -!- SIMILARITY: Belongs to the CobB/CbiA family. {ECO:0000256|HAMAP-
CC Rule:MF_00027}.
CC -!- SIMILARITY: Belongs to the CobB/CobQ family. CobQ subfamily.
CC {ECO:0000256|ARBA:ARBA00006205}.
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DR EMBL; CP003236; AFK54605.1; -; Genomic_DNA.
DR RefSeq; WP_014746282.1; NC_017956.1.
DR AlphaFoldDB; I3TPB7; -.
DR STRING; 1110502.TMO_2767; -.
DR KEGG; tmo:TMO_2767; -.
DR PATRIC; fig|1110502.3.peg.2837; -.
DR eggNOG; COG1797; Bacteria.
DR HOGENOM; CLU_022752_0_0_5; -.
DR UniPathway; UPA00148; UER00231.
DR Proteomes; UP000005258; 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-UniRule.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 1.
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 3: Inferred from homology;
KW ATP-binding {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|HAMAP-
KW Rule:MF_00027}; Cobalamin biosynthesis {ECO:0000256|HAMAP-Rule:MF_00027};
KW Glutamine amidotransferase {ECO:0000256|ARBA:ARBA00022962,
KW ECO:0000256|HAMAP-Rule:MF_00027};
KW Ligase {ECO:0000256|ARBA:ARBA00022598, ECO:0000256|HAMAP-Rule:MF_00027};
KW Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|HAMAP-Rule:MF_00027};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|HAMAP-
KW Rule:MF_00027}; Reference proteome {ECO:0000313|Proteomes:UP000005258}.
FT DOMAIN 8..193
FT /note="CobQ/CobB/MinD/ParA nucleotide binding"
FT /evidence="ECO:0000259|Pfam:PF01656"
FT DOMAIN 252..441
FT /note="CobB/CobQ-like glutamine amidotransferase"
FT /evidence="ECO:0000259|Pfam:PF07685"
FT ACT_SITE 335
FT /note="Nucleophile"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
FT SITE 436
FT /note="Increases nucleophilicity of active site Cys"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
SQ SEQUENCE 446 AA; 45912 MW; 33D9261C4252A77D CRC64;
MTPPPALILA APASSGGKTT MTLGLLRAFR RRGLAPAAAK IGPDYIDPAF HEVAAGRPSV
NLDGWAMAPD RLARLIETQA PSGLLAIEGV MGLFDGAPAP GASGDGSAAA LARMFSLPVL
LVVDAGAQAR SAAALIHGFR SFDPAVQVAA VIFNRVGGPG HRRVLAAAAA EAGVPALGFV
PRRADIALPS RHLGLVQARE TTDLDALLDR LADLVAAHVD LDAVVALARP ASPGARLVAA
EPGPAVPPPG GRIALARDDA FAFIYPHLLA DWHAAGAEVL PFSPLAGQAP DPSADAVWLP
GGYPELHAGR LATDRAWVRG LVAARDRGAV IFGECGGYMA LGEVLTDADG RDWPMAGLLG
LSTSFAARRL HLGYRLGRMV TGPLEGRLWR GHEFHYATII AERGDPLWSS VEDATGAAVE
GARGLRAGRV AGSFLHLIAA GQSVAG
//
