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Protein

Pyrimidine-nucleoside phosphorylase

Gene

pdp

Organism
Geobacillus stearothermophilus (Bacillus stearothermophilus)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes phosphorolysis of the pyrimidine nucleosides uridine, thymidine and 2'-deoxyuridine with the formation of the corresponding pyrimidine base and ribose-1-phosphate.1 Publication

Catalytic activityi

Uridine + phosphate = uracil + alpha-D-ribose 1-phosphate.1 Publication
Thymidine + phosphate = thymine + 2'-deoxy-alpha-D-ribose 1-phosphate.1 Publication
2'-deoxyuridine + phosphate = uracil + 2'-deoxy-alpha-D-ribose 1-phosphate.1 Publication

Cofactori

K+1 PublicationNote: Binds 1 K+ ion per subunit.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi88Potassium; via carbonyl oxygenCombined sources1 Publication1
Metal bindingi90PotassiumCombined sources1 Publication1
Binding sitei92PhosphateCombined sources1 Publication1
Binding sitei120PhosphateCombined sources1 Publication1
Binding sitei168SubstrateCombined sources1 Publication1
Binding sitei187SubstrateCombined sources1 Publication1
Metal bindingi243Potassium; via carbonyl oxygenCombined sources1 Publication1
Metal bindingi246Potassium; via carbonyl oxygenCombined sources1 Publication1
Metal bindingi255PotassiumCombined sources1 Publication1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Glycosyltransferase, Transferase

Keywords - Ligandi

Metal-binding, Potassium

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-17881.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyrimidine-nucleoside phosphorylase1 Publication (EC:2.4.2.21 Publication)
Short name:
PYNP1 Publication
Short name:
Py-NPase1 Publication
Gene namesi
Name:pdp
Synonyms:pyn
OrganismiGeobacillus stearothermophilus (Bacillus stearothermophilus)
Taxonomic identifieri1422 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000590831 – 433Pyrimidine-nucleoside phosphorylaseAdd BLAST433

Proteomic databases

PRIDEiP77836.

Interactioni

Subunit structurei

Homodimer.1 Publication

Structurei

Secondary structure

1433
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 11Combined sources9
Helixi18 – 29Combined sources12
Helixi35 – 48Combined sources14
Helixi52 – 64Combined sources13
Beta strandi79 – 83Combined sources5
Helixi91 – 100Combined sources10
Turni101 – 103Combined sources3
Beta strandi106 – 110Combined sources5
Helixi120 – 124Combined sources5
Helixi136 – 146Combined sources11
Beta strandi147 – 152Combined sources6
Helixi159 – 170Combined sources12
Helixi177 – 191Combined sources15
Beta strandi194 – 203Combined sources10
Helixi211 – 227Combined sources17
Beta strandi231 – 238Combined sources8
Beta strandi243 – 249Combined sources7
Helixi250 – 260Combined sources11
Helixi266 – 282Combined sources17
Beta strandi285 – 288Combined sources4
Helixi289 – 302Combined sources14
Helixi304 – 315Combined sources12
Helixi320 – 322Combined sources3
Helixi326 – 328Combined sources3
Beta strandi333 – 339Combined sources7
Beta strandi341 – 349Combined sources9
Helixi351 – 361Combined sources11
Beta strandi377 – 381Combined sources5
Beta strandi393 – 402Combined sources10
Helixi405 – 412Combined sources8
Beta strandi415 – 420Combined sources6
Beta strandi427 – 432Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1BRWX-ray2.10A/B1-432[»]
ProteinModelPortaliP77836.
SMRiP77836.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP77836.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni81 – 83Phosphate bindingCombined sources1 Publication3
Regioni108 – 110Phosphate bindingCombined sources1 Publication3

Sequence similaritiesi

Phylogenomic databases

KOiK00756.

