Q96T60 (PNKP_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Bifunctional polynucleotide phosphatase/kinase

Alternative name(s):
DNA 5'-kinase/3'-phosphatase
Polynucleotide kinase-3'-phosphatase

Including the following 2 domains:

1. Polynucleotide 3'-phosphatase
   EC=3.1.3.32
   Alternative name(s):
   2'(3')-polynucleotidase
2. Polynucleotide 5'-hydroxyl-kinase
   EC=2.7.1.78

Gene names

Name:

PNKP

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	521 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Plays a key role in the repair of DNA damage, functioning as part of both the non-homologous end-joining (NHEJ) and base excision repair (BER) pathways. Through its two catalytic activities, PNK ensures that DNA termini are compatible with extension and ligation by either removing 3'-phosphates from, or by phosphorylating 5'-hydroxyl groups on, the ribose sugar of the DNA backbone. Ref.1
Catalytic activity	A 3'-phosphopolynucleotide + H2O = a polynucleotide + phosphate. ATP + 5'-dephospho-DNA = ADP + 5'-phospho-DNA.
Subunit structure	Monomer By similarity.
Subcellular location	Nucleus Ref.2.
Tissue specificity	Expressed in many tissues with highest expression in spleen and testis, and lowest expression in small intestine (Ref.1). Expressed in higher amount in pancreas, heart and kidney and at lower levels in brain, lung and liver (Ref.2). Ref.1 Ref.2
Domain	The FHA domain binds threonine-phosphorylated peptides from XRCC1/4, and is responsible for the recruitment of PNKP to the sites of DNA repair. The affinity is ten times greater if peptides are also phosphorylated on the serine preceeding the phosphothreonine. Ref.14
Involvement in disease	Epileptic encephalopathy, early infantile, 10 (EIEE10) [MIM:613402]: A disease characterized by infantile-onset seizures, microcephaly, severe intellectual disability and delayed motor milestones with absent speech or only achieving a few words. Most patients also have behavioral problems with hyperactivity. Microcephaly is progressive and without neuronal migration or structural abnormalities, consistent with primary microcephaly. Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.15
Sequence similarities	In the N-terminal section; belongs to the DNA 3' phosphatase family. Contains 1 FHA domain.
Sequence caution	The sequence AAD47379.1 differs from that shown. Reason: Frameshift at several positions.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Cellular component	Nucleus
Coding sequence diversity	Polymorphism
Disease	Disease mutation Primary microcephaly
Ligand	ATP-binding Nucleotide-binding
Molecular function	Hydrolase Kinase Transferase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Multifunctional enzyme Reference proteome
Gene Ontology (GO)
Biological_process	DNA damage response, detection of DNA damage Inferred from direct assay Ref.1. Source: UniProtKB DNA-dependent DNA replication Non-traceable author statement Ref.1. Source: UniProtKB nucleotide-excision repair, DNA damage removal Non-traceable author statement Ref.2. Source: UniProtKB response to oxidative stress Inferred from direct assay Ref.1. Source: UniProtKB response to radiation Non-traceable author statement Ref.2. Source: UniProtKB
Cellular_component	nucleolus Inferred from direct assay. Source: HPA
Molecular_function	ATP binding Non-traceable author statement Ref.1. Source: UniProtKB ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity Inferred from direct assay Ref.2. Source: UniProtKB damaged DNA binding Non-traceable author statement Ref.2. Source: UniProtKB double-stranded DNA binding Traceable author statement Ref.2. Source: UniProtKB endonuclease activity Non-traceable author statement Ref.1. Source: UniProtKB nucleotide kinase activity Inferred from direct assay Ref.1Ref.2. Source: UniProtKB polynucleotide 3'-phosphatase activity Inferred from direct assay Ref.1Ref.2. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 521

521

Bifunctional polynucleotide phosphatase/kinase

PRO_0000058478

Regions

Domain

6 – 110

105

FHA

Nucleotide binding

372 – 379

8

ATP Potential

Region

146 – 337

192

Phosphatase By similarity

Region

341 – 516

176

Kinase By similarity

Amino acid modifications

Modified residue

114

1

Phosphoserine Ref.13

Modified residue

118

1

Phosphothreonine Ref.9 Ref.10 Ref.11 Ref.13

Modified residue

122

1

Phosphothreonine Ref.8 Ref.9 Ref.10

Natural variations

Natural variant

20

1

P → S. Ref.5
Corresponds to variant rs3739168 [ dbSNP | Ensembl ].

VAR_019260

Natural variant

63

1

A → V. Ref.5
Corresponds to variant rs3739173 [ dbSNP | Ensembl ].

VAR_019261

Natural variant

176

1

L → F in EIEE10. Ref.15

VAR_063835

Natural variant

180

1

R → S. Ref.5
Corresponds to variant rs3739185 [ dbSNP | Ensembl ].

VAR_019262

Natural variant

196

1

Y → N. Ref.5
Corresponds to variant rs3739186 [ dbSNP | Ensembl ].

