COBB_RHILO
ID COBB_RHILO Reviewed; 439 AA.
AC Q98KP1;
DT 23-APR-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2001, sequence version 1.
DT 25-MAY-2022, entry version 99.
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=mlr1387;
OS Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
OS (Mesorhizobium loti (strain MAFF 303099)).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Phyllobacteriaceae; Mesorhizobium.
OX NCBI_TaxID=266835;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LMG 29417 / CECT 9101 / MAFF 303099;
RX PubMed=11214968; DOI=10.1093/dnares/7.6.331;
RA Kaneko T., Nakamura Y., Sato S., Asamizu E., Kato T., Sasamoto S.,
RA Watanabe A., Idesawa K., Ishikawa A., Kawashima K., Kimura T., Kishida Y.,
RA Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Mochizuki Y.,
RA Nakayama S., Nakazaki N., Shimpo S., Sugimoto M., Takeuchi C., Yamada M.,
RA Tabata S.;
RT "Complete genome structure of the nitrogen-fixing symbiotic bacterium
RT Mesorhizobium loti.";
RL DNA Res. 7:331-338(2000).
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}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; BA000012; BAB48773.1; -; Genomic_DNA.
DR RefSeq; WP_010910126.1; NC_002678.2.
DR AlphaFoldDB; Q98KP1; -.
DR SMR; Q98KP1; -.
DR STRING; 266835.14022163; -.
DR EnsemblBacteria; BAB48773; BAB48773; BAB48773.
DR KEGG; mlo:mlr1387; -.
DR PATRIC; fig|266835.9.peg.1118; -.
DR eggNOG; COG1797; Bacteria.
DR HOGENOM; CLU_022752_0_0_5; -.
DR OMA; QPFKCGP; -.
DR OrthoDB; 692368at2; -.
DR UniPathway; UPA00148; UER00220.
DR Proteomes; UP000000552; 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; -; 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.
FT CHAIN 1..439
FT /note="Hydrogenobyrinate a,c-diamide synthase"
FT /id="PRO_0000141266"
FT DOMAIN 247..439
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 439 AA; 45879 MW; DCFB9F997D2948B8 CRC64;
MTARAIIIGA PRSGSGKTSV TIGILRALTR RGLKVRGAKS GPDYIDPGFH TAATGLSGVN
LDSWAMPPSL LNALAAQQAD DTDFVILESA MGLFDGIPAA PGRTGSAADL ARLYGLPVLL
VLDVSGQSTT AAAVAKGFAT YDPDVRMAGV VLNRLGSERH RKLSGDAIEA IGLPVVGAIL
RDPTLNLPER HLGLVQAGEY DDLMAHLDRL ADMAEKSLDL DAVMRLATPL APAAGGFADA
LQPPGQRIAL AEDGAFTFLY PHVAAYWRKA GAEIVPFSPL ADEAPDDSCD VCWLPGGYPE
LHAGKLAAAE TFKAGMARFA ATKPIHGECG GFMVLGEALE DASGETHRML GLLGHATSFA
KRKMNLGYRE ARLRADCPLG AQGALIRGHE FHYAQMTATG NDEPLADLAD GLGNPIGASG
YRRGHVSGTF FHAIARASA
