ID A0A126RD18_9SPHN Unreviewed; 435 AA.
AC A0A126RD18;
DT 11-MAY-2016, integrated into UniProtKB/TrEMBL.
DT 11-MAY-2016, sequence version 1.
DT 27-MAR-2024, entry version 40.
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=K663_18431 {ECO:0000313|EMBL:AMK20047.1};
OS Sphingobium sp. MI1205.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Sphingobium.
OX NCBI_TaxID=407020 {ECO:0000313|EMBL:AMK20047.1, ECO:0000313|Proteomes:UP000060707};
RN [1] {ECO:0000313|Proteomes:UP000060707}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MI1205 {ECO:0000313|Proteomes:UP000060707};
RA Tabata M.;
RT "Genome sequence of gamma-HCH degrading bacterium Sphingobium sp. MI1205.";
RL Submitted (APR-2013) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:AMK20047.1, ECO:0000313|Proteomes:UP000060707}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MI1205 {ECO:0000313|EMBL:AMK20047.1,
RC ECO:0000313|Proteomes:UP000060707};
RX PubMed=27056230;
RA Tabata M., Ohhata S., Nikawadori Y., Sato T., Kishida K., Ohtsubo Y.,
RA Tsuda M., Nagata Y.;
RT "Complete Genome Sequence of a gamma-Hexachlorocyclohexane-Degrading
RT Bacterium, Sphingobium sp. Strain MI1205.";
RL Genome Announc. 4:0-0(2016).
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; CP005189; AMK20047.1; -; Genomic_DNA.
DR RefSeq; WP_062121512.1; NZ_CP005189.1.
DR AlphaFoldDB; A0A126RD18; -.
DR STRING; 407020.K663_18431; -.
DR KEGG; spmi:K663_18431; -.
DR PATRIC; fig|407020.3.peg.3850; -.
DR OrthoDB; 9764035at2; -.
DR UniPathway; UPA00148; UER00231.
DR Proteomes; UP000060707; Chromosome 2.
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 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 5..191
FT /note="CobQ/CobB/MinD/ParA nucleotide binding"
FT /evidence="ECO:0000259|Pfam:PF01656"
FT DOMAIN 245..432
FT /note="CobB/CobQ-like glutamine amidotransferase"
FT /evidence="ECO:0000259|Pfam:PF07685"
FT ACT_SITE 327
FT /note="Nucleophile"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
FT SITE 429
FT /note="Increases nucleophilicity of active site Cys"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
SQ SEQUENCE 435 AA; 45301 MW; 99700E53B57C68C5 CRC64;
MTPGILVAAP RSGSGKTVIT LGLLRALARR GVRVQPYKCG PDYIDTGYHR LASGRAAFNL
DSWAMDGAMI RGLAAQAVTA DLALAEGAMG LFDGAAATGA SGNGSSADIA AALGWPVILV
IDVSGQSQSA AALAHGFRTL RPDLRVVGVI LNRVASPRHD AMIRRAMEEI ALPVLGAVPR
SAALSLPERH LGLVQAGEQE RADERIDAIA DVVEAHVGLS ALLACAGALP CAASCGTGWR
PPGQRVALAQ DAAFSFTYAH MLAGWQSAGA EILRFSPLAD EAPDPHADAV WLPGGYPELH
APRLAEATRF IDGLRRHAQD RPVHGECGGY MVLGQAIIDA QGQTHAMAGL LGLVSSFAER
RLHLGYRRAR LLAPMGGYGE GADLRGHEFH YSTVVEQPDQ PLAHVTDAAG DAVASTGSRR
GLVTGSFFHL VAGAA
//
