Reviewed, UniProtKB/Swiss-Prot Q9JLV6 (PNKP_MOUSE)

Names and origin

Protein names

Recommended name:
    Bifunctional polynucleotide phosphatase/kinase
Alternative name(s):
    Polynucleotide kinase-3'-phosphatase
    DNA 5'-kinase/3'-phosphatase
Including the following 2 domains:
    1- Recommended name:
            Polynucleotide 3'-phosphatase
              EC=3.1.3.32
        Alternative name(s):
            2'(3')-polynucleotidase
    2- Recommended name:
            Polynucleotide 5'-hydroxyl-kinase
              EC=2.7.1.78

Gene names

Name:

Pnkp

Organism

Mus musculus (Mouse)

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus

Protein attributes

Sequence length	522 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Catalyzes the phosphorylation of DNA at 5'-hydroxyl termini and can dephosphorylate its 3'-phosphate termini. Plays an important function in DNA repair following ionizing radiation or oxidative damage By similarity.
Catalytic activity	A 3'-phosphopolynucleotide + H2O = a polynucleotide + phosphate. ATP + 5'-dephospho-DNA = ADP + 5'-phospho-DNA.
Subcellular location	Nucleus By similarity.
Post-translational modification	Phosphorylated upon DNA damage, probably by ATM or ATR. Ref.3
Sequence similarities	In the N-terminal section; belongs to the DNA 3' phosphatase family.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Ligand	ATP-binding Nucleotide-binding
Molecular function	Hydrolase Kinase Transferase
PTM	Phosphoprotein
Technical term	3D-structure Multifunctional enzyme
Gene Ontology (GO)
Biological process	DNA repair Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity Inferred from electronic annotation. Source: EC polynucleotide 3'-phosphatase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q9JLV6-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: Q9JLV6-2)

The sequence of this isoform differs from the canonical sequence as follows:
     163-191: QGKVAAFDLDGTLITTRSGKVFPTSPSDW → RA

Note: No experimental confirmation available.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 522

522

Bifunctional polynucleotide phosphatase/kinase

PRO_0000058479

Regions

Nucleotide binding

371 – 378

8

ATP Potential

Amino acid modifications

Modified residue

114

1

Phosphoserine Ref.3

Modified residue

122

1

Phosphothreonine Ref.3

Natural variations

Alternative sequence

163 – 191

29

QGKVA…SPSDW → RA in isoform 2.

VSP_010771

Experimental info

Sequence conflict

77

1

H → Q in AAF36487. Ref.1

Sequence conflict

216

1

Missing in AAF36487. Ref.1

Secondary structure

1

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522

Helix Strand Turn

Details...

