ID   COBB_AGRFC              Reviewed;         438 AA.
AC   Q8UBQ8;
DT   23-APR-2003, integrated into UniProtKB/Swiss-Prot.
DT   01-JUN-2002, sequence version 1.
DT   03-AUG-2022, entry version 95.
DE   RecName: Full=Hydrogenobyrinate a,c-diamide synthase {ECO:0000255|HAMAP-Rule:MF_00027};
DE            EC=6.3.5.9 {ECO:0000255|HAMAP-Rule:MF_00027};
DE   AltName: Full=Hydrogenobyrinic acid a,c-diamide synthase {ECO:0000255|HAMAP-Rule:MF_00027};
GN   Name=cobB {ECO:0000255|HAMAP-Rule:MF_00027}; OrderedLocusNames=Atu2793;
GN   ORFNames=AGR_C_5069;
OS   Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens
OS   (strain C58)).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC   Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium;
OC   Agrobacterium tumefaciens complex.
OX   NCBI_TaxID=176299;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=C58 / ATCC 33970;
RX   PubMed=11743193; DOI=10.1126/science.1066804;
RA   Wood D.W., Setubal J.C., Kaul R., Monks D.E., Kitajima J.P., Okura V.K.,
RA   Zhou Y., Chen L., Wood G.E., Almeida N.F. Jr., Woo L., Chen Y.,
RA   Paulsen I.T., Eisen J.A., Karp P.D., Bovee D. Sr., Chapman P.,
RA   Clendenning J., Deatherage G., Gillet W., Grant C., Kutyavin T., Levy R.,
RA   Li M.-J., McClelland E., Palmieri A., Raymond C., Rouse G.,
RA   Saenphimmachak C., Wu Z., Romero P., Gordon D., Zhang S., Yoo H., Tao Y.,
RA   Biddle P., Jung M., Krespan W., Perry M., Gordon-Kamm B., Liao L., Kim S.,
RA   Hendrick C., Zhao Z.-Y., Dolan M., Chumley F., Tingey S.V., Tomb J.-F.,
RA   Gordon M.P., Olson M.V., Nester E.W.;
RT   "The genome of the natural genetic engineer Agrobacterium tumefaciens
RT   C58.";
RL   Science 294:2317-2323(2001).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=C58 / ATCC 33970;
RX   PubMed=11743194; DOI=10.1126/science.1066803;
RA   Goodner B., Hinkle G., Gattung S., Miller N., Blanchard M., Qurollo B.,
RA   Goldman B.S., Cao Y., Askenazi M., Halling C., Mullin L., Houmiel K.,
RA   Gordon J., Vaudin M., Iartchouk O., Epp A., Liu F., Wollam C., Allinger M.,
RA   Doughty D., Scott C., Lappas C., Markelz B., Flanagan C., Crowell C.,
RA   Gurson J., Lomo C., Sear C., Strub G., Cielo C., Slater S.;
RT   "Genome sequence of the plant pathogen and biotechnology agent
RT   Agrobacterium tumefaciens C58.";
RL   Science 294:2323-2328(2001).
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:0000255|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:0000255|HAMAP-
CC         Rule:MF_00027};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000255|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:0000255|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:0000255|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:0000255|HAMAP-
CC       Rule:MF_00027}.
CC   -!- SIMILARITY: Belongs to the CobB/CbiA family. {ECO:0000255|HAMAP-
CC       Rule:MF_00027}.
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DR   EMBL; AE007869; AAK88506.1; -; Genomic_DNA.
DR   PIR; A97694; A97694.
DR   PIR; AH2919; AH2919.
DR   RefSeq; NP_355721.1; NC_003062.2.
DR   RefSeq; WP_010972568.1; NC_003062.2.
DR   AlphaFoldDB; Q8UBQ8; -.
DR   SMR; Q8UBQ8; -.
DR   STRING; 176299.Atu2793; -.
DR   EnsemblBacteria; AAK88506; AAK88506; Atu2793.
DR   KEGG; atu:Atu2793; -.
DR   PATRIC; fig|176299.10.peg.2803; -.
DR   eggNOG; COG1797; Bacteria.
DR   HOGENOM; CLU_022752_0_0_5; -.
DR   OMA; QPFKCGP; -.
DR   PhylomeDB; Q8UBQ8; -.
DR   BioCyc; AGRO:ATU2793-MON; -.
DR   UniPathway; UPA00148; UER00220.
DR   Proteomes; UP000000813; Chromosome circular.
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-KW.
DR   Gene3D; 3.40.50.300; -; 1.
DR   Gene3D; 3.40.50.880; -; 1.
DR   HAMAP; MF_00027; CobB_CbiA; 1.
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; IPR027417; P-loop_NTPase.
DR   PANTHER; PTHR43873; PTHR43873; 1.
DR   Pfam; PF01656; CbiA; 1.
DR   Pfam; PF07685; GATase_3; 1.
DR   SUPFAM; SSF52317; SSF52317; 1.
DR   SUPFAM; SSF52540; SSF52540; 1.
DR   TIGRFAMs; TIGR00379; cobB; 1.
DR   PROSITE; PS51274; GATASE_COBBQ; 1.
PE   3: Inferred from homology;
KW   ATP-binding; Cobalamin biosynthesis; Glutamine amidotransferase; Ligase;
KW   Magnesium; Nucleotide-binding; Reference proteome.
FT   CHAIN           1..438
FT                   /note="Hydrogenobyrinate a,c-diamide synthase"
FT                   /id="PRO_0000141252"
FT   DOMAIN          247..438
FT                   /note="GATase cobBQ-type"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00027"
FT   ACT_SITE        329
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00027"
FT   SITE            432
FT                   /note="Increases nucleophilicity of active site Cys"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00027"
SQ   SEQUENCE   438 AA;  46644 MW;  95B937E638A67628 CRC64;
     MTARAIIIGA PRSGSGKTSV TIGLLRAFAR RGVKVRGIKT GPDYIDPGFH AFATGTPGLN
     LDSWAMQPDL LRHLFSQQTE DAELILIESA MGLFDGIPVA ENRTGSAADL ARLFRIPVLL
     VLDVSGQSQT AATIAHGFAH YDPDVTMGAV VLNRAGSERH RTLCTEAIEK IGLPVVGCVL
     RDPSLILPER HLGLVQASEH PEIDPHIDRL ADAMEKSIDL DTLFSLAAPV DMPCGSVAAA
     IAPPGQRIAL AEDAAFTFLY PHLRRHWRAA GAEIVPFSPL ADEAPDESCD ICWLPGGYPE
     LFAGKLADAV GFKAGITRFA ETKPVHGECG GYMVLGERLE DAEGVIHAMT GLLSHATSFA
     TRKMNLGYRQ ATIAADSPLG MAGDVLRGHE FHYARVIDPG RDQPFAHMAD GQGRPLGPSG
     GRRGFVSGTF FHAIAKGG