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P77836

- PDP_GEOSE

UniProt

P77836 - PDP_GEOSE

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Protein
Pyrimidine-nucleoside phosphorylase
Gene
pdp, pyn
Organism
Geobacillus stearothermophilus (Bacillus stearothermophilus)
Status
Reviewed - Annotation score: 4 out of 5 - Experimental evidence at protein leveli

Functioni

Catalytic activityi

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

Cofactori

Binds 1 potassium ion per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi88 – 881Potassium; via carbonyl oxygen
Metal bindingi90 – 901Potassium
Metal bindingi243 – 2431Potassium; via carbonyl oxygen
Metal bindingi246 – 2461Potassium; via carbonyl oxygen
Metal bindingi255 – 2551Potassium

GO - Molecular functioni

  1. metal ion binding Source: UniProtKB-KW
  2. phosphorylase activity Source: InterPro
  3. pyrimidine-nucleoside phosphorylase activity Source: UniProtKB-EC

GO - Biological processi

  1. pyrimidine nucleobase metabolic process Source: InterPro
  2. pyrimidine nucleoside metabolic process Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Glycosyltransferase, Transferase

Keywords - Ligandi

Metal-binding

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-17881.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyrimidine-nucleoside phosphorylase (EC:2.4.2.2)
Short name:
PYNP
Gene namesi
Name:pdp
Synonyms:pyn
OrganismiGeobacillus stearothermophilus (Bacillus stearothermophilus)
Taxonomic identifieri1422 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 433433Pyrimidine-nucleoside phosphorylase
PRO_0000059083Add
BLAST

Proteomic databases

PRIDEiP77836.

Interactioni

Subunit structurei

Homodimer.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 119
Helixi18 – 2912
Helixi35 – 4814
Helixi52 – 6413
Beta strandi79 – 835
Helixi91 – 10010
Turni101 – 1033
Beta strandi106 – 1105
Helixi120 – 1245
Helixi136 – 14611
Beta strandi147 – 1526
Helixi159 – 17012
Helixi177 – 19115
Beta strandi194 – 20310
Helixi211 – 22717
Beta strandi231 – 2388
Beta strandi243 – 2497
Helixi250 – 26011
Helixi266 – 28217
Beta strandi285 – 2884
Helixi289 – 30214
Helixi304 – 31512
Helixi320 – 3223
Helixi326 – 3283
Beta strandi333 – 3397
Beta strandi341 – 3499
Helixi351 – 36111
Beta strandi377 – 3815
Beta strandi393 – 40210
Helixi405 – 4128
Beta strandi415 – 4206
Beta strandi427 – 4326

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1BRWX-ray2.10A/B1-432[»]
ProteinModelPortaliP77836.
SMRiP77836. Positions 1-432.

Miscellaneous databases

EvolutionaryTraceiP77836.

Family & Domainsi

Sequence similaritiesi

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.
IPR000053. Pyrmidine_PPase.
IPR017872. Pyrmidine_PPase_CS.
[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

MRMVDLIEKK RDGHALTKEE IQFIIEGYTK GDIPDYQMSA LAMAIFFRGM    50
NEEETAELTM AMVHSGDTID LSRIEGIKVD KHSTGGVGDT TTLVLGPLVA 100
SVGVPVAKMS GRGLGHTGGT IDKLESVPGF HVEITNDEFI DLVNKNKIAV 150
VGQSGNLTPA DKKLYALRDV TATVNSIPLI ASSIMSKKIA AGADAIVLDV 200
KTGVGAFMKD LNDAKALAKA MVDIGNRVGR KTMAIISDMS QPLGYAIGNA 250
LEVKEAIDTL KGEGPEDFQE LCLVLGSHMV YLAEKASSLE EARHMLEKAM 300
KDGSALQTFK TFLAAQGGDA SVVDDPSKLP QAKYIIELEA KEDGYVSEIV 350
ADAVGTAAMW LGAGRATKES TIDLAVGLVL RKKVGDAVKK GESLVTIYSN 400
REQVDDVKQK LYENIRISAT PVQAPTLIYD KIS 433
Length:433
Mass (Da):46,332
Last modified:February 1, 1997 - v1
Checksum:i75EF04B8E7B2E0AD
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
D87961 Genomic DNA. Translation: BAA13512.1.
D87959 Genomic DNA. Translation: BAA20903.1.
PIRiJT0875.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
D87961 Genomic DNA. Translation: BAA13512.1 .
D87959 Genomic DNA. Translation: BAA20903.1 .
PIRi JT0875.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1BRW X-ray 2.10 A/B 1-432 [» ]
ProteinModelPortali P77836.
SMRi P77836. Positions 1-432.
ModBasei Search...
MobiDBi Search...

Proteomic databases

PRIDEi P77836.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Enzyme and pathway databases

BioCyci MetaCyc:MONOMER-17881.

Miscellaneous databases

EvolutionaryTracei P77836.

Family and domain databases

Gene3Di 3.40.1030.10. 1 hit.
3.90.1170.30. 1 hit.
InterProi IPR000312. Glycosyl_Trfase_fam3.
IPR017459. Glycosyl_Trfase_fam3_N_dom.
IPR013102. PYNP_C.
IPR018090. Pyrmidine_PPas_bac/euk.
IPR000053. Pyrmidine_PPase.
IPR017872. Pyrmidine_PPase_CS.
[Graphical view ]
PANTHERi PTHR10515. PTHR10515. 1 hit.
Pfami PF02885. Glycos_trans_3N. 1 hit.
PF00591. Glycos_transf_3. 1 hit.
PF07831. PYNP_C. 1 hit.
[Graphical view ]
PIRSFi PIRSF000478. TP_PyNP. 1 hit.
SMARTi SM00941. PYNP_C. 1 hit.
[Graphical view ]
SUPFAMi SSF47648. SSF47648. 1 hit.
SSF52418. SSF52418. 1 hit.
SSF54680. SSF54680. 1 hit.
TIGRFAMsi TIGR02644. Y_phosphoryl. 1 hit.
PROSITEi PS00647. THYMID_PHOSPHORYLASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Molecular cloning and expression of the pyrimidine nucleoside phosphorylase gene from Bacillus stearothermophilus TH 6-2."
    Okuyama K., Hamamoto T., Noguchi T., Midorikawa Y.
    Biosci. Biotechnol. Biochem. 60:1655-1659(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: TH 6-2.
  2. "The crystal structure of pyrimidine nucleoside phosphorylase in a closed conformation."
    Pugmire M.J., Ealick S.E.
    Structure 6:1467-1479(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).

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: September 3, 2014
This is version 96 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

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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