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Protein

Uridine phosphorylase

Gene

udp

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 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.

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

  • identical protein binding Source: EcoCyc
  • uridine phosphorylase activity Source: EcoCyc

GO - Biological processi

  • cellular response to DNA damage stimulus Source: EcoliWiki
  • nucleotide catabolic process Source: InterPro
  • UMP salvage Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Glycosyltransferase, Transferase

Enzyme and pathway databases

BioCyciEcoCyc:URPHOS-MONOMER.
ECOL316407:JW3808-MONOMER.
MetaCyc:URPHOS-MONOMER.
BRENDAi2.4.2.3. 2026.
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:b3831, JW3808
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11045. udp.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: UniProtKB
  • membrane Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi5D → A, E or N: No change in activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved3 Publications
ChainiPRO_00000631832 – 253Uridine phosphorylaseAdd BLAST252

Proteomic databases

EPDiP12758.
PaxDbiP12758.
PRIDEiP12758.

2D gel databases

SWISS-2DPAGEP12758.

Interactioni

Subunit structurei

Homohexamer. The homohexamer shows 4-fold, 6-fold or 8-fold symmetry.

GO - Molecular functioni

  • identical protein binding Source: EcoCyc

Protein-protein interaction databases

BioGridi4263299. 4 interactors.
DIPiDIP-11075N.
IntActiP12758. 4 interactors.
MINTiMINT-6478293.
STRINGi511145.b3831.

Structurei

Secondary structure

1253
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi6 – 9Combined sources4
Helixi13 – 16Combined sources4
Beta strandi21 – 23Combined sources3
Helixi28 – 30Combined sources3
Helixi31 – 35Combined sources5
Beta strandi38 – 47Combined sources10
Beta strandi50 – 57Combined sources8
Beta strandi60 – 65Combined sources6
Helixi71 – 83Combined sources13
Beta strandi88 – 97Combined sources10
Beta strandi107 – 116Combined sources10
Helixi119 – 122Combined sources4
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 – 222Combined sources11
Turni223 – 225Combined sources3
Helixi231 – 251Combined sources21

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1K3FX-ray2.50A/B/C/D/E/F1-253[»]
1LX7X-ray2.00A/B1-253[»]
1RXCX-ray2.35A/B/C/D/E/F/G/H/I/J/K/L1-253[»]
1RXSX-ray2.80A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/a/b/c/d/e/h/i/j/k/l/m/o1-253[»]
1RXUX-ray3.10A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R1-253[»]
1RXYX-ray1.70A/B1-253[»]
1T0UX-ray2.20A/B1-253[»]
1TGVX-ray2.20A/B1-253[»]
1TGYX-ray2.20A/B1-253[»]
1U1CX-ray2.20A/B/C/D/E/F2-253[»]
1U1DX-ray2.00A/B/C/D/E/F2-253[»]
1U1EX-ray2.00A/B/C/D/E/F2-253[»]
1U1FX-ray2.30A/B/C/D/E/F2-253[»]
1U1GX-ray1.95A/B/C/D/E/F2-253[»]
3KVVX-ray1.80A/B/C/D/E/F1-253[»]
ProteinModelPortaliP12758.
SMRiP12758.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP12758.

Family & Domainsi

Sequence similaritiesi

Belongs to the PNP/UDP phosphorylase family.Curated

Phylogenomic databases

eggNOGiENOG4108I5U. Bacteria.
COG2820. LUCA.
HOGENOMiHOG000274897.
InParanoidiP12758.
KOiK00757.
OMAiPHIGITA.
PhylomeDBiP12758.

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.

