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Description:
Bifunctional polynucleotide phosphatase/kinase (Polynucleotide kinase-3'-phosphatase) (DNA 5'-kinase/3'-phosphatase) [Includes:Polynucleotide 3'-phosphatase (EC 3.1.3.32) (2'(3')-polynucleotidase);Polynucleotide 5'-hydroxyl-kinase (EC 2.7.1.78)].
Molecular weight: 57076
View which proteins in this organism that is involved with DNA Repair;
classified after biological processes (using data from the GOA project):
nucleotide-excision repair, DNA damage removal( GO:0000718 ) DNA repair( GO:0006281 )
Important dates:
19-JUL-2004, integrated into UniProtKB/Swiss-Prot.
01-DEC-2001, sequence version 1.
07-MAR-2006, entry version 29.
Phylogenetic order:
Eukaryota Metazoa Chordata Craniata Vertebrata Euteleostomi Mammalia Eutheria Euarchontoglires Primates Catarrhini Hominidae Homo.
To calculate the pI (Isoelectric point - the pH where a protein has a neutral charge),
go to this page and enter the protein ID (e.g 3MG_ECOLI): http://us.expasy.org/tools/pi_tool.html
Links to references in other databases for protein PNKP_HUMAN:
| Database | Pointer | Add. info#1 | Add. info#2 |
| EMBL | AF126486 | AAD51135.1 | - |
| EMBL | AF125807 | AAD50639.1 | - |
| EMBL | AF354258 | AAK57340.1 | - |
| EMBL | AY133033 | AAM82170.1 | - |
| EMBL | AC018766 | AAF44716.1 | - |
| EMBL | BC033822 | AAH33822.1 | - |
| PDB | 2BRF | X-ray | A=1-110. |
| SMR | Q96T60 | 141-521.1 | |
| Ensembl | ENSG00000039650 | Homo sapiens.1 | |
| HGNC | HGNC:9154 | PNKP.1 | |
| MIM | 605610 | gene. | |
| GO | GO:0005634 | C:nucleus | IDA. |
| GO | GO:0005524 | F:ATP binding | NAS. |
| GO | GO:0003684 | F:damaged DNA binding | NAS. |
| GO | GO:0003690 | F:double-stranded DNA binding | TAS. |
| GO | GO:0004519 | F:endonuclease activity | NAS. |
| GO | GO:0019201 | F:nucleotide kinase activity | IDA. |
| GO | GO:0046403 | F:polynucleotide 3'-phosphatase activity | IDA. |
| GO | GO:0046404 | F:polynucleotide 5'-hydroxyl-kinase activity | IDA. |
| GO | GO:0017076 | F:purine nucleotide binding | NAS. |
| GO | GO:0016311 | P:dephosphorylation | IDA. |
| GO | GO:0042769 | P:DNA damage response, perception of DNA damage | IDA. |
| GO | GO:0006281 | P:DNA repair | IGI. |
| GO | GO:0006261 | P:DNA-dependent DNA replication | NAS. |
| GO | GO:0046939 | P:nucleotide phosphorylation | IDA. |
| GO | GO:0000718 | P:nucleotide-excision repair, DNA damage removal | NAS. |
| GO | GO:0006979 | P:response to oxidative stress | IDA. |
| GO | GO:0009314 | P:response to radiation | TAS. |
| InterPro | IPR006551 | DNA-3-Pase. | |
| InterPro | IPR006549 | HAD_SF-IIIA. | |
| InterPro | IPR006550 | PNK-3Pase. | |
| TIGRFAMs | TIGR01664 | DNA-3-Pase | 1. |
| TIGRFAMs | TIGR01662 | HAD-SF-IIIA | 1. |
| TIGRFAMs | TIGR01663 | PNK-3Pase | 1. |
Keywords:
3D-structure; ATP-binding; Direct protein sequencing; DNA damage; DNA repair; Hydrolase; Kinase; Multifunctional enzyme; Nuclear protein; Nucleotide-binding; Polymorphism; Transferase.
References:
RN [1]
RP NUCLEOTIDE SEQUENCE, FUNCTION, AND TISSUE SPECIFICITY.
