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P77836

- PDP_GEOSE

UniProt

P77836 - PDP_GEOSE

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Protein

Pyrimidine-nucleoside phosphorylase

Gene

pdp

Organism
Geobacillus stearothermophilus (Bacillus stearothermophilus)
Status
Reviewed - Annotation score: 3 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

K(+)Note: 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 phosphorylasePRO_0000059083Add
BLAST

Proteomic databases

PRIDEiP77836.

Interactioni

Subunit structurei

Homodimer.

Structurei

Secondary structure

1
433
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 119Combined sources
Helixi18 – 2912Combined sources
Helixi35 – 4814Combined sources
Helixi52 – 6413Combined sources
Beta strandi79 – 835Combined sources
Helixi91 – 10010Combined sources
Turni101 – 1033Combined sources
Beta strandi106 – 1105Combined sources
Helixi120 – 1245Combined sources
Helixi136 – 14611Combined sources
Beta strandi147 – 1526Combined sources
Helixi159 – 17012Combined sources
Helixi177 – 19115Combined sources
Beta strandi194 – 20310Combined sources
Helixi211 – 22717Combined sources
Beta strandi231 – 2388Combined sources
Beta strandi243 – 2497Combined sources
Helixi250 – 26011Combined sources
Helixi266 – 28217Combined sources
Beta strandi285 – 2884Combined sources
Helixi289 – 30214Combined sources
Helixi304 – 31512Combined sources
Helixi320 – 3223Combined sources
Helixi326 – 3283Combined sources
Beta strandi333 – 3397Combined sources
Beta strandi341 – 3499Combined sources
Helixi351 – 36111Combined sources
Beta strandi377 – 3815Combined sources
Beta strandi393 – 40210Combined sources
Helixi405 – 4128Combined sources
Beta strandi415 – 4206Combined sources
Beta strandi427 – 4326Combined sources

3D structure databases

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

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

        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.

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 .
PIRi JT0875.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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: November 26, 2014
This is version 98 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