Family and domain databases

Gene3Di3.40.1030.10. 1 hit.
3.90.1170.30. 1 hit.
InterProiIPR000312. Glycosyl_Trfase_fam3.
IPR017459. Glycosyl_Trfase_fam3_N_dom.
IPR013102. PYNP_C.
IPR018090. Pyrmidine_PPas_bac/euk.
IPR017872. Pyrmidine_PPase_CS.
IPR000053. Thymidine/pyrmidine_PPase.
[Graphical view]
PANTHERiPTHR10515. PTHR10515. 1 hit.
PfamiPF02885. Glycos_trans_3N. 1 hit.
PF00591. Glycos_transf_3. 1 hit.
PF07831. PYNP_C. 1 hit.
[Graphical view]
PIRSFiPIRSF000478. TP_PyNP. 1 hit.
SMARTiSM00941. PYNP_C. 1 hit.
[Graphical view]
SUPFAMiSSF47648. SSF47648. 1 hit.
SSF52418. SSF52418. 1 hit.
SSF54680. SSF54680. 1 hit.
TIGRFAMsiTIGR02644. Y_phosphoryl. 1 hit.
PROSITEiPS00647. THYMID_PHOSPHORYLASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P77836-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRMVDLIEKK RDGHALTKEE IQFIIEGYTK GDIPDYQMSA LAMAIFFRGM
60 70 80 90 100
NEEETAELTM AMVHSGDTID LSRIEGIKVD KHSTGGVGDT TTLVLGPLVA
110 120 130 140 150
SVGVPVAKMS GRGLGHTGGT IDKLESVPGF HVEITNDEFI DLVNKNKIAV
160 170 180 190 200
VGQSGNLTPA DKKLYALRDV TATVNSIPLI ASSIMSKKIA AGADAIVLDV
210 220 230 240 250
KTGVGAFMKD LNDAKALAKA MVDIGNRVGR KTMAIISDMS QPLGYAIGNA
260 270 280 290 300
LEVKEAIDTL KGEGPEDFQE LCLVLGSHMV YLAEKASSLE EARHMLEKAM
310 320 330 340 350
KDGSALQTFK TFLAAQGGDA SVVDDPSKLP QAKYIIELEA KEDGYVSEIV
360 370 380 390 400
ADAVGTAAMW LGAGRATKES TIDLAVGLVL RKKVGDAVKK GESLVTIYSN
410 420 430
REQVDDVKQK LYENIRISAT PVQAPTLIYD KIS
Length:433
Mass (Da):46,332
Last modified:February 1, 1997 - v1
Checksum:i75EF04B8E7B2E0AD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D87961 Genomic DNA. Translation: BAA13512.1.
D87959 Genomic DNA. Translation: BAA20903.1.
PIRiJT0875.

Genome annotation databases

KEGGiag:BAA13512.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D87961 Genomic DNA. Translation: BAA13512.1.
D87959 Genomic DNA. Translation: BAA20903.1.
PIRiJT0875.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1BRWX-ray2.10A/B1-432[»]
ProteinModelPortaliP77836.
SMRiP77836.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiP77836.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

KEGGiag:BAA13512.

Phylogenomic databases

KOiK00756.

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-17881.

Miscellaneous databases

EvolutionaryTraceiP77836.

Family and domain databases

Gene3Di3.40.1030.10. 1 hit.
3.90.1170.30. 1 hit.
InterProiIPR000312. Glycosyl_Trfase_fam3.
IPR017459. Glycosyl_Trfase_fam3_N_dom.
IPR013102. PYNP_C.
IPR018090. Pyrmidine_PPas_bac/euk.
IPR017872. Pyrmidine_PPase_CS.
IPR000053. Thymidine/pyrmidine_PPase.
[Graphical view]
PANTHERiPTHR10515. PTHR10515. 1 hit.
PfamiPF02885. Glycos_trans_3N. 1 hit.
PF00591. Glycos_transf_3. 1 hit.
PF07831. PYNP_C. 1 hit.
[Graphical view]
PIRSFiPIRSF000478. TP_PyNP. 1 hit.
SMARTiSM00941. PYNP_C. 1 hit.
[Graphical view]
SUPFAMiSSF47648. SSF47648. 1 hit.
SSF52418. SSF52418. 1 hit.
SSF54680. SSF54680. 1 hit.
TIGRFAMsiTIGR02644. Y_phosphoryl. 1 hit.
PROSITEiPS00647. THYMID_PHOSPHORYLASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPDP_GEOSE
AccessioniPrimary (citable) accession number: P77836
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: February 1, 1997
Last modified: November 2, 2016
This is version 106 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, Direct protein sequencing

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.