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Database: UniProt
Entry: S3X0W9_9ACTN
LinkDB: S3X0W9_9ACTN
Original site: S3X0W9_9ACTN 
ID   S3X0W9_9ACTN            Unreviewed;       831 AA.
AC   S3X0W9;
DT   18-SEP-2013, integrated into UniProtKB/TrEMBL.
DT   18-SEP-2013, sequence version 1.
DT   24-JAN-2024, entry version 51.
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=HMPREF1531_01222 {ECO:0000313|EMBL:EPH03796.1};
OS   Propionibacterium sp. oral taxon 192 str. F0372.
OC   Bacteria; Actinomycetota; Actinomycetes; Propionibacteriales;
OC   Propionibacteriaceae; Propionibacterium.
OX   NCBI_TaxID=1203605 {ECO:0000313|EMBL:EPH03796.1, ECO:0000313|Proteomes:UP000014567};
RN   [1] {ECO:0000313|EMBL:EPH03796.1, ECO:0000313|Proteomes:UP000014567}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=F0372 {ECO:0000313|EMBL:EPH03796.1,
RC   ECO:0000313|Proteomes:UP000014567};
RG   The Broad Institute Genomics Platform;
RA   Earl A., Ward D., Feldgarden M., Gevers D., Kirega A., Socransky S.S.,
RA   Dewhirst F.E., Izard J., Walker B., Young S., Zeng Q., Gargeya S.,
RA   Fitzgerald M., Haas B., Abouelleil A., Allen A.W., Alvarado L.,
RA   Arachchi H.M., Berlin A.M., Chapman S.B., Gainer-Dewar J., Goldberg J.,
RA   Griggs A., Gujja S., Hansen M., Howarth C., Imamovic A., Ireland A.,
RA   Larimer J., McCowan C., Murphy C., Pearson M., Poon T.W., Priest M.,
RA   Roberts A., Saif S., Shea T., Sisk P., Sykes S., Wortman J., Nusbaum C.,
RA   Birren B.;
RT   "The Genome Sequence of Propionibacterium sp. oral taxon 192 str. F0372.";
RL   Submitted (MAY-2013) 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:EPH03796.1}.
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DR   EMBL; ATFL01000010; EPH03796.1; -; Genomic_DNA.
DR   RefSeq; WP_016669022.1; NZ_KE340297.1.
DR   AlphaFoldDB; S3X0W9; -.
DR   STRING; 1203605.HMPREF1531_01222; -.
DR   PATRIC; fig|1203605.3.peg.1267; -.
DR   eggNOG; COG0079; Bacteria.
DR   eggNOG; COG1797; Bacteria.
DR   HOGENOM; CLU_348794_0_0_11; -.
DR   OrthoDB; 9764035at2; -.
DR   UniPathway; UPA00148; UER00220.
DR   Proteomes; UP000014567; 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:0030170; F:pyridoxal phosphate binding; IEA:InterPro.
DR   GO; GO:0009236; P:cobalamin biosynthetic process; IEA:UniProtKB-UniRule.
DR   GO; GO:0006541; P:glutamine metabolic process; IEA:UniProtKB-UniRule.
DR   CDD; cd00609; AAT_like; 1.
DR   CDD; cd03130; GATase1_CobB; 1.
DR   Gene3D; 3.40.50.880; -; 1.
DR   Gene3D; 3.90.1150.10; Aspartate Aminotransferase, domain 1; 1.
DR   Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 1.
DR   Gene3D; 3.40.640.10; Type I PLP-dependent aspartate aminotransferase-like (Major domain); 1.
DR   HAMAP; MF_00027; CobB_CbiA; 1.
DR   InterPro; IPR004839; Aminotransferase_I/II.
DR   InterPro; IPR004484; CbiA_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; IPR004838; NHTrfase_class1_PyrdxlP-BS.
DR   InterPro; IPR027417; P-loop_NTPase.
DR   InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR   InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR   InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
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; PF00155; Aminotran_1_2; 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   SUPFAM; SSF53383; PLP-dependent transferases; 1.
DR   PROSITE; PS00105; AA_TRANSFER_CLASS_1; 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:UP000014567}.
FT   DOMAIN          6..207
FT                   /note="CobQ/CobB/MinD/ParA nucleotide binding"
FT                   /evidence="ECO:0000259|Pfam:PF01656"
FT   DOMAIN          277..459
FT                   /note="CobB/CobQ-like glutamine amidotransferase"
FT                   /evidence="ECO:0000259|Pfam:PF07685"
FT   DOMAIN          537..816
FT                   /note="Aminotransferase class I/classII"
FT                   /evidence="ECO:0000259|Pfam:PF00155"
FT   ACT_SITE        360
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
FT   SITE            457
FT                   /note="Increases nucleophilicity of active site Cys"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
SQ   SEQUENCE   831 AA;  86981 MW;  39CB89D5E91E05CE CRC64;
     MRIPRIVVAA PNSSSGKTTI SIGLMGALTA AGHRVAPFKV GPDYIDPGYH TLATGHPGRN
     LDAWLCGTEL ITPLLAHGAL LPDDQYGPAE LSIIEGVMGF LDGRLGVTDG VRGFGSTAHV
     ASLTCSPVVL VADATGVSRT LAATVGGLAR SGDLLGGGLV APHIAGVIIN KCGSARAVGE
     LRDAFKAVGL PVLGAVPRST DLVVPSRHLG LVPAAERDQA RAAVDAAAYL VAEHVDLDAV
     LRVATAAPEL EVTPWSPVSH LRDALQQAGS VPHPGTRIAV AAGRAFTFRY AETVELFRAA
     GAEVVEFDPM TDEHLPSDVH GLYLGGGFPE IYAEELAANL PLLEEVRRAV ADGVPTWAEC
     AGMLYLCRRL DGMDMAGALP IDATMTPRLT LGYRTLTATT DSLMTRAGEQ VNSHEFHRTA
     TTLLDDSLPA AWQVSSPGNP TKTEGLVGVN VLACYQHIHP VGAPGIVAGF VAGAHARAIR
     GRAAVRIATT TGRRPEPDLR HHGDGDLAPG LVDLAVNVHP STDWLIDEIV EDRSAWGAYP
     DPAATEAILA AHHAVRPEQV LCTAGGADAF TLIARYFAGG RTTIVHPQFT EPEQAARTSG
     HQVSRVLLRA DDGFRLDPQQ IPGTAELVVV GNPTNPTGVL HPAETIASLA RPGRTVVVDE
     AFMDFVDDAP SLICRFMEGI LVVRSVTKMW GIPGLRAGYL VGPAELIARL RALQAPWPVS
     APALRAMSLI GDSRAADHAA QVRALTATRR EVLIGTLTDI GLSVVAGSRA PFILVDASAL
     GDDPVARLAE NGFAVRRGDT FPGLGPGWIR VAVRDDAVSA ALGQALRRVL G
//
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