COBT_SALTY
ID COBT_SALTY Reviewed; 356 AA.
AC Q05603;
DT 01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2002, sequence version 5.
DT 03-AUG-2022, entry version 161.
DE RecName: Full=Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase;
DE Short=NN:DBI PRT;
DE EC=2.4.2.21 {ECO:0000269|PubMed:8206834};
DE AltName: Full=N(1)-alpha-phosphoribosyltransferase;
GN Name=cobT; OrderedLocusNames=STM2016;
OS Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=99287;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=LT2;
RX PubMed=7883701; DOI=10.1128/jb.177.6.1461-1469.1995;
RA Chen P., Ailion M., Weyand N., Roth J.R.;
RT "The end of the cob operon: evidence that the last gene (cobT) catalyzes
RT synthesis of the lower ligand of vitamin B12, dimethylbenzimidazole.";
RL J. Bacteriol. 177:1461-1469(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=11677609; DOI=10.1038/35101614;
RA McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P.,
RA Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D.,
RA Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E.,
RA Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R.,
RA Wilson R.K.;
RT "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.";
RL Nature 413:852-856(2001).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-242.
RC STRAIN=LT2;
RX PubMed=8501034; DOI=10.1128/jb.175.11.3303-3316.1993;
RA Roth J.R., Lawrence J.G., Rubenfield M., Kieffer-Higgins S., Church G.M.;
RT "Characterization of the cobalamin (vitamin B12) biosynthetic genes of
RT Salmonella typhimurium.";
RL J. Bacteriol. 175:3303-3316(1993).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, AND DISRUPTION PHENOTYPE.
RC STRAIN=LT2;
RX PubMed=8206834; DOI=10.1128/jb.176.12.3568-3575.1994;
RA Trzebiatowski J.R., O'Toole G.A., Escalante-Semerena J.C.;
RT "The cobT gene of Salmonella typhimurium encodes the NaMN: 5,6-
RT dimethylbenzimidazole phosphoribosyltransferase responsible for the
RT synthesis of N1-(5-phospho-alpha-D-ribosyl)-5,6-dimethylbenzimidazole, an
RT intermediate in the synthesis of the nucleotide loop of cobalamin.";
RL J. Bacteriol. 176:3568-3575(1994).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH SUBSTRATE OR
RP PRODUCTS, SEQUENCE REVISION TO 158, FUNCTION, SUBUNIT, AND SITE.
RX PubMed=10587435; DOI=10.1021/bi991752c;
RA Cheong C.-G., Escalante-Semerena J.C., Rayment I.;
RT "The three-dimensional structures of nicotinate mononucleotide:5,6-
RT dimethylbenzimidazole phosphoribosyltransferase (CobT) from Salmonella
RT typhimurium complexed with 5,6-dimethybenzimidazole and its reaction
RT products determined to 1.9-A resolution.";
RL Biochemistry 38:16125-16135(1999).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH SUBSTRATES OR
RP PRODUCTS, FUNCTION, AND SUBSTRATE SPECIFICITY.
RX PubMed=11441022; DOI=10.1074/jbc.m105390200;
RA Cheong C.G., Escalante-Semerena J.C., Rayment I.;
RT "Structural investigation of the biosynthesis of alternative lower ligands
RT for cobamides by nicotinate mononucleotide: 5,6-dimethylbenzimidazole
RT phosphoribosyltransferase from Salmonella enterica.";
RL J. Biol. Chem. 276:37612-37620(2001).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF APOPROTEIN AND IN COMPLEX WITH
RP NICOTINATE MONONUCLEOTIDE AND SUBSTRATE ANALOGS, FUNCTION, POSSIBLE
RP REACTION MECHANISM, AND SUBUNIT.
RX DOI=10.1074/jbc.M203535200;
RA Cheong C.G., Escalante-Semerena J.C., Rayment I.;
RT "Capture of a labile substrate by expulsion of water molecules from the
RT active site of nicotinate mononucleotide:5,6-dimethylbenzimidazole
RT phosphoribosyltransferase (CobT) from Salmonella enterica.";
RL J. Biol. Chem. 277:41120-41127(2002).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.40 ANGSTROMS) OF MUTANT PROTEINS IN COMPLEX WITH
RP NICOTINATE MONONUCLEOTIDE, FUNCTION, SUBUNIT, AND MUTAGENESIS OF SER-80;
RP GLN-88; GLU-174; LEU-175 AND GLU-317.
