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Protein

Uridine phosphorylase

Gene

udp

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1-phosphate. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis (By similarity).By similarity

Catalytic activityi

Uridine + phosphate = uracil + alpha-D-ribose 1-phosphate.

Pathwayi: UMP biosynthesis via salvage pathway

This protein is involved in step 1 of the subpathway that synthesizes uracil from uridine (phosphorylase route).
Proteins known to be involved in this subpathway in this organism are:
  1. Uridine phosphorylase (udp)
This subpathway is part of the pathway UMP biosynthesis via salvage pathway, which is itself part of Pyrimidine metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes uracil from uridine (phosphorylase route), the pathway UMP biosynthesis via salvage pathway and in Pyrimidine metabolism.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Glycosyltransferase, Transferase

Enzyme and pathway databases

BRENDAi2.4.2.3. 5542.
UniPathwayiUPA00574; UER00633.

Names & Taxonomyi

Protein namesi
Recommended name:
Uridine phosphorylase (EC:2.4.2.3)
Short name:
UPase
Short name:
UrdPase
Gene namesi
Name:udp
Ordered Locus Names:STM3968
ORF Names:STMD1.21
OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Taxonomic identifieri99287 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
Proteomesi
  • UP000001014 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00000631852 – 253Uridine phosphorylaseAdd BLAST252

Proteomic databases

PaxDbiP0A1F6.
PRIDEiP0A1F6.

Interactioni

Subunit structurei

Homohexamer.By similarity

Protein-protein interaction databases

STRINGi99287.STM3968.

Structurei

Secondary structure

1253
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni7 – 9Combined sources3
Helixi13 – 16Combined sources4
Beta strandi21 – 26Combined sources6
Helixi28 – 30Combined sources3
Helixi31 – 35Combined sources5
Beta strandi38 – 47Combined sources10
Beta strandi50 – 57Combined sources8
Beta strandi60 – 65Combined sources6
Helixi71 – 83Combined sources13
Beta strandi88 – 95Combined sources8
Beta strandi107 – 118Combined sources12
Helixi119 – 122Combined sources4
Beta strandi126 – 128Combined sources3
Helixi134 – 146Combined sources13
Beta strandi151 – 160Combined sources10
Helixi164 – 166Combined sources3
Beta strandi171 – 173Combined sources3
Helixi178 – 180Combined sources3
Helixi183 – 189Combined sources7
Beta strandi194 – 198Combined sources5
Helixi199 – 207Combined sources9
Turni208 – 210Combined sources3
Beta strandi212 – 219Combined sources8
Turni223 – 225Combined sources3
Helixi231 – 234Combined sources4
Turni235 – 239Combined sources5
Helixi240 – 252Combined sources13

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1RYZX-ray2.90A/B/C/D/E/F1-253[»]
1SJ9X-ray2.50A/B/C/D/E/F1-253[»]
1Y1QX-ray2.35A/B/C/D/E/F1-253[»]
1Y1RX-ray2.11A/B/C/D/E/F1-253[»]
1Y1SX-ray2.55A/B/C/D/E/F1-253[»]
1Y1TX-ray1.77A/F1-253[»]
1ZL2X-ray1.85A/B/C/D/E/F1-253[»]
2HN9X-ray2.12A/B/C/D/E/F1-253[»]
2HRDX-ray1.70A/B/C/D/E/F1-253[»]
2HSWX-ray1.99A/B1-253[»]
2HWUX-ray2.91A/B/C/D/E/F1-253[»]
2I8AX-ray1.64A/B/C/D/E/F2-253[»]
2IQ5X-ray1.90A/B2-253[»]
2OECX-ray2.19A/B/C/D/E/F2-253[»]
2OXFX-ray1.76A/F4-253[»]
2PGAX-ray1.74A/B/C/D/E/F1-253[»]
2QDKX-ray1.62A/B/C/D/E/F2-253[»]
2RJ3X-ray2.51A/B/C/D/E/F2-253[»]
3C74X-ray2.38A/B/C/D/E/F2-253[»]
3DDOX-ray1.50A/B/C/D/E/F1-253[»]
3DPSX-ray1.80A/F1-253[»]
3FWPX-ray1.86A/B/C/D/E/F1-253[»]
4E1VX-ray2.15A/B/C/D/E/F/G/H/I1-253[»]
4OGKX-ray2.40A/B/C/D/E/F1-253[»]
ProteinModelPortaliP0A1F6.
SMRiP0A1F6.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A1F6.

Family & Domainsi

Sequence similaritiesi

Belongs to the PNP/UDP phosphorylase family.Curated

Phylogenomic databases

eggNOGiENOG4107SXA. Bacteria.
COG2820. LUCA.
HOGENOMiHOG000274897.
KOiK00757.
OMAiPHIGITA.
PhylomeDBiP0A1F6.

