ID Q6N821_RHOPA Unreviewed; 453 AA.
AC Q6N821;
DT 05-JUL-2004, integrated into UniProtKB/TrEMBL.
DT 05-JUL-2004, sequence version 1.
DT 27-MAR-2024, entry version 120.
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 ECO:0000313|EMBL:CAE27524.1};
GN OrderedLocusNames=RPA2083 {ECO:0000313|EMBL:CAE27524.1};
OS Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009).
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales;
OC Nitrobacteraceae; Rhodopseudomonas.
OX NCBI_TaxID=258594 {ECO:0000313|EMBL:CAE27524.1, ECO:0000313|Proteomes:UP000001426};
RN [1] {ECO:0000313|EMBL:CAE27524.1, ECO:0000313|Proteomes:UP000001426}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-98 / CGA009 {ECO:0000313|Proteomes:UP000001426};
RX PubMed=14704707; DOI=10.1038/nbt923;
RA Larimer F.W., Chain P., Hauser L., Lamerdin J., Malfatti S., Do L.,
RA Land M.L., Pelletier D.A., Beatty T.J., Lang A.S., Tabita F.R.,
RA Gibson J.L., Hanson T.E., Torres y Torres J., Peres C., Harrison F.H.,
RA Gibson J., Harwood C.S.;
RT "Complete genome sequence of the metabolically versatile photosynthetic
RT bacterium Rhodopseudomonas palustris.";
RL Nat. Biotechnol. 22:55-61(2004).
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 -!- SIMILARITY: Belongs to the CobB/CobQ family. CobQ subfamily.
CC {ECO:0000256|ARBA:ARBA00006205}.
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; BX572599; CAE27524.1; -; Genomic_DNA.
DR RefSeq; WP_011157638.1; NZ_CP116810.1.
DR AlphaFoldDB; Q6N821; -.
DR STRING; 258594.RPA2083; -.
DR GeneID; 66893128; -.
DR eggNOG; COG1797; Bacteria.
DR HOGENOM; CLU_022752_0_0_5; -.
DR PhylomeDB; Q6N821; -.
DR UniPathway; UPA00148; UER00220.
DR Proteomes; UP000001426; 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-UniRule.
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 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; 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:UP000001426}.
FT DOMAIN 19..196
FT /note="CobQ/CobB/MinD/ParA nucleotide binding"
FT /evidence="ECO:0000259|Pfam:PF01656"
FT DOMAIN 259..445
FT /note="CobB/CobQ-like glutamine amidotransferase"
FT /evidence="ECO:0000259|Pfam:PF07685"
FT ACT_SITE 341
FT /note="Nucleophile"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
FT SITE 443
FT /note="Increases nucleophilicity of active site Cys"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
SQ SEQUENCE 453 AA; 47801 MW; EB37876AD43EBA0F CRC64;
MTVTDHILPT ATNGRPPGLI IAAPSTNSGK TTVTLALHAA LRRRSLTVQP YKCGPDYIDP
AFHEIAAGRP CYNLDSWAFG QDRITYLLDA AAGADLCLAE GVMGLFDGGS ARGAWGNGAT
ADIAAFTGWP VVLVIDVAGQ AQSAAALALG FARYRSDVRI AGVILNNVAS ARHEALVRDG
FAAQDIPVLG GFERQRDLTL KNRHLGLVQA RETARLDIRL QQLADSAVRG IDLDALIRAA
QPARPIASTI RPLTPPGQRI ALAHDDAFSF IYPHLTAGWR AAGAEIVPFS PLNDEGPDPS
CDAAWLPGGY PELHAGRLAA ATRFKAALGA FAETRAVHGE CGGYMTLGAG LIDADGTRHA
MAGLLGLETD FASRKLHLGY RLATLHADAA GKAAGSVLRG HEYHYARVVT VADEPLAEIR
DPAGQLTDET GSRRGHVTGT FFHLIDVAEE AIA
//