RC STRAIN=LT2;
RX PubMed=24121107; DOI=10.1016/j.bbagen.2013.09.038;
RA Chan C.H., Newmister S.A., Talyor K., Claas K.R., Rayment I.,
RA Escalante-Semerena J.C.;
RT "Dissecting cobamide diversity through structural and functional analyses
RT of the base-activating CobT enzyme of Salmonella enterica.";
RL Biochim. Biophys. Acta 1840:464-475(2014).
CC -!- FUNCTION: Catalyzes the synthesis of alpha-ribazole-5'-phosphate from
CC nicotinate mononucleotide (NAMN) and 5,6-dimethylbenzimidazole (DMB)
CC (PubMed:8206834, PubMed:10587435, PubMed:11441022, Ref.7,
CC PubMed:24121107). Able to use a variety of other nucleotide bases as
CC substrate to create alternative lower ligands for cobamide
CC (PubMed:11441022, Ref.7, PubMed:24121107).
CC {ECO:0000269|PubMed:10587435, ECO:0000269|PubMed:11441022,
CC ECO:0000269|PubMed:24121107, ECO:0000269|PubMed:8206834,
CC ECO:0000269|Ref.7}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5,6-dimethylbenzimidazole + nicotinate beta-D-ribonucleotide =
CC alpha-ribazole 5'-phosphate + H(+) + nicotinate;
CC Xref=Rhea:RHEA:11196, ChEBI:CHEBI:15378, ChEBI:CHEBI:15890,
CC ChEBI:CHEBI:32544, ChEBI:CHEBI:57502, ChEBI:CHEBI:57918; EC=2.4.2.21;
CC Evidence={ECO:0000269|PubMed:8206834};
CC -!- PATHWAY: Nucleoside biosynthesis; alpha-ribazole biosynthesis; alpha-
CC ribazole from 5,6-dimethylbenzimidazole: step 1/2.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:10587435,
CC ECO:0000269|PubMed:24121107, ECO:0000269|Ref.7}.
CC -!- DISRUPTION PHENOTYPE: No growth on cobinamide (CBI); double cobB-cobT
CC deletion mutants do not grow on CBI and DMB (PubMed:8206834).
CC {ECO:0000269|PubMed:8206834}.
CC -!- MISCELLANEOUS: In vitro assays of this enzyme are performed at pH 10
CC because at physiological pH (7.0) its activity is undetectable; this
CC makes it difficult to assess the role of mutagenesis of potential
CC proton acceptor active site residues (Glu-174 and Glu-317)
CC (PubMed:24121107). {ECO:0000305|PubMed:24121107}.
CC -!- SIMILARITY: Belongs to the CobT family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA27271.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC Sequence=AAA69297.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; L35477; AAA69297.1; ALT_INIT; Genomic_DNA.
DR EMBL; AE006468; AAL20920.1; -; Genomic_DNA.
DR EMBL; L12006; AAA27271.1; ALT_INIT; Genomic_DNA.
DR RefSeq; NP_460961.1; NC_003197.2.
DR RefSeq; WP_001193983.1; NC_003197.2.
DR PDB; 1D0S; X-ray; 1.90 A; A=1-356.
DR PDB; 1D0V; X-ray; 1.90 A; A=1-356.
DR PDB; 1JH8; X-ray; 1.80 A; A=1-356.
DR PDB; 1JHA; X-ray; 2.00 A; A=1-356.
DR PDB; 1JHM; X-ray; 2.20 A; A=1-356.
DR PDB; 1JHO; X-ray; 2.00 A; A=1-356.
DR PDB; 1JHP; X-ray; 2.20 A; A=1-356.
DR PDB; 1JHQ; X-ray; 2.00 A; A=1-356.
DR PDB; 1JHR; X-ray; 2.00 A; A=1-356.
DR PDB; 1JHU; X-ray; 2.00 A; A=1-356.
DR PDB; 1JHV; X-ray; 2.00 A; A=1-356.
DR PDB; 1JHX; X-ray; 2.00 A; A=1-356.
DR PDB; 1JHY; X-ray; 2.00 A; A=1-356.
DR PDB; 1L4B; X-ray; 1.70 A; A=1-356.
DR PDB; 1L4E; X-ray; 2.00 A; A=1-356.
DR PDB; 1L4F; X-ray; 2.10 A; A=1-356.
DR PDB; 1L4G; X-ray; 2.10 A; A=1-356.
DR PDB; 1L4H; X-ray; 2.10 A; A=1-356.
DR PDB; 1L4K; X-ray; 2.20 A; A=1-356.
DR PDB; 1L4L; X-ray; 2.00 A; A=1-356.
