COBB_SINSX
ID COBB_SINSX Reviewed; 434 AA.
AC P21632;
DT 01-MAY-1991, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 93.
DE RecName: Full=Hydrogenobyrinate a,c-diamide synthase {ECO:0000255|HAMAP-Rule:MF_00027, ECO:0000305|PubMed:2172209};
DE EC=6.3.5.9 {ECO:0000255|HAMAP-Rule:MF_00027, ECO:0000269|PubMed:2172209};
DE AltName: Full=Hydrogenobyrinic acid a,c-diamide synthase {ECO:0000255|HAMAP-Rule:MF_00027, ECO:0000305|PubMed:2172209};
GN Name=cobB {ECO:0000255|HAMAP-Rule:MF_00027, ECO:0000303|PubMed:2211520};
OS Sinorhizobium sp.
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Rhizobiaceae; Sinorhizobium/Ensifer group; Sinorhizobium.
OX NCBI_TaxID=42445;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 2-16.
RC STRAIN=SC510;
RX PubMed=2211520; DOI=10.1128/jb.172.10.5968-5979.1990;
RA Crouzet J., Cauchois L., Blanche F., Debussche L., Thibaut D.,
RA Rouyez M.-C., Rigault S., Mayaux J.-F., Cameron B.;
RT "Nucleotide sequence of a Pseudomonas denitrificans 5.4-kilobase DNA
RT fragment containing five cob genes and identification of structural genes
RT encoding S-adenosyl-L-methionine: uroporphyrinogen III methyltransferase
RT and cobyrinic acid a,c-diamide synthase.";
RL J. Bacteriol. 172:5968-5979(1990).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, COFACTOR,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RC STRAIN=SC510;
RX PubMed=2172209; DOI=10.1128/jb.172.11.6239-6244.1990;
RA Debussche L., Thibaut D., Cameron B., Crouzet J., Blanche F.;
RT "Purification and characterization of cobyrinic acid a,c-diamide synthase
RT from Pseudomonas denitrificans.";
RL J. Bacteriol. 172:6239-6244(1990).
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. To a much lesser extent,
CC can also use cobyrinate as substrate in vitro, but the physiological
CC substrate is indeed hydrogenobyrinate, as part of the aerobic pathway
CC for cobalamin biosynthesis. {ECO:0000255|HAMAP-Rule:MF_00027,
CC ECO:0000269|PubMed:2172209, ECO:0000305}.
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, ECO:0000269|PubMed:2172209};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00027,
CC ECO:0000269|PubMed:2172209};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.41 uM for hydrogenobyrinate {ECO:0000269|PubMed:2172209};
CC KM=0.21 uM for hydrogenobyrinate c-monoamide
CC {ECO:0000269|PubMed:2172209};
CC KM=30.2 uM for ATP {ECO:0000269|PubMed:2172209};
CC KM=20.3 uM for glutamine {ECO:0000269|PubMed:2172209};
CC KM=12 mM for ammonia {ECO:0000269|PubMed:2172209};
CC KM=250 uM for cobyrinate {ECO:0000269|PubMed:2172209};
CC Vmax=1390 nmol/h/mg enzyme with hydrogenobyrinate as substrate
CC {ECO:0000269|PubMed:2172209};
CC Vmax=574 nmol/h/mg enzyme with hydrogenobyrinate c-monoamide as
CC substrate {ECO:0000269|PubMed:2172209};
CC Vmax=800 nmol/h/mg enzyme with cobyrinate as substrate
CC {ECO:0000269|PubMed:2172209};
CC pH dependence:
CC Optimum pH is around 7.3. {ECO:0000269|PubMed:2172209};
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, ECO:0000305}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:2172209}.
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 likely
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, ECO:0000269|PubMed:2172209}.
CC -!- SIMILARITY: Belongs to the CobB/CbiA family. {ECO:0000255|HAMAP-
CC Rule:MF_00027}.
CC -!- CAUTION: Was originally thought to originate from Pseudomonas
CC denitrificans, but similarity searches show that the sequence is much
CC closer to Sinorhizobium. The entry's taxonomy has been changed.
CC {ECO:0000305}.
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DR EMBL; M59236; AAA25774.1; -; Genomic_DNA.
DR AlphaFoldDB; P21632; -.
DR SMR; P21632; -.
DR BioCyc; MetaCyc:MON-116; -.
DR SABIO-RK; P21632; -.
DR UniPathway; UPA00148; UER00220.
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 1: Evidence at protein level;
KW ATP-binding; Cobalamin biosynthesis; Direct protein sequencing;
KW Glutamine amidotransferase; Ligase; Magnesium; Nucleotide-binding.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:2211520"
FT CHAIN 2..434
FT /note="Hydrogenobyrinate a,c-diamide synthase"
FT /id="PRO_0000141265"
FT DOMAIN 243..434
FT /note="GATase cobBQ-type"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00027"
FT ACT_SITE 326
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00027"
FT SITE 426
FT /note="Increases nucleophilicity of active site Cys"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00027"
SQ SEQUENCE 434 AA; 45705 MW; DE3D15D099BC0BCA CRC64;
MSGLLIAAPA SGSGKTTVTL GLMRALKRRG VAIAPGKAGP DYIDPAFHAA ATGEPCFNYD
PWAMRPELLL ANASHVASGG RTLIVEAMMG LHDGAADGSG TPADLAATLN LAVILVVDCA
RMSQSVAALV RGYADHRDDI RVVGVILNKV GSDRHEMMLR DALGKVRMPV FGVLRQDSAL
QLPERHLGLV QAGEHSALEG FIEAAAARVE AACDLDAIRL IATIFPQVPA AADAERLRPL
GQRIAVARDI AFAFCYEHLL YGWRQGGAEI SFFSPLADEG PDAAADAVYL PGGYPELHAG
QLSAAARFRS GMHSAAERGA RIFGECGGYM VLGEGLVAAD GTRYDMLGLL PLVTSFAERR
RHLGYRRVVP VDNAFFDGPM TAHEFHYATI VAEGAADRLF AVSDAAGEDL GQAGLRRGPV
AGSFMHLIDV AGAA