Beta strand

6 – 13

8

Beta strand

31 – 36

6

Turn

37 – 40

4

Beta strand

51 – 56

6

Turn

57 – 60

4

Beta strand

61 – 66

6

Beta strand

68 – 70

3

Beta strand

84 – 88

5

Beta strand

92 – 96

5

Beta strand

99 – 108

10

Beta strand

146 – 149

4

Beta strand

152 – 156

5

Beta strand

166 – 169

4

Turn

172 – 174

3

Beta strand

175 – 177

3

Beta strand

179 – 181

3

Beta strand

192 – 194

3

Helix

198 – 208

11

Beta strand

211 – 217

7

Helix

219 – 222

4

Helix

228 – 242

15

Beta strand

247 – 251

5

Beta strand

253 – 258

6

Helix

263 – 270

8

Beta strand

272 – 275

4

Helix

280 – 282

3

Beta strand

284 – 286

3

Helix

308 – 316

9

Helix

323 – 326

4

Helix

342 – 344

3

Beta strand

351 – 354

4

Beta strand

366 – 370

5

Helix

377 – 384

8

Helix

386 – 388

3

Beta strand

391 – 394

4

Helix

395 – 398

4

Helix

401 – 413

13

Beta strand

418 – 422

5

Helix

427 – 440

14

Beta strand

444 – 449

6

Helix

453 – 466

14

Helix

475 – 484

10

Helix

490 – 492

3

Beta strand

497 – 500

4

Helix

510 – 516

7

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified July 19, 2004. Version 2. Checksum: C691C0A6DA9F47FE	FASTA	522	57,223
	10 20 30 40 50 60 MSQLGSRGRL WLQSPTGGPP PIFLPSDGQA LVLGRGPLTQ VTDRKCSRNQ VELIADPESR 70 80 90 100 110 120 TVAVKQLGVN PSTVGVHELK PGLSGSLSLG DVLYLVNGLY PLTLRWEELS TSGSQPDAPP 130 140 150 160 170 180 DTPGDPEEGE DTEPQKKRVR KSSLGWESLK KLLVFTASGV KPQGKVAAFD LDGTLITTRS 190 200 210 220 230 240 GKVFPTSPSD WRILYPEIPK KLQELAAEGY KLVIFTNQMG IGRGKLPAEV FKGKVEAVLE 250 260 270 280 290 300 KLGVPFQVLV ATHAGLNRKP VSGMWDHLQE QANEGIPISV EDSVFVGDAA GRLANWAPGR 310 320 330 340 350 360 KKKDFSCADR LFALNVGLPF ATPEEFFLKW PAARFELPAF DPRTISSAGP LYLPESSSLL 370 380 390 400 410 420 SPNPEVVVAV GFPGAGKSTF IQEHLVSAGY VHVNRDTLGS WQRCVSSCQA ALRQGKRVVI 430 440 450 460 470 480 DNTNPDVPSR ARYIQCAKDA GVPCRCFNFC ATIEQARHNN RFREMTDPSH APVSDMVMFS 490 500 510 520 YRKQFEPPTL AEGFLEILEI PFRLQEHLDP ALQRLYRQFS EG
	Isoform 2. Checksum: 6FE381B1531C953C	FASTA	495	54,373
	10 20 30 40 50 60 MSQLGSRGRL WLQSPTGGPP PIFLPSDGQA LVLGRGPLTQ VTDRKCSRNQ VELIADPESR 70 80 90 100 110 120 TVAVKQLGVN PSTVGVHELK PGLSGSLSLG DVLYLVNGLY PLTLRWEELS TSGSQPDAPP 130 140 150 160 170 180 DTPGDPEEGE DTEPQKKRVR KSSLGWESLK KLLVFTASGV KPRARILYPE IPKKLQELAA 190 200 210 220 230 240 EGYKLVIFTN QMGIGRGKLP AEVFKGKVEA VLEKLGVPFQ VLVATHAGLN RKPVSGMWDH 250 260 270 280 290 300 LQEQANEGIP ISVEDSVFVG DAAGRLANWA PGRKKKDFSC ADRLFALNVG LPFATPEEFF 310 320 330 340 350 360 LKWPAARFEL PAFDPRTISS AGPLYLPESS SLLSPNPEVV VAVGFPGAGK STFIQEHLVS 370 380 390 400 410 420 AGYVHVNRDT LGSWQRCVSS CQAALRQGKR VVIDNTNPDV PSRARYIQCA KDAGVPCRCF 430 440 450 460 470 480 NFCATIEQAR HNNRFREMTD PSHAPVSDMV MFSYRKQFEP PTLAEGFLEI LEIPFRLQEH 490 LDPALQRLYR QFSEG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	Beaulieu N., Lasko D.D. Submitted (FEB-1999) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2). Strain: C57BL/6J. Tissue: Spleen.
[2]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Strain: C57BL/6J. Tissue: Mammary tumor.
[3]	"ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage." Matsuoka S., Ballif B.A., Smogorzewska A., McDonald E.R. III, Hurov K.E., Luo J., Bakalarski C.E., Zhao Z., Solimini N., Lerenthal Y., Shiloh Y., Gygi S.P., Elledge S.J. Science 316:1160-1166(2007) [PubMed: 17525332] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-114 AND THR-122, MASS SPECTROMETRY.
[4]	"The forkhead-associated (FHA) domain-like structure from mouse polynucleotide kinase 3'-phosphatase." RIKEN structural genomics initiative (RSGI) Submitted (FEB-2004) to the PDB data bank Cited for: STRUCTURE BY NMR OF 1-106.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF129451 mRNA. Translation: AAF36487.1.
BC057659 mRNA. Translation: AAH57659.1.

IPI

IPI00124762.
IPI00454118.

UniGene

Mm.238254

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1UJX	NMR	-	A	1-106	[»]
1YJ5	X-ray	2.80	A/B	140-522	[»]
			C	1-143	[»]
1YJM	X-ray	2.20	A/B/C	1-110	[»]

ModBase

Search...

Protein-protein interaction databases

STRING

Q9JLV6.

PTM databases

PhosphoSite

Q9JLV6.

Proteomic databases

PRIDE

Q9JLV6.

Genome annotation databases

Ensembl

ENSMUST00000003044; ENSMUSP00000003044; ENSMUSG00000002963; Mus musculus. [Genome view]
ENSMUST00000085410; ENSMUSP00000082531; ENSMUSG00000002963; Mus musculus. [Genome view]
ENSMUST00000107876; ENSMUSP00000103508; ENSMUSG00000002963; Mus musculus. [Genome view]

UCSC

uc009grf.1. mouse.

Organism-specific databases

MGI

MGI:1891698. Pnkp.

Phylogenomic databases

HOGENOM

HBG714111.

HOVERGEN

Q9JLV6.

InParanoid

Q9JLV6.

Enzyme and pathway databases

BRENDA

2.7.1.78. 244.
3.1.3.32. 244.

Gene expression databases

ArrayExpress

Q9JLV6.

Bgee

Q9JLV6.

CleanEx

MM_PNKP.

Genevestigator

Q9JLV6.

GermOnline

ENSMUSG00000002963. Mus musculus.

Family and domain databases

InterPro

IPR006551. DNA-3-Pase.
IPR006549. HAD-SF_hydro_IIIA.
IPR006550. PNK-3Pase.
IPR015636. PNK_3Pase.
IPR008984. SMAD_FHA_domain.
[Graphical view]

PANTHER

PTHR12083. PNK_3Pase. 1 hit.

TIGRFAMs

TIGR01664. DNA-3_-Pase. 1 hit.
TIGR01662. HAD-SF-IIIA. 1 hit.
TIGR01663. PNK-3_Pase. 1 hit.

ProtoNet

Search...

Other Resources

SOURCE

Search...

Entry information

Entry name

PNKP_MOUSE

Accession

Primary (citable) accession number: Q9JLV6
Secondary accession number(s): Q6PFA3

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 19, 2004
Last sequence update:	July 19, 2004
Last modified:	February 9, 2010
This is version 67 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)