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Protein

DNA polymerase kappa

Gene

Polk

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Depending on the context, it inserts the correct base, but causes frequent base transitions, transversions and frameshifts. Lacks 3'-5' proofreading exonuclease activity. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but does not have lyase activity (By similarity).By similarity1 Publication

Catalytic activityi

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Divalent metal cations. Prefers Mg2+, but can also use Mn2+.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi106 – 1061MagnesiumBy similarity
Metal bindingi197 – 1971MagnesiumBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri619 – 64527UBZ-type 1Add
BLAST
Zinc fingeri761 – 78727UBZ-type 2Add
BLAST

GO - Molecular functioni

  • damaged DNA binding Source: InterPro
  • DNA-directed DNA polymerase activity Source: MGI
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

  • DNA repair Source: MGI
  • DNA replication Source: UniProtKB-KW
  • nucleotide-excision repair, DNA gap filling Source: MGI
Complete GO annotation...

Keywords - Molecular functioni

DNA-directed DNA polymerase, Mutator protein, Nucleotidyltransferase, Transferase

Keywords - Biological processi

DNA damage, DNA repair, DNA replication, DNA synthesis

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, Schiff base, Zinc

Enzyme and pathway databases

ReactomeiR-MMU-5655862. Translesion synthesis by POLK.
R-MMU-5656169. Termination of translesion DNA synthesis.
R-MMU-5685942. HDR through Homologous Recombination (HRR).
R-MMU-5696397. Gap-filling DNA repair synthesis and ligation in GG-NER.
R-MMU-5696400. Dual Incision in GG-NER.
R-MMU-6782135. Dual incision in TC-NER.
R-MMU-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase kappa (EC:2.7.7.7)
Alternative name(s):
DINB protein
Short name:
DINP
Gene namesi
Name:Polk
Synonyms:Dinb1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 13

Organism-specific databases

MGIiMGI:1349767. Polk.

Subcellular locationi

  • Nucleus By similarity

  • Note: Detected throughout the nucleus and at replication foci.By similarity

GO - Cellular componenti

  • intracellular membrane-bounded organelle Source: MGI
  • nucleoplasm Source: MGI
  • nucleus Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 852852DNA polymerase kappaPRO_0000173991Add
BLAST

Proteomic databases

EPDiQ9QUG2.
MaxQBiQ9QUG2.
PaxDbiQ9QUG2.
PRIDEiQ9QUG2.

PTM databases

iPTMnetiQ9QUG2.
PhosphoSiteiQ9QUG2.

Expressioni

Tissue specificityi

Detected at low levels in heart, brain, lung, liver, kidney and testis.1 Publication

Gene expression databases

BgeeiQ9QUG2.
CleanExiMM_POLK.
ExpressionAtlasiQ9QUG2. baseline and differential.
GenevisibleiQ9QUG2. MM.

Interactioni

Subunit structurei

Interacts with PCNA (By similarity). Interacts with REV1.By similarity1 Publication

Protein-protein interaction databases

BioGridi205098. 6 interactions.
IntActiQ9QUG2. 1 interaction.
STRINGi10090.ENSMUSP00000022172.

Structurei

Secondary structure

1
852
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi566 – 5716Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2LSJNMR-B560-582[»]
4FJOX-ray2.72B565-574[»]
ProteinModelPortaliQ9QUG2.
SMRiQ9QUG2. Positions 20-515.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini102 – 357256UmuCAdd
BLAST

Domaini

The catalytic core consists of fingers, palm and thumb subdomains, but the fingers and thumb subdomains are much smaller than in high-fidelity polymerases; residues from five sequence motifs of the Y-family cluster around an active site cleft that can accommodate DNA and nucleotide substrates with relaxed geometric constraints, with consequently higher rates of misincorporation and low processivity.

