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Protein

Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase

Gene

cobT

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide (NAMN) and 5,6-dimethylbenzimidazole (DMB) (PubMed:8206834, PubMed:10587435, PubMed:11441022, Ref. 7, PubMed:24121107). Able to use a variety of other nucleotide bases as substrate to create alternative lower ligands for cobamide (PubMed:11441022, Ref. 7, PubMed:24121107).5 Publications

Catalytic activityi

Beta-nicotinate D-ribonucleotide + 5,6-dimethylbenzimidazole = nicotinate + alpha-ribazole 5'-phosphate.1 Publication

Pathwayi: alpha-ribazole biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes alpha-ribazole from 5,6-dimethylbenzimidazole.
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase (cobT)
  2. Adenosylcobalamin/alpha-ribazole phosphatase (cobC)
This subpathway is part of the pathway alpha-ribazole biosynthesis, which is itself part of Nucleoside biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes alpha-ribazole from 5,6-dimethylbenzimidazole, the pathway alpha-ribazole biosynthesis and in Nucleoside biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei88 – 881Substrate1 Publication
Sitei174 – 1741Important for substrate positioning, might be proton acceptor1 Publication
Binding sitei203 – 2031Nicotinate mononucleotide; via amide nitrogen2 Publications
Binding sitei265 – 2651Nicotinate mononucleotide; via amide nitrogen2 Publications
Binding sitei291 – 2911Nicotinate mononucleotide2 Publications
Sitei317 – 3171Important for substrate positioning, might be proton acceptor2 Publications1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi174 – 1807Nicotinate mononucleotide2 Publications
Nucleotide bindingi314 – 3152Nicotinate mononucleotide2 Publications

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Glycosyltransferase, Transferase

Keywords - Biological processi

Cobalamin biosynthesis

Keywords - Ligandi

Nucleotide-binding

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-13214.
SENT99287:GCTI-2028-MONOMER.
BRENDAi2.4.2.21. 2169.
UniPathwayiUPA00061; UER00516.

Names & Taxonomyi

Protein namesi
Recommended name:
Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase (EC:2.4.2.211 Publication)
Short name:
NN:DBI PRT
Alternative name(s):
N(1)-alpha-phosphoribosyltransferase
Gene namesi
Name:cobT
Ordered Locus Names:STM2016
OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Taxonomic identifieri99287 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
Proteomesi
  • UP000001014 Componenti: Chromosome

Pathology & Biotechi

Disruption phenotypei

No growth on cobinamide (CBI); double cobB-cobT deletion mutants do not grow on CBI and DMB (PubMed:8206834).1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi80 – 801S → Y: Alters specificity to use phenolic compounds as substrate; when associated with M-88 and M-175. 1 Publication
Mutagenesisi88 – 881Q → M: Alters specificity to use phenolic compounds as substrate; when associated with Y-80 and M-175. 1 Publication
Mutagenesisi174 – 1741E → A: Decreases specific activity for DMB and adenine about 20-fold. Decreases specific activity 1600- to 15000-fold; when associated with A-317. 1 Publication
Mutagenesisi175 – 1751L → M: Alters specificity to use phenolic compounds as substrate; when associated with Y-80 and M-88. 1 Publication
Mutagenesisi317 – 3171E → A: Decreases specific activity for DMB and adenine about 50-fold; crystals bind substrate less well. Decreases specific activity 1600- to 15000-fold; when associated with A-174. 1 Publication

Chemistry

DrugBankiDB00173. Adenine.
DB03255. Phenol.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 356356Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferasePRO_0000167069Add
BLAST

Proteomic databases

PaxDbiQ05603.
PRIDEiQ05603.

Interactioni

Subunit structurei

Homodimer.3 Publications

Protein-protein interaction databases

STRINGi99287.STM2016.