VAR_019263

Natural variant

326

1

E → K in EIEE10. Ref.15

VAR_063836

Natural variant

478

1

V → G. Ref.5
Corresponds to variant rs3739206 [ dbSNP | Ensembl ].

VAR_019264

Experimental info

Sequence conflict

6

1

A → P in AAD50639. Ref.2

Sequence conflict

18

1

G → E in AAD51135. Ref.1

Sequence conflict

458

1

R → C in AAD47379. Ref.3

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

521

Helix Strand Turn

Details...

Beta strand

9 – 13

5

Beta strand

31 – 33

3

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 – 107

9

Sequences

	Sequence		Length	Mass (Da)
	Q96T60 [UniParc]. Last modified December 1, 2001. Version 1. Checksum: 22B5C94D41E62516	FASTA	521	57,076
	10 20 30 40 50 60 MGEVEAPGRL WLESPPGGAP PIFLPSDGQA LVLGRGPLTQ VTDRKCSRTQ VELVADPETR 70 80 90 100 110 120 TVAVKQLGVN PSTTGTQELK PGLEGSLGVG DTLYLVNGLH PLTLRWEETR TPESQPDTPP 130 140 150 160 170 180 GTPLVSQDEK RDAELPKKRM RKSNPGWENL EKLLVFTAAG VKPQGKVAGF DLDGTLITTR 190 200 210 220 230 240 SGKVFPTGPS DWRILYPEIP RKLRELEAEG YKLVIFTNQM SIGRGKLPAE EFKAKVEAVV 250 260 270 280 290 300 EKLGVPFQVL VATHAGLYRK PVTGMWDHLQ EQANDGTPIS IGDSIFVGDA AGRPANWAPG 310 320 330 340 350 360 RKKKDFSCAD RLFALNLGLP FATPEEFFLK WPAAGFELPA FDPRTVSRSG PLCLPESRAL 370 380 390 400 410 420 LSASPEVVVA VGFPGAGKST FLKKHLVSAG YVHVNRDTLG SWQRCVTTCE TALKQGKRVA 430 440 450 460 470 480 IDNTNPDAAS RARYVQCARA AGVPCRCFLF TATLEQARHN NRFREMTDSS HIPVSDMVMY 490 500 510 520 GYRKQFEAPT LAEGFSAILE IPFRLWVEPR LGRLYCQFSE G

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Molecular cloning of the human gene, PNKP, encoding a polynucleotide kinase 3'-phosphatase and evidence for its role in repair of DNA strand breaks caused by oxidative damage." Jilani A., Ramotar D., Slack C., Ong C., Yang X.M., Scherer S.W., Lasko D.D. J. Biol. Chem. 274:24176-24186(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY.
[2]	"Molecular characterization of a human DNA kinase." Karimi-Busheri F., Daly G., Robins P., Canas B., Pappin D.J.C., Sgouros J., Miller G.G., Fakhrai H., Davis E.M., Le Beau M.M., Weinfeld M. J. Biol. Chem. 274:24187-24194(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], PARTIAL PROTEIN SEQUENCE, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, CHARACTERIZATION.
[3]	"Cloning a cDNA which is differently expressed in malignancies." Yang H.W., Piao H.Y., Chen Y.Z., Hayashi Y. Submitted (JUL-1998) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[4]	"Genomic organization, physical mapping and expression analysis of the human polynucleotide kinase-3'-phosphatase (PNKP) gene." Scorilas A., Katsaros N. Submitted (FEB-2001) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[5]	NIEHS SNPs program Submitted (JUL-2002) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANTS SER-20; VAL-63; SER-180; ASN-196 AND GLY-478.
[6]	"The DNA sequence and biology of human chromosome 19." Grimwood J., Gordon L.A., Olsen A.S., Terry A., Schmutz J., Lamerdin J.E., Hellsten U., Goodstein D., Couronne O., Tran-Gyamfi M., Aerts A., Altherr M., Ashworth L., Bajorek E., Black S., Branscomb E., Caenepeel S., Carrano A.V. , Caoile C., Chan Y.M., Christensen M., Cleland C.A., Copeland A., Dalin E., Dehal P., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Garcia C., Georgescu A.M., Glavina T., Gomez M., Gonzales E., Groza M., Hammon N., Hawkins T., Haydu L., Ho I., Huang W., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Larionov V., Leem S.-H., Lopez F., Lou Y., Lowry S., Malfatti S., Martinez D., McCready P.M., Medina C., Morgan J., Nelson K., Nolan M., Ovcharenko I., Pitluck S., Pollard M., Popkie A.P., Predki P., Quan G., Ramirez L., Rash S., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., She X., Smith D., Slezak T., Solovyev V., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wagner M., Wheeler J., Wu K., Xie G., Yang J., Dubchak I., Furey T.S., DeJong P., Dickson M., Gordon D., Eichler E.E., Pennacchio L.A., Richardson P., Stubbs L., Rokhsar D.S., Myers R.M., Rubin E.M., Lucas S.M. Nature 428:529-535(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[7]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Blood.
[8]	"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks." Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M. Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-122, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[9]	"A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-118 AND THR-122, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[10]	"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions." Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K. Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-118 AND THR-122, MASS SPECTROMETRY. Tissue: Leukemic T-cell.
[11]	"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis." Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M. Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-118, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[12]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[13]	"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation." Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B. Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-114 AND THR-118, MASS SPECTROMETRY.
[14]	"Specific recognition of a multiply phosphorylated motif in the DNA repair scaffold XRCC1 by the FHA domain of human PNK." Ali A.A., Jukes R.M., Pearl L.H., Oliver A.W. Nucleic Acids Res. 37:1701-1712(2009) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS) OF 1-110 ALONE AND IN COMPLEX WITH XRCC1 PHOSPHOPEPTIDE, DOMAIN FHA.
[15]	"Mutations in PNKP cause microcephaly, seizures and defects in DNA repair." Shen J., Gilmore E.C., Marshall C.A., Haddadin M., Reynolds J.J., Eyaid W., Bodell A., Barry B., Gleason D., Allen K., Ganesh V.S., Chang B.S., Grix A., Hill R.S., Topcu M., Caldecott K.W., Barkovich A.J., Walsh C.A. Nat. Genet. 42:245-249(2010) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANTS EIEE10 PHE-176 AND LYS-326.
+	Additional computationally mapped references.

