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Protein

Purine nucleoside phosphorylase DeoD-type

Gene

deoD

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Cleavage of adenosine and its derivatives.

Catalytic activityi

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

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

Enzyme and pathway databases

BioCyciBSUB:BSU19630-MONOMER.
BRENDAi2.4.2.1. 658.
SABIO-RKO34925.

Names & Taxonomyi

Protein namesi
Recommended name:
Purine nucleoside phosphorylase DeoD-type (EC:2.4.2.1)
Short name:
PNP
Alternative name(s):
Purine nucleoside phosphorylase II
Short name:
PU-NPase II
Gene namesi
Name:deoD
Synonyms:punB
Ordered Locus Names:BSU19630
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000631211 – 233Purine nucleoside phosphorylase DeoD-typeAdd BLAST233

Proteomic databases

PaxDbiO34925.
PRIDEiO34925.

Interactioni

Subunit structurei

Homohexamer.By similarity

Protein-protein interaction databases

IntActiO34925. 1 interactor.
MINTiMINT-8366691.
STRINGi224308.Bsubs1_010100010841.

Structurei

Secondary structure

1233
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi9 – 11Combined sources3
Beta strandi14 – 18Combined sources5
Helixi22 – 32Combined sources11
Beta strandi34 – 40Combined sources7
Helixi42 – 44Combined sources3
Beta strandi47 – 52Combined sources6
Beta strandi55 – 60Combined sources6
Helixi66 – 80Combined sources15
Beta strandi84 – 93Combined sources10
Beta strandi95 – 98Combined sources4
Beta strandi103 – 112Combined sources10
Helixi115 – 120Combined sources6
Helixi131 – 144Combined sources14
Beta strandi148 – 155Combined sources8
Helixi166 – 171Combined sources6
Beta strandi176 – 180Combined sources5
Helixi181 – 190Combined sources10
Beta strandi194 – 204Combined sources11
Turni205 – 207Combined sources3
Helixi213 – 227Combined sources15
Turni228 – 230Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4D8VX-ray2.35A/B1-233[»]
4D8XX-ray2.65A1-233[»]
4D8YX-ray1.61A/B/C/D/E/F1-233[»]
4D98X-ray1.70A/B1-233[»]
4D9HX-ray1.91A/B1-233[»]
4DA0X-ray2.95A1-233[»]
4DA6X-ray1.70A1-233[»]
4DA7X-ray2.05A1-233[»]
4DA8X-ray2.60A1-233[»]
4DABX-ray1.85A1-233[»]
4DAEX-ray2.35A1-233[»]
4DANX-ray2.56A/B1-233[»]
4DAOX-ray2.22A/B1-233[»]
4DARX-ray3.15A1-233[»]
ProteinModelPortaliO34925.
SMRiO34925.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni87 – 90Phosphate bindingBy similarity4
Regioni178 – 180Purine nucleoside bindingBy similarity3
Regioni202 – 203Purine nucleoside bindingBy similarity2

Sequence similaritiesi

Belongs to the PNP/UDP phosphorylase family.Curated

Phylogenomic databases

eggNOGiENOG4105D3A. Bacteria.
COG0813. LUCA.
HOGENOMiHOG000274896.
InParanoidiO34925.
KOiK03784.
OMAiVECYNEV.
PhylomeDBiO34925.

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.

O34925-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSVHIGAEKG QIADTVLLPG DPLRAKFIAE TYLENVECYN EVRGMYGFTG
60 70 80 90 100
TYKGKKISVQ GTGMGVPSIS IYVNELIQSY DVQNLIRVGS CGAIRKDVKV
110 120 130 140 150
RDVILAMTSS TDSQMNRVAF GSVDFAPCAD FELLKNAYDA AKDKGVPVTV
160 170 180 190 200
GSVFTADQFY NDDSQIEKLA KYGVLGVEME TTALYTLAAK HGRKALSILT
210 220 230
VSDHVLTGEE TTAEERQTTF HDMIEVALHS VSQ
Length:233
Mass (Da):25,378
Last modified:January 1, 1998 - v1
Checksum:i645FD21146E8F613
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF015775 Genomic DNA. Translation: AAB72065.1.
AF006665 Genomic DNA. Translation: AAB81164.1.
AL009126 Genomic DNA. Translation: CAB13854.1.
PIRiD69614.
RefSeqiNP_389844.1. NC_000964.3.
WP_003231176.1. NZ_JNCM01000036.1.

Genome annotation databases

EnsemblBacteriaiCAB13854; CAB13854; BSU19630.
GeneIDi940038.
KEGGibsu:BSU19630.
PATRICi18975779. VBIBacSub10457_2080.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF015775 Genomic DNA. Translation: AAB72065.1.
AF006665 Genomic DNA. Translation: AAB81164.1.
AL009126 Genomic DNA. Translation: CAB13854.1.
PIRiD69614.
RefSeqiNP_389844.1. NC_000964.3.
WP_003231176.1. NZ_JNCM01000036.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4D8VX-ray2.35A/B1-233[»]
4D8XX-ray2.65A1-233[»]
4D8YX-ray1.61A/B/C/D/E/F1-233[»]
4D98X-ray1.70A/B1-233[»]
4D9HX-ray1.91A/B1-233[»]
4DA0X-ray2.95A1-233[»]
4DA6X-ray1.70A1-233[»]
4DA7X-ray2.05A1-233[»]
4DA8X-ray2.60A1-233[»]
4DABX-ray1.85A1-233[»]
4DAEX-ray2.35A1-233[»]
4DANX-ray2.56A/B1-233[»]
4DAOX-ray2.22A/B1-233[»]
4DARX-ray3.15A1-233[»]
ProteinModelPortaliO34925.
SMRiO34925.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiO34925. 1 interactor.
MINTiMINT-8366691.
STRINGi224308.Bsubs1_010100010841.

Proteomic databases

PaxDbiO34925.
PRIDEiO34925.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB13854; CAB13854; BSU19630.
GeneIDi940038.
KEGGibsu:BSU19630.
PATRICi18975779. VBIBacSub10457_2080.

Phylogenomic databases

eggNOGiENOG4105D3A. Bacteria.
COG0813. LUCA.
HOGENOMiHOG000274896.
InParanoidiO34925.
KOiK03784.
OMAiVECYNEV.
PhylomeDBiO34925.

Enzyme and pathway databases

BioCyciBSUB:BSU19630-MONOMER.
BRENDAi2.4.2.1. 658.
SABIO-RKO34925.

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 nameiDEOD_BACSU
AccessioniPrimary (citable) accession number: O34925
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: January 1, 1998
Last modified: November 2, 2016
This is version 112 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. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  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.