Structurei

Secondary structure

1
356
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 96Combined sources
Helixi16 – 2712Combined sources
Beta strandi29 – 313Combined sources
Turni33 – 364Combined sources
Helixi37 – 4711Combined sources
Helixi50 – 523Combined sources
Beta strandi60 – 689Combined sources
Helixi71 – 755Combined sources
Helixi84 – 9310Combined sources
Helixi98 – 1069Combined sources
Beta strandi109 – 1168Combined sources
Beta strandi118 – 1203Combined sources
Beta strandi125 – 1273Combined sources
Beta strandi131 – 1344Combined sources
Turni137 – 1393Combined sources
Helixi145 – 16420Combined sources
Beta strandi167 – 1759Combined sources
Turni177 – 1793Combined sources
Helixi180 – 19112Combined sources
Helixi195 – 1984Combined sources
Turni202 – 2043Combined sources
Helixi207 – 2093Combined sources
Helixi210 – 22415Combined sources
Helixi231 – 2388Combined sources
Helixi241 – 25515Combined sources
Helixi265 – 27713Combined sources
Helixi279 – 2846Combined sources
Helixi296 – 3027Combined sources
Helixi319 – 33719Combined sources
Helixi341 – 3444Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1D0SX-ray1.90A1-356[»]
1D0VX-ray1.90A1-356[»]
1JH8X-ray1.80A1-356[»]
1JHAX-ray2.00A1-356[»]
1JHMX-ray2.20A1-356[»]
1JHOX-ray2.00A1-356[»]
1JHPX-ray2.20A1-356[»]
1JHQX-ray2.00A1-356[»]
1JHRX-ray2.00A1-356[»]
1JHUX-ray2.00A1-356[»]
1JHVX-ray2.00A1-356[»]
1JHXX-ray2.00A1-356[»]
1JHYX-ray2.00A1-356[»]
1L4BX-ray1.70A1-356[»]
1L4EX-ray2.00A1-356[»]
1L4FX-ray2.10A1-356[»]
1L4GX-ray2.10A1-356[»]
1L4HX-ray2.10A1-356[»]
1L4KX-ray2.20A1-356[»]
1L4LX-ray2.00A1-356[»]
1L4MX-ray2.00A1-356[»]
1L4NX-ray2.00A1-356[»]
1L5FX-ray1.90A1-356[»]
1L5KX-ray2.00A1-356[»]
1L5LX-ray2.00A1-356[»]
1L5MX-ray2.00A1-356[»]
1L5NX-ray1.90A1-356[»]
1L5OX-ray1.60A1-356[»]
4KQFX-ray1.90A1-356[»]
4KQGX-ray1.90A1-356[»]
4KQHX-ray1.90A1-356[»]
4KQIX-ray1.40A1-356[»]
4KQJX-ray1.95A1-356[»]
4KQKX-ray1.47A/B1-356[»]
ProteinModelPortaliQ05603.
SMRiQ05603. Positions 3-350.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ05603.

Family & Domainsi

Sequence similaritiesi

Belongs to the CobT family.Curated

Phylogenomic databases

eggNOGiENOG4105CUP. Bacteria.
COG2038. LUCA.
HOGENOMiHOG000263499.
KOiK00768.
OMAiMNNMATF.
PhylomeDBiQ05603.

Family and domain databases

CDDicd02439. DMB-PRT_CobT. 1 hit.
Gene3Di1.10.1610.10. 1 hit.
HAMAPiMF_00230. CobT. 1 hit.
InterProiIPR003200. Nict_dMeBzImd_PRibTrfase-like.
IPR023195. Nict_dMeBzImd_PRibTrfase_N.
IPR017846. Nict_dMeBzImd_PRibTrfase_pro.
[Graphical view]
PfamiPF02277. DBI_PRT. 1 hit.
[Graphical view]
SUPFAMiSSF52733. SSF52733. 1 hit.
TIGRFAMsiTIGR03160. cobT_DBIPRT. 1 hit.

Sequencei

Sequence statusi: Complete.

Q05603-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQTLHALLRD IPAPDAEAMA RAQQHIDGLL KPPGSLGRLE TLAVQLAGMP
60 70 80 90 100
GLNGTPQVGE KAVLVMCADH GVWDEGVAVS PKIVTAIQAA NMTRGTTGVC
110 120 130 140 150
VLAAQAGAKV HVIDVGIDAE PIPGVVNMRV ARGCGNIAVG PAMSRLQAEA
160 170 180 190 200
LLLEVSRYTC DLAQRGVTLF GVGELGMANT TPAAAMVSVF TGSDAKEVVG
210 220 230 240 250
IGANLPPSRI DNKVDVVRRA IAINQPNPRD GIDVLSKVGG FDLVGMTGVM
260 270 280 290 300
LGAARCGLPV LLDGFLSYSA ALAACQIAPA VRPYLIPSHF SAEKGARIAL
310 320 330 340 350
AHLSMEPYLH MAMRLGEGSG AALAMPIVEA ACAMFHNMGE LAASNIVLPE

GNANAT
Length:356
Mass (Da):36,613
Last modified:January 23, 2002 - v5
Checksum:i3665FD3BB1B8A44C
GO

Sequence cautioni

The sequence AAA27271 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
The sequence AAA69297 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti22 – 221A → T in AAA69297 (PubMed:7883701).Curated
Sequence conflicti22 – 221A → T in AAA27271 (PubMed:8501034).Curated
Sequence conflicti158 – 1592YT → CA in AAA69297 (PubMed:7883701).Curated
Sequence conflicti158 – 1592YT → CA in AAA27271 (PubMed:8501034).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L35477 Genomic DNA. Translation: AAA69297.1. Different initiation.
AE006468 Genomic DNA. Translation: AAL20920.1.
L12006 Genomic DNA. Translation: AAA27271.1. Different initiation.
RefSeqiNP_460961.1. NC_003197.1.
WP_001193983.1. NC_003197.1.

