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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)DescriptionActionsGraphical viewLength
Binding sitei88Substrate1 Publication1
Sitei174Important for substrate positioning, might be proton acceptor1 Publication1
Binding sitei203Nicotinate mononucleotide; via amide nitrogen2 Publications1
Binding sitei265Nicotinate mononucleotide; via amide nitrogen2 Publications1
Binding sitei291Nicotinate mononucleotide2 Publications1
Sitei317Important for substrate positioning, might be proton acceptor2 Publications1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi174 – 180Nicotinate mononucleotide2 Publications7
Nucleotide bindingi314 – 315Nicotinate mononucleotide2 Publications2

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.
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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
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)DescriptionActionsGraphical viewLength
Mutagenesisi80S → Y: Alters specificity to use phenolic compounds as substrate; when associated with M-88 and M-175. 1 Publication1
Mutagenesisi88Q → M: Alters specificity to use phenolic compounds as substrate; when associated with Y-80 and M-175. 1 Publication1
Mutagenesisi174E → A: Decreases specific activity for DMB and adenine about 20-fold. Decreases specific activity 1600- to 15000-fold; when associated with A-317. 1 Publication1
Mutagenesisi175L → M: Alters specificity to use phenolic compounds as substrate; when associated with Y-80 and M-88. 1 Publication1
Mutagenesisi317E → 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 Publication1

Chemistry databases

DrugBankiDB00173. Adenine.
DB03255. Phenol.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001670691 – 356Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferaseAdd BLAST356

Proteomic databases

PaxDbiQ05603.
PRIDEiQ05603.

Interactioni

Subunit structurei

Homodimer.3 Publications

Protein-protein interaction databases

STRINGi99287.STM2016.

Structurei

Secondary structure

1356
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi4 – 9Combined sources6
Helixi16 – 27Combined sources12
Beta strandi29 – 31Combined sources3
Turni33 – 36Combined sources4
Helixi37 – 47Combined sources11
Helixi50 – 52Combined sources3
Beta strandi60 – 68Combined sources9
Helixi71 – 75Combined sources5
Helixi84 – 93Combined sources10
Helixi98 – 106Combined sources9
Beta strandi109 – 116Combined sources8
Beta strandi118 – 120Combined sources3
Beta strandi125 – 127Combined sources3
Beta strandi131 – 134Combined sources4
Turni137 – 139Combined sources3
Helixi145 – 164Combined sources20
Beta strandi167 – 175Combined sources9
Turni177 – 179Combined sources3
Helixi180 – 191Combined sources12
Helixi195 – 198Combined sources4
Turni202 – 204Combined sources3
Helixi207 – 209Combined sources3
Helixi210 – 224Combined sources15
Helixi231 – 238Combined sources8
Helixi241 – 255Combined sources15
Helixi265 – 277Combined sources13
Helixi279 – 284Combined sources6
Helixi296 – 302Combined sources7
Helixi319 – 337Combined sources19
Helixi341 – 344Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
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)DescriptionActionsGraphical viewLength
Sequence conflicti22A → T in AAA69297 (PubMed:7883701).Curated1
Sequence conflicti22A → T in AAA27271 (PubMed:8501034).Curated1
Sequence conflicti158 – 159YT → CA in AAA69297 (PubMed:7883701).Curated2
Sequence conflicti158 – 159YT → CA in AAA27271 (PubMed:8501034).Curated2

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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi99287.STM2016.

Chemistry databases

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.
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: November 2, 2016
This is version 134 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.