DR PDB; 1L4M; X-ray; 2.00 A; A=1-356.
DR PDB; 1L4N; X-ray; 2.00 A; A=1-356.
DR PDB; 1L5F; X-ray; 1.90 A; A=1-356.
DR PDB; 1L5K; X-ray; 2.00 A; A=1-356.
DR PDB; 1L5L; X-ray; 2.00 A; A=1-356.
DR PDB; 1L5M; X-ray; 2.00 A; A=1-356.
DR PDB; 1L5N; X-ray; 1.90 A; A=1-356.
DR PDB; 1L5O; X-ray; 1.60 A; A=1-356.
DR PDB; 4KQF; X-ray; 1.90 A; A=1-356.
DR PDB; 4KQG; X-ray; 1.90 A; A=1-356.
DR PDB; 4KQH; X-ray; 1.90 A; A=1-356.
DR PDB; 4KQI; X-ray; 1.40 A; A=1-356.
DR PDB; 4KQJ; X-ray; 1.95 A; A=1-356.
DR PDB; 4KQK; X-ray; 1.47 A; A/B=1-356.
DR PDBsum; 1D0S; -.
DR PDBsum; 1D0V; -.
DR PDBsum; 1JH8; -.
DR PDBsum; 1JHA; -.
DR PDBsum; 1JHM; -.
DR PDBsum; 1JHO; -.
DR PDBsum; 1JHP; -.
DR PDBsum; 1JHQ; -.
DR PDBsum; 1JHR; -.
DR PDBsum; 1JHU; -.
DR PDBsum; 1JHV; -.
DR PDBsum; 1JHX; -.
DR PDBsum; 1JHY; -.
DR PDBsum; 1L4B; -.
DR PDBsum; 1L4E; -.
DR PDBsum; 1L4F; -.
DR PDBsum; 1L4G; -.
DR PDBsum; 1L4H; -.
DR PDBsum; 1L4K; -.
DR PDBsum; 1L4L; -.
DR PDBsum; 1L4M; -.
DR PDBsum; 1L4N; -.
DR PDBsum; 1L5F; -.
DR PDBsum; 1L5K; -.
DR PDBsum; 1L5L; -.
DR PDBsum; 1L5M; -.
DR PDBsum; 1L5N; -.
DR PDBsum; 1L5O; -.
DR PDBsum; 4KQF; -.
DR PDBsum; 4KQG; -.
DR PDBsum; 4KQH; -.
DR PDBsum; 4KQI; -.
DR PDBsum; 4KQJ; -.
DR PDBsum; 4KQK; -.
DR AlphaFoldDB; Q05603; -.
DR SMR; Q05603; -.
DR STRING; 99287.STM2016; -.
DR DrugBank; DB02163; 2,5-Xylidine.
DR DrugBank; DB04533; 2-Amino-4-methylphenol.
DR DrugBank; DB01726; 2-Aminophenol.
DR DrugBank; DB03018; 3,4-dimethylaniline.
DR DrugBank; DB04052; 3,4-Xylenol.
DR DrugBank; DB03180; 4,5-Dimethyl-1,2-phenylenediamine.
DR DrugBank; DB04120; 4-Methyl-1,2-Benzenediol.
DR DrugBank; DB02591; 5,6-Dimethylbenzimidazole.
DR DrugBank; DB04130; 5-Methoxybenzimidazole.
DR DrugBank; DB03177; 5-methylbenzimidazole.
DR DrugBank; DB02770; 7-alpha-D-Ribofuranosyl-2-aminopurine-5'-phosphate.
DR DrugBank; DB03200; 7-Alpha-D-Ribofuranosyl-Purine-5'-Phosphate.
DR DrugBank; DB00173; Adenine.
DR DrugBank; DB03887; Alpha-Adenosine Monophosphate.
DR DrugBank; DB02030; Alpha-Ribazole-5'-Phosphate.
DR DrugBank; DB03079; Alpha-Ribazole-5'-Phosphate Derivative.
DR DrugBank; DB02962; Benzimidazole.
DR DrugBank; DB03366; Imidazole.
DR DrugBank; DB04532; Indole.
DR DrugBank; DB02819; Mono-[3,4-Dihydroxy-5-(5-Methyl-Benzoimidazol-1-Yl)-Tetrahydor-Furan-2-Ylmethyl] Ester.
DR DrugBank; DB02905; N7-(5'-Phospho-alpha-ribosyl)-2-hydroxypurine.
DR DrugBank; DB02382; Namn.
DR DrugBank; DB01688; P-Cresol.
