P77836 (PDP_GEOSE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Pyrimidine-nucleoside phosphorylase
Short name=PYNP
EC=2.4.2.2

Gene names

Name:	pdp
Synonyms:	pyn

Organism

Geobacillus stearothermophilus (Bacillus stearothermophilus)

Taxonomic identifier

1422 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Firmicutes › Bacilli › Bacillales › Bacillaceae › Geobacillus

Protein attributes

Sequence length	433 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Catalytic activity	A pyrimidine nucleoside + phosphate = a pyrimidine base + alpha-D-ribose 1-phosphate.
Cofactor	Binds 1 potassium ion per subunit.
Subunit structure	Homodimer.
Sequence similarities	Belongs to the thymidine/pyrimidine-nucleoside phosphorylase family.

Ontologies

Keywords
Ligand	Metal-binding
Molecular function	Glycosyltransferase Transferase
Technical term	3D-structure
Gene Ontology (GO)
Biological_process	pyrimidine nucleobase metabolic process Inferred from electronic annotation. Source: InterPro pyrimidine nucleoside metabolic process Inferred from electronic annotation. Source: InterPro
Molecular_function	metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW phosphorylase activity Inferred from electronic annotation. Source: InterPro pyrimidine-nucleoside phosphorylase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 433

433

Pyrimidine-nucleoside phosphorylase

PRO_0000059083

Sites

Metal binding

88

1

Potassium; via carbonyl oxygen

Metal binding

90

1

Potassium

Metal binding

243

1

Potassium; via carbonyl oxygen

Metal binding

246

1

Potassium; via carbonyl oxygen

Metal binding

255

1

Potassium

Secondary structure

1

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433

Helix Strand Turn

Details...

Helix

3 – 11

9

Helix

18 – 29

12

Helix

35 – 48

14

Helix

52 – 64

13

Beta strand

79 – 83

5

Helix

91 – 100

10

Turn

101 – 103

3

Beta strand

106 – 110

5

Helix

120 – 124

5

Helix

136 – 146

11

Beta strand

147 – 152

6

Helix

159 – 170

12

Helix

177 – 191

15

Beta strand

194 – 203

10

Helix

211 – 227

17

Beta strand

231 – 238

8

Beta strand

243 – 249

7

Helix

250 – 260

11

Helix

266 – 282

17

Beta strand

285 – 288

4

Helix

289 – 302

14

Helix

304 – 315

12

Helix

320 – 322

3

Helix

326 – 328

3

Beta strand

333 – 339

7

Beta strand

341 – 349

9

Helix

351 – 361

11

Beta strand

377 – 381

5

Beta strand

393 – 402

10

Helix

405 – 408

4

Sequences

	Sequence		Length	Mass (Da)
	P77836 [UniParc]. Last modified February 1, 1997. Version 1. Checksum: 75EF04B8E7B2E0AD	FASTA	433	46,332
	10 20 30 40 50 60 MRMVDLIEKK RDGHALTKEE IQFIIEGYTK GDIPDYQMSA LAMAIFFRGM NEEETAELTM 70 80 90 100 110 120 AMVHSGDTID LSRIEGIKVD KHSTGGVGDT TTLVLGPLVA SVGVPVAKMS GRGLGHTGGT 130 140 150 160 170 180 IDKLESVPGF HVEITNDEFI DLVNKNKIAV VGQSGNLTPA DKKLYALRDV TATVNSIPLI 190 200 210 220 230 240 ASSIMSKKIA AGADAIVLDV KTGVGAFMKD LNDAKALAKA MVDIGNRVGR KTMAIISDMS 250 260 270 280 290 300 QPLGYAIGNA LEVKEAIDTL KGEGPEDFQE LCLVLGSHMV YLAEKASSLE EARHMLEKAM 310 320 330 340 350 360 KDGSALQTFK TFLAAQGGDA SVVDDPSKLP QAKYIIELEA KEDGYVSEIV ADAVGTAAMW 370 380 390 400 410 420 LGAGRATKES TIDLAVGLVL RKKVGDAVKK GESLVTIYSN REQVDDVKQK LYENIRISAT 430 PVQAPTLIYD KIS

References

[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).

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

D87961 Genomic DNA. Translation: BAA13512.1.
D87959 Genomic DNA. Translation: BAA20903.1.

PIR

JT0875.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1BRW	X-ray	2.10	A/B	1-408	[»]

ProteinModelPortal

P77836.

SMR

P77836. Positions 1-432.

ModBase

Search...

Proteomic databases

PRIDE

P77836.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

Gene3D

3.40.1030.10. 1 hit.
3.90.1170.30. 1 hit.

InterPro

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]

PANTHER

PTHR10515. PTHR10515. 1 hit.

Pfam

PF02885. Glycos_trans_3N. 1 hit.
PF00591. Glycos_transf_3. 1 hit.
PF07831. PYNP_C. 1 hit.
[Graphical view]

PIRSF

PIRSF000478. TP_PyNP. 1 hit.

SMART

SM00941. PYNP_C. 1 hit.
[Graphical view]

SUPFAM

SSF47648. Glyco_trans_3. 1 hit.
SSF52418. Glyco_trans_3. 1 hit.
SSF54680. PYNP_C. 1 hit.

TIGRFAMs

TIGR02644. Y_phosphoryl. 1 hit.

PROSITE

PS00647. THYMID_PHOSPHORYLASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P77836.

Entry information

Entry name

PDP_GEOSE

Accession

Primary (citable) accession number: P77836

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	February 1, 1997
Last modified:	April 3, 2013
This is version 89 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program