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Protein

Purine nucleoside phosphorylase DeoD-type 1

Gene

deoD1

Organism
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
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 sitei5Purine nucleoside; shared with dimeric partnerCombined sources1
Binding sitei21Phosphate; via amide nitrogenCombined sources1
Binding sitei25PhosphateCombined sources1
Binding sitei44Phosphate; shared with dimeric partnerCombined sources1

GO - Molecular functioni

  • purine-nucleoside phosphorylase activity Source: TIGR

GO - Biological processi

  • nucleobase-containing compound metabolic process Source: TIGR
  • purine nucleoside metabolic process Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Glycosyltransferase, Transferase

Enzyme and pathway databases

BioCyciVCHO:VC2347-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Purine nucleoside phosphorylase DeoD-type 1UniRule annotation (EC:2.4.2.1UniRule annotation)
Short name:
PNP 1UniRule annotation
Gene namesi
Name:deoD1UniRule annotation
Ordered Locus Names:VC_2347
OrganismiVibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Taxonomic identifieri243277 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
Proteomesi
  • UP000000584 Componenti: Chromosome 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000631691 – 241Purine nucleoside phosphorylase DeoD-type 1Add BLAST241

Interactioni

Subunit structurei

Homohexamer.UniRule annotation

Protein-protein interaction databases

STRINGi243277.VC2347.

Structurei

Secondary structure

1241
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi15 – 19Combined sources5
Helixi23 – 33Combined sources11
Beta strandi34 – 41Combined sources8
Helixi43 – 45Combined sources3
Beta strandi48 – 53Combined sources6
Beta strandi56 – 61Combined sources6
Helixi67 – 81Combined sources15
Beta strandi85 – 94Combined sources10
Beta strandi104 – 113Combined sources10
Helixi116 – 120Combined sources5
Turni121 – 123Combined sources3
Helixi132 – 144Combined sources13
Beta strandi150 – 156Combined sources7
Helixi166 – 173Combined sources8
Beta strandi178 – 182Combined sources5
Helixi183 – 193Combined sources11
Beta strandi196 – 206Combined sources11
Turni207 – 209Combined sources3
Helixi215 – 237Combined sources23

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1VHJX-ray2.23A/B/C/D/E/F2-241[»]
1VHWX-ray1.54A/B/C/D/E/F2-241[»]
3OF3X-ray1.83A/B/C/D/E/F/G/H/I/J/K/L1-241[»]
ProteinModelPortaliQ9KPM0.
SMRiQ9KPM0.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9KPM0.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni88 – 91Phosphate bindingCombined sources4
Regioni180 – 182Purine nucleoside bindingCombined sources3
Regioni204 – 205Purine nucleoside bindingBy similarity2

Sequence similaritiesi

Belongs to the PNP/UDP phosphorylase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105D3A. Bacteria.
COG0813. LUCA.
KOiK03784.
OMAiKDHDFSA.

Family and domain databases

Gene3Di3.40.50.1580. 1 hit.
HAMAPiMF_01627. Pur_nucleosid_phosp. 1 hit.
InterProiIPR004402. DeoD-type.
IPR018017. Nucleoside_phosphorylase.
IPR018016. Nucleoside_phosphorylase_CS.
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.
PROSITEiPS01232. PNP_UDP_1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9KPM0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MATPHINAQM GDFADVVLMP GDPLRAKYIA ENFLDNAVQV CDVRNMFGYT
60 70 80 90 100
GTYKGRKISV MGHGMGIPSC SIYVTELIKD YGVKKIIRVG SCGAVNEGIK
110 120 130 140 150
VRDVVIGMGA CTDSKVNRIR FKDHDFAAIA DYKMVKAAEE AAKARGIDVK
160 170 180 190 200
VGNLFSAELF YTPDPSMFDV MDKYGIVGVE MEAAGIYGVA AEYGAKALAI
210 220 230 240
CTVSDHIKTG EQTTSEERQN TFNEMIEIAL DSVLIGDQAG Y
Length:241
Mass (Da):26,124
Last modified:October 1, 2000 - v1
Checksum:i6E55A07972166241
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE003852 Genomic DNA. Translation: AAF95490.1.
PIRiC82087.
RefSeqiNP_231977.1. NC_002505.1.
WP_000224887.1. NC_002505.1.

Genome annotation databases

EnsemblBacteriaiAAF95490; AAF95490; VC_2347.
GeneIDi2613143.
KEGGivch:VC2347.
PATRICi20083719. VBIVibCho83274_2234.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE003852 Genomic DNA. Translation: AAF95490.1.
PIRiC82087.
RefSeqiNP_231977.1. NC_002505.1.
WP_000224887.1. NC_002505.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1VHJX-ray2.23A/B/C/D/E/F2-241[»]
1VHWX-ray1.54A/B/C/D/E/F2-241[»]
3OF3X-ray1.83A/B/C/D/E/F/G/H/I/J/K/L1-241[»]
ProteinModelPortaliQ9KPM0.
SMRiQ9KPM0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243277.VC2347.

Protocols and materials databases

DNASUi2613143.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAF95490; AAF95490; VC_2347.
GeneIDi2613143.
KEGGivch:VC2347.
PATRICi20083719. VBIVibCho83274_2234.

Phylogenomic databases

eggNOGiENOG4105D3A. Bacteria.
COG0813. LUCA.
KOiK03784.
OMAiKDHDFSA.

Enzyme and pathway databases

BioCyciVCHO:VC2347-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ9KPM0.

Family and domain databases

Gene3Di3.40.50.1580. 1 hit.
HAMAPiMF_01627. Pur_nucleosid_phosp. 1 hit.
InterProiIPR004402. DeoD-type.
IPR018017. Nucleoside_phosphorylase.
IPR018016. Nucleoside_phosphorylase_CS.
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.
PROSITEiPS01232. PNP_UDP_1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDEOD1_VIBCH
AccessioniPrimary (citable) accession number: Q9KPM0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 24, 2006
Last sequence update: October 1, 2000
Last modified: November 2, 2016
This is version 88 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.