Web resources

NIEHS-SNPs

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF126486 mRNA. Translation: AAD51135.1.
AF125807 mRNA. Translation: AAD50639.1.
AF120499 mRNA. Translation: AAD47379.1. Frameshift.
AF354258 Genomic DNA. Translation: AAK57340.1.
AY133033 Genomic DNA. Translation: AAM82170.1.
AC018766 Genomic DNA. Translation: AAF44716.1.
BC033822 mRNA. Translation: AAH33822.1.

IPI

IPI00290684.

RefSeq

NP_009185.2. NM_007254.3.

UniGene

Hs.78016.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2BRF	X-ray	1.40	A	1-110	[»]
2W3O	X-ray	1.85	A/B	1-110	[»]

ProteinModelPortal

Q96T60.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q96T60. 6 interactions.

MINT

MINT-1199136.

STRING

9606.ENSP00000323511.

PTM databases

PhosphoSite

Q96T60.

Polymorphism databases

DMDM

50401132.

Proteomic databases

PaxDb

Q96T60.

PRIDE

Q96T60.

Protocols and materials databases

DNASU

11284.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000322344; ENSP00000323511; ENSG00000039650.
ENST00000596014; ENSP00000472300; ENSG00000039650.

GeneID

11284.

KEGG

hsa:11284.

UCSC

uc002pqg.3. human.

Organism-specific databases

CTD

11284.

GeneCards

GC19M050364.

HGNC

HGNC:9154. PNKP.

HPA

HPA006782.

MIM

605610. gene.
613402. phenotype.

neXtProt

NX_Q96T60.

Orphanet

228418. Microcephaly - seizures - developmental delay.

PharmGKB

PA33477.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG0241.

HOGENOM

HOG000031466.

HOVERGEN

HBG053624.

InParanoid

Q96T60.

KO

K08073.

OMA

SWQRCVT.

OrthoDB

EOG4TF0K0.

PhylomeDB

Q96T60.

Gene expression databases

Bgee

Q96T60.

CleanEx

HS_PNKP.

Genevestigator

Q96T60.

GermOnline

ENSG00000039650. Homo sapiens.

Family and domain databases

Gene3D

2.60.200.20. 1 hit.
3.40.50.1000. 1 hit.

InterPro

IPR000253. FHA_dom.
IPR023214. HAD-like_dom.
IPR006549. HAD-SF_hydro_IIIA.
IPR027417. P-loop_NTPase.
IPR013954. PNK3P.
IPR015636. PNK_3Pase_euk.
IPR006550. PNK_3Pase_met.
IPR006551. Polynucleotide_phosphatase.
IPR008984. SMAD_FHA_domain.
[Graphical view]

PANTHER

PTHR12083. PTHR12083. 1 hit.

Pfam

PF08645. PNK3P. 1 hit.
[Graphical view]

SUPFAM

SSF56784. HAD-like_dom. 1 hit.
SSF49879. SMAD_FHA. 1 hit.
SSF52540. SSF52540. 1 hit.

TIGRFAMs

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

PROSITE

PS50006. FHA_DOMAIN. False negative.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q96T60.

GenomeRNAi

11284.

NextBio

42959.

SOURCE

Search...

Entry information

Entry name

PNKP_HUMAN

Accession

Primary (citable) accession number: Q96T60
Secondary accession number(s): Q9P1V2 , Q9UKU8, Q9UNF8, Q9UNI0

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 19, 2004
Last sequence update:	December 1, 2001
Last modified:	May 29, 2013
This is version 114 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.