DR DrugBank; DB04176; Phosporic Acid Mono-[3,4-Dihydroxy-5-(5-Methoxy-Benzoimidazol-1-Yl)-Tetrahydro-Furan-2-Ylmethyl] Ester.
DR PaxDb; Q05603; -.
DR EnsemblBacteria; AAL20920; AAL20920; STM2016.
DR GeneID; 1253537; -.
DR KEGG; stm:STM2016; -.
DR PATRIC; fig|99287.12.peg.2138; -.
DR HOGENOM; CLU_002982_0_0_6; -.
DR OMA; AIWYAGW; -.
DR PhylomeDB; Q05603; -.
DR BioCyc; MetaCyc:MON-13214; -.
DR BioCyc; SENT99287:STM2016-MON; -.
DR BRENDA; 2.4.2.21; 2169.
DR UniPathway; UPA00061; UER00516.
DR EvolutionaryTrace; Q05603; -.
DR Proteomes; UP000001014; Chromosome.
DR GO; GO:0008939; F:nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity; IDA:CACAO.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0009236; P:cobalamin biosynthetic process; IEA:UniProtKB-KW.
DR CDD; cd02439; DMB-PRT_CobT; 1.
DR Gene3D; 1.10.1610.10; -; 1.
DR Gene3D; 3.40.50.10210; -; 1.
DR HAMAP; MF_00230; CobT; 1.
DR InterPro; IPR003200; Nict_dMeBzImd_PRibTrfase.
DR InterPro; IPR017846; Nict_dMeBzImd_PRibTrfase_bact.
DR InterPro; IPR023195; Nict_dMeBzImd_PRibTrfase_N.
DR InterPro; IPR036087; Nict_dMeBzImd_PRibTrfase_sf.
DR Pfam; PF02277; DBI_PRT; 1.
DR SUPFAM; SSF52733; SSF52733; 1.
DR TIGRFAMs; TIGR03160; cobT_DBIPRT; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cobalamin biosynthesis; Glycosyltransferase;
KW Nucleotide-binding; Reference proteome; Transferase.
FT CHAIN 1..356
FT /note="Nicotinate-nucleotide--dimethylbenzimidazole
FT phosphoribosyltransferase"
FT /id="PRO_0000167069"
FT BINDING 88
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:11441022"
FT BINDING 174..180
FT /ligand="nicotinate beta-D-ribonucleotide"
FT /ligand_id="ChEBI:CHEBI:57502"
FT /evidence="ECO:0000269|PubMed:24121107, ECO:0000269|Ref.7"
FT BINDING 203
FT /ligand="nicotinate beta-D-ribonucleotide"
FT /ligand_id="ChEBI:CHEBI:57502"
FT /evidence="ECO:0000269|PubMed:24121107, ECO:0000269|Ref.7"
FT BINDING 265
FT /ligand="nicotinate beta-D-ribonucleotide"
FT /ligand_id="ChEBI:CHEBI:57502"
FT /evidence="ECO:0000269|PubMed:24121107, ECO:0000269|Ref.7"
FT BINDING 291
FT /ligand="nicotinate beta-D-ribonucleotide"
FT /ligand_id="ChEBI:CHEBI:57502"
FT /evidence="ECO:0000269|PubMed:24121107, ECO:0000269|Ref.7"
FT BINDING 314..315
FT /ligand="nicotinate beta-D-ribonucleotide"
FT /ligand_id="ChEBI:CHEBI:57502"
FT /evidence="ECO:0000269|PubMed:24121107, ECO:0000269|Ref.7"
FT SITE 174
FT /note="Important for substrate positioning, might be proton
FT acceptor"
FT /evidence="ECO:0000269|PubMed:24121107"
FT SITE 317
FT /note="Important for substrate positioning, might be proton
FT acceptor"
FT /evidence="ECO:0000269|PubMed:24121107,
FT ECO:0000305|PubMed:10587435, ECO:0000305|Ref.7"
FT MUTAGEN 80
FT /note="S->Y: Alters specificity to use phenolic compounds
FT as substrate; when associated with M-88 and M-175."
FT /evidence="ECO:0000269|PubMed:24121107"
FT MUTAGEN 88
FT /note="Q->M: Alters specificity to use phenolic compounds
FT as substrate; when associated with Y-80 and M-175."
FT /evidence="ECO:0000269|PubMed:24121107"
FT MUTAGEN 174
FT /note="E->A: Decreases specific activity for DMB and
FT adenine about 20-fold. Decreases specific activity 1600- to
FT 15000-fold; when associated with A-317."