RX MEDLINE=99377055; PubMed=10446192; DOI=10.1074/jbc.274.34.24176;
RA Jilani A., Ramotar D., Slack C., Ong C., Yang X.M., Scherer S.W.,
RA Lasko D.D.;
RT "Molecular cloning of the human gene, PNKP, encoding a polynucleotide
RT kinase 3'-phosphatase and evidence for its role in repair of DNA
RT strand breaks caused by oxidative damage.";
RL J. Biol. Chem. 274:24176-24186(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE, PARTIAL PROTEIN SEQUENCE, SUBCELLULAR LOCATION,
RP TISSUE SPECIFICITY, AND CHARACTERIZATION.
RX MEDLINE=99377056; PubMed=10446193; DOI=10.1074/jbc.274.34.24187;
RA Karimi-Busheri F., Daly G., Robins P., Canas B., Pappin D.J.C.,
RA Sgouros J., Miller G.G., Fakhrai H., Davis E.M., Le Beau M.M.,
RA Weinfeld M.;
RT "Molecular characterization of a human DNA kinase.";
RL J. Biol. Chem. 274:24187-24194(1999).
RN [3]
RP NUCLEOTIDE SEQUENCE.
RA Scorilas A., Katsaros N.;
RT "Genomic organization, physical mapping and expression analysis of the
RT human polynucleotide kinase-3'-phosphatase (PNKP) gene.";
RL Submitted (FEB-2001) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANTS SER-20; VAL-63;
RP SER-180; ASN-196 AND GLY-478.
RA Rieder M.J., Livingston R.J., Braun A.C., Montoya M.A., Chung M.-W.,
RA Miyamoto K.E., Nguyen C.P., Nguyen D.A., Poel C.L., Robertson P.D.,
RA Schackwitz W.S., Sherwood J.K., Witrak L.A., Nickerson D.A.;
RT "NIEHS-SNPs, environmental genome project, NIEHS ES15478, Department
RT of Genome Sciences, Seattle, WA (URL: http://egp.gs.washington.edu).";
RL Submitted (JUL-2002) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=15057824; DOI=10.1038/nature02399;
RA Grimwood J., Gordon L.A., Olsen A.S., Terry A., Schmutz J.,
RA Lamerdin J.E., Hellsten U., Goodstein D., Couronne O., Tran-Gyamfi M.,
RA Aerts A., Altherr M., Ashworth L., Bajorek E., Black S., Branscomb E.,
RA Caenepeel S., Carrano A.V., Caoile C., Chan Y.M., Christensen M.,
RA Cleland C.A., Copeland A., Dalin E., Dehal P., Denys M., Detter J.C.,
RA Escobar J., Flowers D., Fotopulos D., Garcia C., Georgescu A.M.,
RA Glavina T., Gomez M., Gonzales E., Groza M., Hammon N., Hawkins T.,
RA Haydu L., Ho I., Huang W., Israni S., Jett J., Kadner K., Kimball H.,
RA Kobayashi A., Larionov V., Leem S.-H., Lopez F., Lou Y., Lowry S.,
RA Malfatti S., Martinez D., McCready P.M., Medina C., Morgan J.,
RA Nelson K., Nolan M., Ovcharenko I., Pitluck S., Pollard M.,
RA Popkie A.P., Predki P., Quan G., Ramirez L., Rash S., Retterer J.,
RA Rodriguez A., Rogers S., Salamov A., Salazar A., She X., Smith D.,
RA Slezak T., Solovyev V., Thayer N., Tice H., Tsai M., Ustaszewska A.,
RA Vo N., Wagner M., Wheeler J., Wu K., Xie G., Yang J., Dubchak I.,
RA Furey T.S., DeJong P., Dickson M., Gordon D., Eichler E.E.,
RA Pennacchio L.A., Richardson P., Stubbs L., Rokhsar D.S., Myers R.M.,
RA Rubin E.M., Lucas S.M.;
RT "The DNA sequence and biology of human chromosome 19.";
RL Nature 428:529-535(2004).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Blood;
RX MEDLINE=22388257; PubMed=12477932; DOI=10.1073/pnas.242603899;
RA Strausberg R.L., Feingold E.A., Grouse L.H., Derge J.G.,
RA Klausner R.D., Collins F.S., Wagner L., Shenmen C.M., Schuler G.D.,
RA Altschul S.F., Zeeberg B., Buetow K.H., Schaefer C.F., Bhat N.K.,
RA Hopkins R.F., Jordan H., Moore T., Max S.I., Wang J., Hsieh F.,
RA Diatchenko L., Marusina K., Farmer A.A., Rubin G.M., Hong L.,
RA Stapleton M., Soares M.B., Bonaldo M.F., Casavant T.L., Scheetz T.E.,
RA Brownstein M.J., Usdin T.B., Toshiyuki S., Carninci P., Prange C.,
RA Raha S.S., Loquellano N.A., Peters G.J., Abramson R.D., Mullahy S.J.,
RA Bosak S.A., McEwan P.J., McKernan K.J., Malek J.A., Gunaratne P.H.,
RA Richards S., Worley K.C., Hale S., Garcia A.M., Gay L.J., Hulyk S.W.,
RA Villalon D.K., Muzny D.M., Sodergren E.J., Lu X., Gibbs R.A.,
RA Fahey J., Helton E., Ketteman M., Madan A., Rodrigues S., Sanchez A.,
RA Whiting M., Madan A., Young A.C., Shevchenko Y., Bouffard G.G.,
RA Blakesley R.W., Touchman J.W., Green E.D., Dickson M.C.,
RA Rodriguez A.C., Grimwood J., Schmutz J., Myers R.M.,
RA Butterfield Y.S.N., Krzywinski M.I., Skalska U., Smailus D.E.,
RA Schnerch A., Schein J.E., Jones S.J.M., Marra M.A.;
RT "Generation and initial analysis of more than 15,000 full-length human
RT and mouse cDNA sequences.";
RL Proc. Natl. Acad. Sci. U.S.A. 99:16899-16903(2002).
