ID I4D6H0_DESAJ Unreviewed; 509 AA.
AC I4D6H0;
DT 05-SEP-2012, integrated into UniProtKB/TrEMBL.
DT 05-SEP-2012, sequence version 1.
DT 27-MAR-2024, entry version 65.
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 OrderedLocusNames=Desaci_2444 {ECO:0000313|EMBL:AFM41394.1};
OS Desulfosporosinus acidiphilus (strain DSM 22704 / JCM 16185 / SJ4).
OC Bacteria; Bacillota; Clostridia; Eubacteriales; Desulfitobacteriaceae;
OC Desulfosporosinus.
OX NCBI_TaxID=646529 {ECO:0000313|EMBL:AFM41394.1, ECO:0000313|Proteomes:UP000002892};
RN [1] {ECO:0000313|EMBL:AFM41394.1, ECO:0000313|Proteomes:UP000002892}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 22704 / JCM 16185 / SJ4
RC {ECO:0000313|Proteomes:UP000002892};
RX PubMed=23105050; DOI=10.1128/JB.01392-12;
RA Pester M., Brambilla E., Alazard D., Rattei T., Weinmaier T., Han J.,
RA Lucas S., Lapidus A., Cheng J.F., Goodwin L., Pitluck S., Peters L.,
RA Ovchinnikova G., Teshima H., Detter J.C., Han C.S., Tapia R., Land M.L.,
RA Hauser L., Kyrpides N.C., Ivanova N.N., Pagani I., Huntmann M., Wei C.L.,
RA Davenport K.W., Daligault H., Chain P.S., Chen A., Mavromatis K.,
RA Markowitz V., Szeto E., Mikhailova N., Pati A., Wagner M., Woyke T.,
RA Ollivier B., Klenk H.P., Spring S., Loy A.;
RT "Complete genome sequences of Desulfosporosinus orientis DSM765T,
RT Desulfosporosinus youngiae DSM17734T, Desulfosporosinus meridiei DSM13257T,
RT and Desulfosporosinus acidiphilus DSM22704T.";
RL J. Bacteriol. 194:6300-6301(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}.
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DR EMBL; CP003639; AFM41394.1; -; Genomic_DNA.
DR RefSeq; WP_014827393.1; NC_018068.1.
DR AlphaFoldDB; I4D6H0; -.
DR STRING; 646529.Desaci_2444; -.
DR KEGG; dai:Desaci_2444; -.
DR eggNOG; COG1797; Bacteria.
DR HOGENOM; CLU_022752_2_0_9; -.
DR OrthoDB; 9764035at2; -.
DR UniPathway; UPA00148; UER00231.
DR Proteomes; UP000002892; 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 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; 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}.
FT DOMAIN 6..189
FT /note="CobQ/CobB/MinD/ParA nucleotide binding"
FT /evidence="ECO:0000259|Pfam:PF01656"
FT DOMAIN 304..491
FT /note="CobB/CobQ-like glutamine amidotransferase"
FT /evidence="ECO:0000259|Pfam:PF07685"
FT ACT_SITE 384
FT /note="Nucleophile"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
FT SITE 486
FT /note="Increases nucleophilicity of active site Cys"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
SQ SEQUENCE 509 AA; 56148 MW; 1FE28C0FD9DF468D CRC64;
MKIPRIVLAG THSGVGKTTL ATGLMAALNK RQRPIQGYKV GPDYIDPSYH AAATGRPSRN
LDRWLLGERL LPAFLQSSQE RWAVIEGVMG MFDGMSGTAG FGSTADVAKL LKAPILLIVD
ASSMSRSVAA LVHGFKTYDP EVNLQGVILN RVKSSAQEKI LRDALIELQI PVLGVLPKET
SLHLPERHLG LIPVGEGGLL EGYIESLAEF IGTYLDLEQI EKIMLKAPDF PETSRADIYD
YLSLDLNSSD NNEILNNSHS NTRENFDNLD KVTVAGGRES GIAKSKGSLA SDFDVSNHRF
RLGLAWDEAF LFYYQDALDM AAGLNCSVVP FSPLHDQSLP KDLDGIFLGG GFPELHLKEL
SANVSFLESL RNFAASGKPI YAECGGYMYL GKSITSFDGT ELPMAGLIPM KAEMTKRLQG
IGYRKGVFRE DNFLGPRGTM VQGHEFHYSR VTYESEVPAV YELYKGDQAD RLEGYARDNL
VASYLHLNFA GQPELMQHWF SSHERRRSS
//
