ID A0A1V2IDS6_9ACTN Unreviewed; 511 AA.
AC A0A1V2IDS6;
DT 07-JUN-2017, integrated into UniProtKB/TrEMBL.
DT 07-JUN-2017, sequence version 1.
DT 27-MAR-2024, entry version 28.
DE RecName: Full=Hydrogenobyrinate a,c-diamide synthase {ECO:0000256|HAMAP-Rule:MF_00027};
DE EC=6.3.5.9 {ECO:0000256|HAMAP-Rule:MF_00027};
DE AltName: Full=Hydrogenobyrinic acid a,c-diamide synthase {ECO:0000256|HAMAP-Rule:MF_00027};
GN Name=cobB {ECO:0000256|HAMAP-Rule:MF_00027};
GN ORFNames=BL253_09765 {ECO:0000313|EMBL:ONH31170.1};
OS Pseudofrankia asymbiotica.
OC Bacteria; Actinomycetota; Actinomycetes; Frankiales; Frankiaceae;
OC Pseudofrankia.
OX NCBI_TaxID=1834516 {ECO:0000313|EMBL:ONH31170.1, ECO:0000313|Proteomes:UP000188929};
RN [1] {ECO:0000313|Proteomes:UP000188929}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NRRL B-16386 {ECO:0000313|Proteomes:UP000188929};
RA Ghodhbane-Gtari F., Swanson E., Gueddou A., Hezbri K., Ktari K.,
RA Nouioui I., Morris K., Simpson S., Abebe-Akele F., Thomas K., Gtari M.,
RA Tisa L.S.;
RT "Frankia sp. NRRL B-16386 Genome sequencing.";
RL Submitted (OCT-2016) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Catalyzes the ATP-dependent amidation of the two carboxylate
CC groups at positions a and c of hydrogenobyrinate, using either L-
CC glutamine or ammonia as the nitrogen source. {ECO:0000256|HAMAP-
CC Rule:MF_00027}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 ATP + 2 H2O + hydrogenobyrinate + 2 L-glutamine = 2 ADP + 2
CC H(+) + hydrogenobyrinate a,c-diamide + 2 L-glutamate + 2 phosphate;
CC Xref=Rhea:RHEA:12544, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:29985, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:58359, ChEBI:CHEBI:77873, ChEBI:CHEBI:77874,
CC ChEBI:CHEBI:456216; EC=6.3.5.9; 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 precorrin-2 (aerobic route): step 9/10.
CC {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 hydrogenobyrinate and catalyzes the
CC ultimate 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 hydrogenobyrinate are
CC activated for nucleophilic attack via formation of a phosphorylated
CC intermediate by ATP. CobB catalyzes first the amidation of the c-
CC carboxylate, and then that of the a-carboxylate. {ECO:0000256|HAMAP-
CC Rule:MF_00027}.
CC -!- SIMILARITY: Belongs to the CobB/CbiA family. {ECO:0000256|HAMAP-
CC Rule:MF_00027}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:ONH31170.1}.
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DR EMBL; MOMC01000017; ONH31170.1; -; Genomic_DNA.
DR RefSeq; WP_076815711.1; NZ_MOMC01000017.1.
DR AlphaFoldDB; A0A1V2IDS6; -.
DR STRING; 1834516.BL253_09765; -.
DR OrthoDB; 9764035at2; -.
DR UniPathway; UPA00148; UER00220.
DR Proteomes; UP000188929; Unassembled WGS sequence.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0042242; F:cobyrinic acid a,c-diamide synthase activity; IEA:InterPro.
DR GO; GO:0043802; F:hydrogenobyrinic acid a,c-diamide synthase (glutamine-hydrolysing) 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; 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 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:UP000188929}.
FT DOMAIN 6..192
FT /note="CobQ/CobB/MinD/ParA nucleotide binding"
FT /evidence="ECO:0000259|Pfam:PF01656"
FT DOMAIN 294..485
FT /note="CobB/CobQ-like glutamine amidotransferase"
FT /evidence="ECO:0000259|Pfam:PF07685"
FT REGION 266..292
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 376
FT /note="Nucleophile"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
FT SITE 481
FT /note="Increases nucleophilicity of active site Cys"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
SQ SEQUENCE 511 AA; 51076 MW; BEB3FE1C56583659 CRC64;
MRIPRIVLAA PASGAGKTSI ATGLLAALRA RGLAVSPHKV GPDYIDPGYH ALAAGRTGRN
LDPWLVGERR ITPLFLHGAL TPRRADVAVI EGVMGLFDGH ATRAGFGSTA HVATLLAAPV
VLVVDARSAG RSVAATVHGF RSFDPAVRIG GVVFNQVGTE RHAEILRAAM AEIGMPVLGV
LGRRDSLVTP SRHLGLVPAA ERAAPARAAV AELADAIGAS LDLDALLALA ATAPDLTAEP
WDPRADAAGA FGVPGTAEAA GISGAAETSG GLAPTAPTPP APASGRGRGP RPVVAVAGGP
AFTFGYAETP ELLAAAGAEV ARFDPTADEA LPDGTSALVI GGGFPQVHAG ALAANAALRA
QVRAFAATGA PVVAECAGLL YLSRALDGEP MCGVLAEVTA AMAPRLTLGY REAVAATDSA
LAARGTVARG HEFHRTVAVP PAGGMDGAPR GSAPAWTWRG AAGDEVAEGF VRGGVHASYL
HTHWAGLPGT AARLVAAARA AQANGSNRAA G
//