Sequence similaritiesi

Belongs to the DNA polymerase type-Y family.Curated
Contains 2 UBZ-type zinc fingers.Curated
Contains 1 umuC domain.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri619 – 64527UBZ-type 1Add
BLAST
Zinc fingeri761 – 78727UBZ-type 2Add
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG2094. Eukaryota.
COG0389. LUCA.
GeneTreeiENSGT00530000062942.
HOGENOMiHOG000082711.
HOVERGENiHBG101212.
InParanoidiQ9QUG2.
KOiK03511.
OMAiNWPEDKR.
OrthoDBiEOG73Z2SP.
PhylomeDBiQ9QUG2.
TreeFamiTF314387.

Family and domain databases

Gene3Di3.30.1490.100. 1 hit.
HAMAPiMF_01113. DNApol_IV.
InterProiIPR017061. DNA_pol_eta/kappa.
IPR017961. DNA_pol_Y-fam_little_finger.
IPR022880. DNApol_IV.
IPR001126. UmuC.
IPR006642. Znf_Rad18_put.
[Graphical view]
PfamiPF00817. IMS. 1 hit.
PF11799. IMS_C. 1 hit.
[Graphical view]
PIRSFiPIRSF036603. DPol_eta. 1 hit.
SMARTiSM00734. ZnF_Rad18. 2 hits.
[Graphical view]
SUPFAMiSSF100879. SSF100879. 1 hit.
PROSITEiPS50173. UMUC. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9QUG2-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MDNTKEKDNF KDDLLLRMGL NDNKAGMEGL DKEKINKIIM EATKGSRFYG
60 70 80 90 100
NELKKEKQVN QRIENMMQQK AQITSQQLRK AQLQVDKFAM ELERNRNLNN
110 120 130 140 150
TIVHVDMDAF YAAVEMRDNP ELKDKPIAVG SMSMLATSNY HARRFGVRAA
160 170 180 190 200
MPGFIAKRLC PQLIIVPPNF DKYRAVSKEV KEILAEYDPN FMAMSLDEAY
210 220 230 240 250
LNITQHLQER QDWPEDKRRY FIKMGNYLKI DTPRQEANEL TEYERSISPL
260 270 280 290 300
LFEDSPPDLQ PQGSPFQLNS EEQNNPQIAQ NSVVFGTSAE EVVKEIRFRI
310 320 330 340 350
EQKTTLTASA GIAPNTMLAK VCSDKNKPNG QYQILPSRSA VMDFIKDLPI
360 370 380 390 400
RKVSGIGKVT EKMLMALGIV TCTELYQQRA LLSLLFSETS WHYFLHIALG
410 420 430 440 450
LGSTDLARDG ERKSMSVERT FSEISKTEEQ YSLCQELCAE LAHDLQKEGL
460 470 480 490 500
KGRTVTIKLK NVNFEVKTRA STVPAAISTA EEIFAIAKEL LRTEVNVGSP
510 520 530 540 550
HPLRLRLMGV RMSTFSSEDD RKHQQRSIIG FLQAGNQALS STGDSLDKTD
560 570 580 590 600
KTELAKPLEM SHKKSFFDKK RSERISNCQD TSRCKTAGQQ ALQILEPSQA
610 620 630 640 650
LKKLSESFET SENSNDCQTF ICPVCFREQE GVSLEAFNEH VDECLDGPST
660 670 680 690 700
SENSKISCYS HASSADIGQK EDVHPSIPLC EKRGHENGEI TLVDGVDLTG
710 720 730 740 750
TEDRSLKAAR MDTLENNRSK EECPDIPDKS CPISLENETI STLSRQDSVQ
760 770 780 790 800
PCTDEVVTGR ALVCPVCNLE QETSDLTLFN IHVDICLNKG IIQELRNSEG
810 820 830 840 850
NSVKQPKESS RSTDRLQKAS GRTKRPGTKT KSSTLKKTKP RDPRHTLDGF