Family and domain databases

Gene3Di3.40.50.1580. 1 hit.
InterProiIPR018017. Nucleoside_phosphorylase.
IPR018016. Nucleoside_phosphorylase_CS.
IPR000845. Nucleoside_phosphorylase_d.
IPR010058. Uridine_phosphorylase.
[Graphical view]
PANTHERiPTHR21234. PTHR21234. 1 hit.
PfamiPF01048. PNP_UDP_1. 1 hit.
[Graphical view]
SUPFAMiSSF53167. SSF53167. 1 hit.
TIGRFAMsiTIGR01718. Uridine-psphlse. 1 hit.
PROSITEiPS01232. PNP_UDP_1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0A1F6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKSDVFHLG LTKNDLQGAQ LAIVPGDPER VEKIAALMDK PVKLASHREF
60 70 80 90 100
TSWRAELDGK AVIVCSTGIG GPSTSIAVEE LAQLGIRTFL RIGTTGAIQP
110 120 130 140 150
HINVGDVLVT TASVRLDGAS LHFAPMEFPA VADFACTTAL VEAAKSIGAT
160 170 180 190 200
THVGVTASSD TFYPGQERYD TYSGRVVRRF KGSMEEWQAM GVMNYEMESA
210 220 230 240 250
TLLTMCASQG LRAGMVAGVI VNRTQQEIPN AETMKQTESH AVKIVVEAAR

RLL
Length:253
Mass (Da):27,139
Last modified:January 23, 2007 - v2
Checksum:i63F26AFB8427BED2
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti200A → R in CAA73795 (PubMed:9661793).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y14282 Genomic DNA. Translation: CAA74658.2.
Y13360 Genomic DNA. Translation: CAA73795.1.
AF233324 Genomic DNA. Translation: AAF33424.1.
AE006468 Genomic DNA. Translation: AAL22812.1.
RefSeqiNP_462853.1. NC_003197.1.
WP_000045169.1. NC_003197.1.

Genome annotation databases

EnsemblBacteriaiAAL22812; AAL22812; STM3968.
GeneIDi1255494.
KEGGistm:STM3968.
PATRICi32386803. VBISalEnt20916_4187.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y14282 Genomic DNA. Translation: CAA74658.2.
Y13360 Genomic DNA. Translation: CAA73795.1.
AF233324 Genomic DNA. Translation: AAF33424.1.
AE006468 Genomic DNA. Translation: AAL22812.1.
RefSeqiNP_462853.1. NC_003197.1.
WP_000045169.1. NC_003197.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1RYZX-ray2.90A/B/C/D/E/F1-253[»]
1SJ9X-ray2.50A/B/C/D/E/F1-253[»]
1Y1QX-ray2.35A/B/C/D/E/F1-253[»]
1Y1RX-ray2.11A/B/C/D/E/F1-253[»]
1Y1SX-ray2.55A/B/C/D/E/F1-253[»]
1Y1TX-ray1.77A/F1-253[»]
1ZL2X-ray1.85A/B/C/D/E/F1-253[»]
2HN9X-ray2.12A/B/C/D/E/F1-253[»]
2HRDX-ray1.70A/B/C/D/E/F1-253[»]
2HSWX-ray1.99A/B1-253[»]
2HWUX-ray2.91A/B/C/D/E/F1-253[»]
2I8AX-ray1.64A/B/C/D/E/F2-253[»]
2IQ5X-ray1.90A/B2-253[»]
2OECX-ray2.19A/B/C/D/E/F2-253[»]
2OXFX-ray1.76A/F4-253[»]
2PGAX-ray1.74A/B/C/D/E/F1-253[»]
2QDKX-ray1.62A/B/C/D/E/F2-253[»]
2RJ3X-ray2.51A/B/C/D/E/F2-253[»]
3C74X-ray2.38A/B/C/D/E/F2-253[»]
3DDOX-ray1.50A/B/C/D/E/F1-253[»]
3DPSX-ray1.80A/F1-253[»]
3FWPX-ray1.86A/B/C/D/E/F1-253[»]
4E1VX-ray2.15A/B/C/D/E/F/G/H/I1-253[»]
4OGKX-ray2.40A/B/C/D/E/F1-253[»]
ProteinModelPortaliP0A1F6.
SMRiP0A1F6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi99287.STM3968.

Proteomic databases

PaxDbiP0A1F6.
PRIDEiP0A1F6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL22812; AAL22812; STM3968.
GeneIDi1255494.
KEGGistm:STM3968.
PATRICi32386803. VBISalEnt20916_4187.

Phylogenomic databases

eggNOGiENOG4107SXA. Bacteria.
COG2820. LUCA.
HOGENOMiHOG000274897.
KOiK00757.
OMAiPHIGITA.
PhylomeDBiP0A1F6.

Enzyme and pathway databases

UniPathwayiUPA00574; UER00633.
BRENDAi2.4.2.3. 5542.

Miscellaneous databases

EvolutionaryTraceiP0A1F6.

Family and domain databases

Gene3Di3.40.50.1580. 1 hit.
InterProiIPR018017. Nucleoside_phosphorylase.
IPR018016. Nucleoside_phosphorylase_CS.
IPR000845. Nucleoside_phosphorylase_d.
IPR010058. Uridine_phosphorylase.
[Graphical view]
PANTHERiPTHR21234. PTHR21234. 1 hit.
PfamiPF01048. PNP_UDP_1. 1 hit.
[Graphical view]
SUPFAMiSSF53167. SSF53167. 1 hit.
TIGRFAMsiTIGR01718. Uridine-psphlse. 1 hit.
PROSITEiPS01232. PNP_UDP_1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiUDP_SALTY
AccessioniPrimary (citable) accession number: P0A1F6
Secondary accession number(s): O08432, O33808, Q9L6M8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 1, 2005
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 88 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.