FT /evidence="ECO:0000269|PubMed:24121107"
FT MUTAGEN 175
FT /note="L->M: Alters specificity to use phenolic compounds
FT as substrate; when associated with Y-80 and M-88."
FT /evidence="ECO:0000269|PubMed:24121107"
FT MUTAGEN 317
FT /note="E->A: Decreases specific activity for DMB and
FT adenine about 50-fold; crystals bind substrate less well.
FT Decreases specific activity 1600- to 15000-fold; when
FT associated with A-174."
FT /evidence="ECO:0000269|PubMed:24121107"
FT CONFLICT 22
FT /note="A -> T (in Ref. 1; AAA69297 and 3; AAA27271)"
FT /evidence="ECO:0000305"
FT CONFLICT 158..159
FT /note="YT -> CA (in Ref. 1; AAA69297 and 3; AAA27271)"
FT /evidence="ECO:0000305"
FT HELIX 4..9
FT /evidence="ECO:0007829|PDB:4KQI"
FT HELIX 16..27
FT /evidence="ECO:0007829|PDB:4KQI"
FT STRAND 29..31
FT /evidence="ECO:0007829|PDB:4KQI"
FT TURN 33..36
FT /evidence="ECO:0007829|PDB:4KQI"
FT HELIX 37..47
FT /evidence="ECO:0007829|PDB:4KQI"
FT HELIX 50..52
FT /evidence="ECO:0007829|PDB:4KQI"
FT STRAND 60..68
FT /evidence="ECO:0007829|PDB:4KQI"
FT HELIX 71..75
FT /evidence="ECO:0007829|PDB:4KQI"
FT HELIX 84..93
FT /evidence="ECO:0007829|PDB:4KQI"
FT HELIX 98..106
FT /evidence="ECO:0007829|PDB:4KQI"
FT STRAND 109..116
FT /evidence="ECO:0007829|PDB:4KQI"
FT STRAND 118..120
FT /evidence="ECO:0007829|PDB:4KQI"
FT STRAND 125..127
FT /evidence="ECO:0007829|PDB:4KQI"
FT STRAND 131..134
FT /evidence="ECO:0007829|PDB:4KQI"
FT TURN 137..139
FT /evidence="ECO:0007829|PDB:4KQI"
FT HELIX 145..164
FT /evidence="ECO:0007829|PDB:4KQI"
FT STRAND 167..175
FT /evidence="ECO:0007829|PDB:4KQI"
FT TURN 177..179
FT /evidence="ECO:0007829|PDB:4KQI"
FT HELIX 180..191
FT /evidence="ECO:0007829|PDB:4KQI"
FT HELIX 195..198
FT /evidence="ECO:0007829|PDB:4KQI"
FT TURN 202..204
FT /evidence="ECO:0007829|PDB:4KQI"
FT HELIX 207..209
FT /evidence="ECO:0007829|PDB:4KQI"
FT HELIX 210..224
FT /evidence="ECO:0007829|PDB:4KQI"
FT HELIX 231..238
FT /evidence="ECO:0007829|PDB:4KQI"
FT HELIX 241..255
FT /evidence="ECO:0007829|PDB:4KQI"
FT HELIX 265..277
FT /evidence="ECO:0007829|PDB:4KQI"
FT HELIX 279..284
FT /evidence="ECO:0007829|PDB:4KQI"
FT HELIX 296..302
FT /evidence="ECO:0007829|PDB:4KQI"
FT HELIX 319..337
FT /evidence="ECO:0007829|PDB:4KQI"
FT HELIX 341..344
FT /evidence="ECO:0007829|PDB:4KQK"
SQ SEQUENCE 356 AA; 36613 MW; 3665FD3BB1B8A44C CRC64;
MQTLHALLRD IPAPDAEAMA RAQQHIDGLL KPPGSLGRLE TLAVQLAGMP GLNGTPQVGE
KAVLVMCADH GVWDEGVAVS PKIVTAIQAA NMTRGTTGVC VLAAQAGAKV HVIDVGIDAE
PIPGVVNMRV ARGCGNIAVG PAMSRLQAEA LLLEVSRYTC DLAQRGVTLF GVGELGMANT
TPAAAMVSVF TGSDAKEVVG IGANLPPSRI DNKVDVVRRA IAINQPNPRD GIDVLSKVGG
FDLVGMTGVM LGAARCGLPV LLDGFLSYSA ALAACQIAPA VRPYLIPSHF SAEKGARIAL
AHLSMEPYLH MAMRLGEGSG AALAMPIVEA ACAMFHNMGE LAASNIVLPE GNANAT