Feature:
CHAIN 1 521 Bifunctional polynucleotide
phosphatase/kinase.
/FTId=PRO_0000058478.
NP_BIND 372 379 ATP (Potential).
VARIANT 20 20 P -> S (in dbSNP:3739168).
/FTId=VAR_019260.
VARIANT 63 63 A -> V (in dbSNP:3739173).
/FTId=VAR_019261.
VARIANT 180 180 R -> S (in dbSNP:3739185).
/FTId=VAR_019262.
VARIANT 196 196 Y -> N (in dbSNP:3739186).
/FTId=VAR_019263.
VARIANT 478 478 V -> G (in dbSNP:3739206).
/FTId=VAR_019264.
CONFLICT 6 6 A -> P (in Ref. 2).
CONFLICT 18 18 G -> E (in Ref. 1).
STRAND 9 13
STRAND 15 15
TURN 16 17
STRAND 18 19
STRAND 22 23
STRAND 26 26
TURN 27 28
STRAND 31 33
STRAND 35 36
TURN 37 40
STRAND 41 41
TURN 44 45
STRAND 46 46
STRAND 48 49
STRAND 51 56
TURN 57 60
STRAND 61 66
STRAND 68 70
STRAND 73 74
STRAND 78 78
TURN 81 82
STRAND 84 88
TURN 89 90
STRAND 92 96
TURN 97 98
STRAND 99 107
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.
-!- CATALYTIC ACTIVITY: A 3'-phosphopolynucleotide + H(2)O = a
polynucleotide + phosphate.
-!- CATALYTIC ACTIVITY: ATP + 5'-dephospho-DNA = ADP + 5'-phospho-DNA.
-!- SUBCELLULAR LOCATION: Nucleus.
-!- 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).
-!- SIMILARITY: In the N-terminal section; belongs to the DNA 3'
phosphatase family.
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Sequence length: 521
MGEVEAPGRL WLESPPGGAP PIFLPSDGQA LVLGRGPLTQ VTDRKCSRTQ VELVADPETR
TVAVKQLGVN PSTTGTQELK PGLEGSLGVG DTLYLVNGLH PLTLRWEETR TPESQPDTPP
GTPLVSQDEK RDAELPKKRM RKSNPGWENL EKLLVFTAAG VKPQGKVAGF DLDGTLITTR
SGKVFPTGPS DWRILYPEIP RKLRELEAEG YKLVIFTNQM SIGRGKLPAE EFKAKVEAVV
EKLGVPFQVL VATHAGLYRK PVTGMWDHLQ EQANDGTPIS IGDSIFVGDA AGRPANWAPG
RKKKDFSCAD RLFALNLGLP FATPEEFFLK WPAAGFELPA FDPRTVSRSG PLCLPESRAL
LSASPEVVVA VGFPGAGKST FLKKHLVSAG YVHVNRDTLG SWQRCVTTCE TALKQGKRVA
IDNTNPDAAS RARYVQCARA AGVPCRCFLF TATLEQARHN NRFREMTDSS HIPVSDMVMY
GYRKQFEAPT LAEGFSAILE IPFRLWVEPR LGRLYCQFSE G