P12758-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKSDVFHLG LTKNDLQGAT LAIVPGDPDR VEKIAALMDK PVKLASHREF
60 70 80 90 100
TTWRAELDGK PVIVCSTGIG GPSTSIAVEE LAQLGIRTFL RIGTTGAIQP
110 120 130 140 150
HINVGDVLVT TASVRLDGAS LHFAPLEFPA VADFECTTAL VEAAKSIGAT
160 170 180 190 200
THVGVTASSD TFYPGQERYD TYSGRVVRHF KGSMEEWQAM GVMNYEMESA
210 220 230 240 250
TLLTMCASQG LRAGMVAGVI VNRTQQEIPN AETMKQTESH AVKIVVEAAR

RLL
Length:253
Mass (Da):27,159
Last modified:January 23, 2007 - v3
Checksum:i7446DE45BA04D88D
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti11L → Y AA sequence (PubMed:8899705).Curated1
Sequence conflicti15D → Y AA sequence (PubMed:8899705).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X15689 Genomic DNA. Translation: CAA33724.1.
M87049 Genomic DNA. Translation: AAA67626.1.
U00096 Genomic DNA. Translation: AAC76834.1.
AP009048 Genomic DNA. Translation: BAE77470.1.
PIRiS05491.
RefSeqiNP_418275.1. NC_000913.3.
WP_000045177.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76834; AAC76834; b3831.
BAE77470; BAE77470; BAE77470.
GeneIDi948987.
KEGGiecj:JW3808.
eco:b3831.
PATRICi32123163. VBIEscCol129921_3947.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X15689 Genomic DNA. Translation: CAA33724.1.
M87049 Genomic DNA. Translation: AAA67626.1.
U00096 Genomic DNA. Translation: AAC76834.1.
AP009048 Genomic DNA. Translation: BAE77470.1.
PIRiS05491.
RefSeqiNP_418275.1. NC_000913.3.
WP_000045177.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1K3FX-ray2.50A/B/C/D/E/F1-253[»]
1LX7X-ray2.00A/B1-253[»]
1RXCX-ray2.35A/B/C/D/E/F/G/H/I/J/K/L1-253[»]
1RXSX-ray2.80A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/a/b/c/d/e/h/i/j/k/l/m/o1-253[»]
1RXUX-ray3.10A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R1-253[»]
1RXYX-ray1.70A/B1-253[»]
1T0UX-ray2.20A/B1-253[»]
1TGVX-ray2.20A/B1-253[»]
1TGYX-ray2.20A/B1-253[»]
1U1CX-ray2.20A/B/C/D/E/F2-253[»]
1U1DX-ray2.00A/B/C/D/E/F2-253[»]
1U1EX-ray2.00A/B/C/D/E/F2-253[»]
1U1FX-ray2.30A/B/C/D/E/F2-253[»]
1U1GX-ray1.95A/B/C/D/E/F2-253[»]
3KVVX-ray1.80A/B/C/D/E/F1-253[»]
ProteinModelPortaliP12758.
SMRiP12758.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263299. 4 interactors.
DIPiDIP-11075N.
IntActiP12758. 4 interactors.
MINTiMINT-6478293.
STRINGi511145.b3831.

2D gel databases

SWISS-2DPAGEP12758.

Proteomic databases

EPDiP12758.
PaxDbiP12758.
PRIDEiP12758.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76834; AAC76834; b3831.
BAE77470; BAE77470; BAE77470.
GeneIDi948987.
KEGGiecj:JW3808.
eco:b3831.
PATRICi32123163. VBIEscCol129921_3947.

Organism-specific databases

EchoBASEiEB1038.
EcoGeneiEG11045. udp.

Phylogenomic databases

eggNOGiENOG4108I5U. Bacteria.
COG2820. LUCA.
HOGENOMiHOG000274897.
InParanoidiP12758.
KOiK00757.
OMAiPHIGITA.
PhylomeDBiP12758.

Enzyme and pathway databases

UniPathwayiUPA00574; UER00633.
BioCyciEcoCyc:URPHOS-MONOMER.
ECOL316407:JW3808-MONOMER.
MetaCyc:URPHOS-MONOMER.
BRENDAi2.4.2.3. 2026.

Miscellaneous databases

EvolutionaryTraceiP12758.
PROiP12758.

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_ECOLI
AccessioniPrimary (citable) accession number: P12758
Secondary accession number(s): Q2M8D6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1989
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 161 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.