Genome annotation databases

EnsemblBacteriaiAAL20920; AAL20920; STM2016.
GeneIDi1253537.
KEGGistm:STM2016.
PATRICi32382615. VBISalEnt20916_2138.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L35477 Genomic DNA. Translation: AAA69297.1. Different initiation.
AE006468 Genomic DNA. Translation: AAL20920.1.
L12006 Genomic DNA. Translation: AAA27271.1. Different initiation.
RefSeqiNP_460961.1. NC_003197.1.
WP_001193983.1. NC_003197.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1D0SX-ray1.90A1-356[»]
1D0VX-ray1.90A1-356[»]
1JH8X-ray1.80A1-356[»]
1JHAX-ray2.00A1-356[»]
1JHMX-ray2.20A1-356[»]
1JHOX-ray2.00A1-356[»]
1JHPX-ray2.20A1-356[»]
1JHQX-ray2.00A1-356[»]
1JHRX-ray2.00A1-356[»]
1JHUX-ray2.00A1-356[»]
1JHVX-ray2.00A1-356[»]
1JHXX-ray2.00A1-356[»]
1JHYX-ray2.00A1-356[»]
1L4BX-ray1.70A1-356[»]
1L4EX-ray2.00A1-356[»]
1L4FX-ray2.10A1-356[»]
1L4GX-ray2.10A1-356[»]
1L4HX-ray2.10A1-356[»]
1L4KX-ray2.20A1-356[»]
1L4LX-ray2.00A1-356[»]
1L4MX-ray2.00A1-356[»]
1L4NX-ray2.00A1-356[»]
1L5FX-ray1.90A1-356[»]
1L5KX-ray2.00A1-356[»]
1L5LX-ray2.00A1-356[»]
1L5MX-ray2.00A1-356[»]
1L5NX-ray1.90A1-356[»]
1L5OX-ray1.60A1-356[»]
4KQFX-ray1.90A1-356[»]
4KQGX-ray1.90A1-356[»]
4KQHX-ray1.90A1-356[»]
4KQIX-ray1.40A1-356[»]
4KQJX-ray1.95A1-356[»]
4KQKX-ray1.47A/B1-356[»]
ProteinModelPortaliQ05603.
SMRiQ05603. Positions 3-350.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi99287.STM2016.

Chemistry

DrugBankiDB00173. Adenine.
DB03255. Phenol.

Proteomic databases

PaxDbiQ05603.
PRIDEiQ05603.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL20920; AAL20920; STM2016.
GeneIDi1253537.
KEGGistm:STM2016.
PATRICi32382615. VBISalEnt20916_2138.

Phylogenomic databases

eggNOGiENOG4105CUP. Bacteria.
COG2038. LUCA.
HOGENOMiHOG000263499.
KOiK00768.
OMAiMNNMATF.
PhylomeDBiQ05603.

Enzyme and pathway databases

UniPathwayiUPA00061; UER00516.
BioCyciMetaCyc:MONOMER-13214.
SENT99287:GCTI-2028-MONOMER.
BRENDAi2.4.2.21. 2169.

Miscellaneous databases

EvolutionaryTraceiQ05603.

Family and domain databases

CDDicd02439. DMB-PRT_CobT. 1 hit.
Gene3Di1.10.1610.10. 1 hit.
HAMAPiMF_00230. CobT. 1 hit.
InterProiIPR003200. Nict_dMeBzImd_PRibTrfase-like.
IPR023195. Nict_dMeBzImd_PRibTrfase_N.
IPR017846. Nict_dMeBzImd_PRibTrfase_pro.
[Graphical view]
PfamiPF02277. DBI_PRT. 1 hit.
[Graphical view]
SUPFAMiSSF52733. SSF52733. 1 hit.
TIGRFAMsiTIGR03160. cobT_DBIPRT. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiCOBT_SALTY
AccessioniPrimary (citable) accession number: Q05603
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: January 23, 2002
Last modified: September 7, 2016
This is version 132 of the entry and version 5 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

In vitro assays of this enzyme are performed at pH 10 because at physiological pH (7.0) its activity is undetectable; this makes it difficult to assess the role of mutagenesis of potential proton acceptor active site residues (Glu-174 and Glu-317) (PubMed:24121107).1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.