COBB_RHOCB
ID COBB_RHOCB Reviewed; 435 AA.
AC O68108; D5AUZ4;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 25-MAY-2022, entry version 103.
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};
GN OrderedLocusNames=RCAP_rcc02032;
OS Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
OC Rhodobacteraceae; Rhodobacter.
OX NCBI_TaxID=272942;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC BAA-309 / NBRC 16581 / SB1003;
RX PubMed=9256491; DOI=10.1073/pnas.94.17.9384;
RA Vlcek C., Paces V., Maltsev N., Paces J., Haselkorn R., Fonstein M.;
RT "Sequence of a 189-kb segment of the chromosome of Rhodobacter capsulatus
RT SB1003.";
RL Proc. Natl. Acad. Sci. U.S.A. 94:9384-9388(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-309 / NBRC 16581 / SB1003;
RX PubMed=20418398; DOI=10.1128/jb.00366-10;
RA Strnad H., Lapidus A., Paces J., Ulbrich P., Vlcek C., Paces V.,
RA Haselkorn R.;
RT "Complete genome sequence of the photosynthetic purple nonsulfur bacterium
RT Rhodobacter capsulatus SB 1003.";
RL J. Bacteriol. 192:3545-3546(2010).
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; AF010496; AAC16198.1; -; Genomic_DNA.
DR EMBL; CP001312; ADE85776.1; -; Genomic_DNA.
DR PIR; T03545; T03545.
DR RefSeq; WP_013067755.1; NC_014034.1.
DR AlphaFoldDB; O68108; -.
DR SMR; O68108; -.
DR STRING; 272942.RCAP_rcc02032; -.
DR EnsemblBacteria; ADE85776; ADE85776; RCAP_rcc02032.
DR GeneID; 31490895; -.
DR KEGG; rcp:RCAP_rcc02032; -.
DR eggNOG; COG1797; Bacteria.
DR HOGENOM; CLU_022752_0_0_5; -.
DR OMA; QPFKCGP; -.
DR OrthoDB; 692368at2; -.
DR UniPathway; UPA00148; UER00220.
DR Proteomes; UP000002361; Chromosome.
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; -; 2.
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..435
FT /note="Hydrogenobyrinate a,c-diamide synthase"
FT /id="PRO_0000141268"
FT DOMAIN 247..435
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 431
FT /note="Increases nucleophilicity of active site Cys"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00027"
SQ SEQUENCE 435 AA; 45303 MW; DE6DB37F8A76FFFA CRC64;
MSEGPKGLAI AAPASGSGKT TLTLGLLRAL TRRGLRVQPF KNGPDYIDPA FHAAAAGRAS
FNLDGWAMDR PQLHALAGQA AGADLVIFEG AMGLYDGPAD PGRSGRGTSA EIARMFGWPV
VLVLDVKGQG QSAAATALGF ARHPEAPPLA GVILNHVASP RHEAMIRAEM DRLGLRVLGA
LPRRSDLSLP ERHLGLVQAE EQAGLEATLE ALADFVAAHV DLEALLSVAG AGPAPGAGAW
AVPPAGRIAL ARDAAFSFVY PHMLEAWRRA GVTVLPFSPL ADQAPDPSAD LVWLPGGYPE
LHAGRIAAAT RFKAGLRAFA ETRSVHGECG GYMVLGARLV DAEGRAHAMA GLLGLVTSYE
KRRLHLGYRS ADLLAPLPGY GAGSRLYGHE FHYSTILEQP DAPLAKVCDA AGAPVAETGS
VRGHVTGSFF HLIAG
