ID K8Y2X3_9LEPT Unreviewed; 461 AA.
AC K8Y2X3;
DT 06-FEB-2013, integrated into UniProtKB/TrEMBL.
DT 06-FEB-2013, sequence version 1.
DT 27-MAR-2024, entry version 56.
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=cbiA {ECO:0000256|HAMAP-Rule:MF_00027};
GN ORFNames=LSS_07144 {ECO:0000313|EMBL:EKT87371.1};
OS Leptospira santarosai serovar Shermani str. LT 821.
OC Bacteria; Spirochaetota; Spirochaetia; Leptospirales; Leptospiraceae;
OC Leptospira.
OX NCBI_TaxID=758847 {ECO:0000313|EMBL:EKT87371.1, ECO:0000313|Proteomes:UP000035800};
RN [1] {ECO:0000313|EMBL:EKT87371.1, ECO:0000313|Proteomes:UP000035800}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LT 821 {ECO:0000313|EMBL:EKT87371.1};
RX PubMed=23041083; DOI=10.1016/j.gene.2012.09.074;
RA Chou L.F., Chen Y.T., Lu C.W., Ko Y.C., Tang C.Y., Pan M.J., Tian Y.C.,
RA Chiu C.H., Hung C.C., Yang C.W.;
RT "Sequence of Leptospira santarosai serovar Shermani genome and prediction
RT of virulence-associated genes.";
RL Gene 511:364-370(2012).
RN [2] {ECO:0000313|Proteomes:UP000035800}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LT821 {ECO:0000313|Proteomes:UP000035800};
RA Chou L.-F., Chen T.-W., Ko Y.-C., Pan M.-J., Tian Y.-C., Chiu C.-H.,
RA Tang P., Hung C.-C., Yang C.-W.;
RT "Potential impact on kidney infection: a whole-genome analysis of
RT Leptospira santarosai serovar Shermani.";
RL Emerg. Microbes Infect. 3:e82-e82(2014).
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}.
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DR EMBL; CP006695; EKT87371.1; -; Genomic_DNA.
DR RefSeq; WP_004459573.1; NZ_CP006695.1.
DR AlphaFoldDB; K8Y2X3; -.
DR STRING; 758847.LSS_07144; -.
DR GeneID; 29740350; -.
DR KEGG; lst:LSS_07144; -.
DR PATRIC; fig|758847.3.peg.1501; -.
DR UniPathway; UPA00148; UER00231.
DR Proteomes; UP000035800; Chromosome II.
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 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 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}.
FT DOMAIN 13..172
FT /note="CobQ/CobB/MinD/ParA nucleotide binding"
FT /evidence="ECO:0000259|Pfam:PF01656"
FT DOMAIN 252..445
FT /note="CobB/CobQ-like glutamine amidotransferase"
FT /evidence="ECO:0000259|Pfam:PF07685"
FT ACT_SITE 334
FT /note="Nucleophile"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
FT SITE 439
FT /note="Increases nucleophilicity of active site Cys"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
SQ SEQUENCE 461 AA; 50516 MW; E2B133DDA1A8DBD8 CRC64;
MQASYAEIKI PRIVIAGTGS GVGKTTIVLA LTLAFQKRGL KVSTFKCGPD YLDPTYHSRT
TGKTCHNLDG WLMGKQAVLN VFHKACHNAD IAIIEGVMGL FDGHSPNSEV GSTAEIAKWI
ASPVLVVVDA SGMARTVAAI LKGLKTFDPD LDLAGAFTNF IGSKSHTQLL RETSPEVPIL
GGFSKHPQQA FPERHLGLYS ASKENVSEEK LIFWGEQGED QLEIDSVLKI AASAPKIQAP
ISKIKSVSNR CRIGIAMDAA FHFYYEDNLT RLREAGAELV PFSPISDSRL PQVDGLYIGG
GYPELFSPAL SKNKSLLNDI LEFSYNKKPI YAECGGLIYL SKKIRLVSGE SYPMAGLIPG
TAVISEKLKA LGYVEVVTKQ KTILGEAGLR FRGHQFRYSD FELDEPHPIE LVYGLRKRKG
NEVSEEGYFH DCVLASYVHA HWASNPNLPE GFVRSCLRVL R
//
