Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Purine nucleoside phosphorylase DeoD-type

Gene

deoD3

Organism
Shewanella oneidensis (strain MR-1)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate.UniRule annotation
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei4Purine nucleoside; shared with dimeric partnerBy similarity1
Binding sitei20Phosphate; via amide nitrogenBy similarity1
Binding sitei24PhosphateBy similarity1
Binding sitei43Phosphate; shared with dimeric partnerBy similarity1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Glycosyltransferase, Transferase

Names & Taxonomyi

Protein namesi
Recommended name:
Purine nucleoside phosphorylase DeoD-typeUniRule annotation (EC:2.4.2.1UniRule annotation)
Short name:
PNPUniRule annotation
Gene namesi
Name:deoD3UniRule annotation
Ordered Locus Names:SO_2719
OrganismiShewanella oneidensis (strain MR-1)
Taxonomic identifieri211586 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaAlteromonadalesShewanellaceaeShewanella
Proteomesi
  • UP000008186 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000631611 – 234Purine nucleoside phosphorylase DeoD-typeAdd BLAST234

Proteomic databases

PaxDbiQ8EDM4.

Interactioni

Subunit structurei

Homohexamer.UniRule annotation

Protein-protein interaction databases

STRINGi211586.SO_2719.

Structurei

Secondary structure

1234
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi14 – 18Combined sources5
Helixi22 – 31Combined sources10
Beta strandi34 – 40Combined sources7
Helixi42 – 44Combined sources3
Beta strandi47 – 52Combined sources6
Beta strandi55 – 60Combined sources6
Helixi66 – 79Combined sources14
Beta strandi84 – 93Combined sources10
Beta strandi103 – 112Combined sources10
Helixi115 – 119Combined sources5
Turni120 – 122Combined sources3
Helixi131 – 143Combined sources13
Beta strandi148 – 155Combined sources8
Helixi166 – 172Combined sources7
Beta strandi177 – 181Combined sources5
Helixi182 – 192Combined sources11
Beta strandi195 – 205Combined sources11
Turni206 – 208Combined sources3
Helixi214 – 232Combined sources19

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4LKRX-ray2.40A1-234[»]
ProteinModelPortaliQ8EDM4.
SMRiQ8EDM4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni87 – 90Phosphate bindingBy similarity4
Regioni179 – 181Purine nucleoside bindingBy similarity3
Regioni203 – 204Purine nucleoside bindingBy similarity2

Sequence similaritiesi

Belongs to the PNP/UDP phosphorylase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4108QW8. Bacteria.
COG0813. LUCA.
HOGENOMiHOG000274896.
KOiK03784.
OMAiMYYDPDE.
OrthoDBiPOG091H02M1.
PhylomeDBiQ8EDM4.

Family and domain databases

Gene3Di3.40.50.1580. 1 hit.
HAMAPiMF_01627. Pur_nucleosid_phosp. 1 hit.
InterProiIPR004402. DeoD-type.
IPR018017. Nucleoside_phosphorylase.
IPR000845. Nucleoside_phosphorylase_d.
[Graphical view]
PANTHERiPTHR21234. PTHR21234. 1 hit.
PfamiPF01048. PNP_UDP_1. 1 hit.
[Graphical view]
SUPFAMiSSF53167. SSF53167. 1 hit.
TIGRFAMsiTIGR00107. deoD. 1 hit.

Sequencei

Sequence statusi: Complete.

Q8EDM4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTAHINAQPT DFAETVIMPG DPLRAKYIAE TYLTDAVEVT NVRNMLGYTG
60 70 80 90 100
YYQGQRISVM GHGMGISSMV LYGHELINFF GVKRIIRIGS LGATQQHVEM
110 120 130 140 150
RDVILAQAAG TDSPTNAKRS SGYHMATSAT FSLLHKAYTK ANEKGISVKV
160 170 180 190 200
GNVFSGDLYY DPDEDMIPAL ERFGVLGIDM EVAGLYGLAH QQGIESLAIL
210 220 230
TVSDHCLTGE ETTAQERQLS FNNMIELALE TALN
Length:234
Mass (Da):25,529
Last modified:March 1, 2003 - v1
Checksum:i666F9D55C6001908
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014299 Genomic DNA. Translation: AAN55747.1.
RefSeqiNP_718303.1. NC_004347.2.
WP_011072663.1. NC_004347.2.

Genome annotation databases

EnsemblBacteriaiAAN55747; AAN55747; SO_2719.
GeneIDi1170418.
KEGGison:SO_2719.
PATRICi23525059. VBISheOne101494_2619.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014299 Genomic DNA. Translation: AAN55747.1.
RefSeqiNP_718303.1. NC_004347.2.
WP_011072663.1. NC_004347.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4LKRX-ray2.40A1-234[»]
ProteinModelPortaliQ8EDM4.
SMRiQ8EDM4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi211586.SO_2719.

Proteomic databases

PaxDbiQ8EDM4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAN55747; AAN55747; SO_2719.
GeneIDi1170418.
KEGGison:SO_2719.
PATRICi23525059. VBISheOne101494_2619.

Phylogenomic databases

eggNOGiENOG4108QW8. Bacteria.
COG0813. LUCA.
HOGENOMiHOG000274896.
KOiK03784.
OMAiMYYDPDE.
OrthoDBiPOG091H02M1.
PhylomeDBiQ8EDM4.

Family and domain databases

Gene3Di3.40.50.1580. 1 hit.
HAMAPiMF_01627. Pur_nucleosid_phosp. 1 hit.
InterProiIPR004402. DeoD-type.
IPR018017. Nucleoside_phosphorylase.
IPR000845. Nucleoside_phosphorylase_d.
[Graphical view]
PANTHERiPTHR21234. PTHR21234. 1 hit.
PfamiPF01048. PNP_UDP_1. 1 hit.
[Graphical view]
SUPFAMiSSF53167. SSF53167. 1 hit.
TIGRFAMsiTIGR00107. deoD. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiDEOD3_SHEON
AccessioniPrimary (citable) accession number: Q8EDM4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 10, 2006
Last sequence update: March 1, 2003
Last modified: November 30, 2016
This is version 82 of the entry and version 1 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.