FK
Length:852
Mass (Da):96,003
Last modified:May 1, 2000 - v1
Checksum:iFD8F33A6E78992F4
GO
Isoform 2 (identifier: Q9QUG2-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     50-185: Missing.
     827-852: GTKTKSSTLKKTKPRDPRHTLDGFFK → RGATSPSAPPCLATMVPLMLPYLPVCISVSCEQMQLELAMMSMKNISLT

Note: No experimental confirmation available.
Show »
Length:739
Mass (Da):82,684
Checksum:i65B4A5A69C4F6E20
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti544 – 5441D → G in strain: C3H/He. 1 Publication
Natural varianti550 – 5501D → A in strain: C3H/He. 1 Publication
Natural varianti606 – 6061E → Q in strain: C3H/He. 1 Publication
Natural varianti692 – 6921L → S in strain: C3H/He. 1 Publication
Natural varianti710 – 7101R → S in strain: C3H/He. 1 Publication
Natural varianti736 – 7361E → A in strain: C3H/He. 1 Publication
Natural varianti747 – 7471D → E in strain: C3H/He. 1 Publication

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei50 – 185136Missing in isoform 2. 1 PublicationVSP_012807Add
BLAST
Alternative sequencei827 – 85226GTKTK…DGFFK → RGATSPSAPPCLATMVPLML PYLPVCISVSCEQMQLELAM MSMKNISLT in isoform 2. 1 PublicationVSP_012808Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB027563 mRNA. Translation: BAA86942.1.
AF163571 mRNA. Translation: AAF02541.1.
AB040765 Genomic DNA. Translation: BAB59059.1.
BC052820 mRNA. Translation: AAH52820.1.
CCDSiCCDS26704.1. [Q9QUG2-1]
RefSeqiNP_036178.1. NM_012048.2. [Q9QUG2-1]
UniGeneiMm.89926.

Genome annotation databases

EnsembliENSMUST00000022172; ENSMUSP00000022172; ENSMUSG00000021668. [Q9QUG2-1]
GeneIDi27015.
KEGGimmu:27015.
UCSCiuc007rne.1. mouse. [Q9QUG2-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB027563 mRNA. Translation: BAA86942.1.
AF163571 mRNA. Translation: AAF02541.1.
AB040765 Genomic DNA. Translation: BAB59059.1.
BC052820 mRNA. Translation: AAH52820.1.
CCDSiCCDS26704.1. [Q9QUG2-1]
RefSeqiNP_036178.1. NM_012048.2. [Q9QUG2-1]
UniGeneiMm.89926.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2LSJNMR-B560-582[»]
4FJOX-ray2.72B565-574[»]
ProteinModelPortaliQ9QUG2.
SMRiQ9QUG2. Positions 20-515.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi205098. 6 interactions.
IntActiQ9QUG2. 1 interaction.
STRINGi10090.ENSMUSP00000022172.

PTM databases

iPTMnetiQ9QUG2.
PhosphoSiteiQ9QUG2.

Proteomic databases

EPDiQ9QUG2.
MaxQBiQ9QUG2.
PaxDbiQ9QUG2.
PRIDEiQ9QUG2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000022172; ENSMUSP00000022172; ENSMUSG00000021668. [Q9QUG2-1]
GeneIDi27015.
KEGGimmu:27015.
UCSCiuc007rne.1. mouse. [Q9QUG2-1]

Organism-specific databases

CTDi51426.
MGIiMGI:1349767. Polk.

Phylogenomic databases

eggNOGiKOG2094. Eukaryota.
COG0389. LUCA.
GeneTreeiENSGT00530000062942.
HOGENOMiHOG000082711.
HOVERGENiHBG101212.
InParanoidiQ9QUG2.
KOiK03511.
OMAiNWPEDKR.
OrthoDBiEOG73Z2SP.
PhylomeDBiQ9QUG2.
TreeFamiTF314387.

Enzyme and pathway databases

ReactomeiR-MMU-5655862. Translesion synthesis by POLK.
R-MMU-5656169. Termination of translesion DNA synthesis.
R-MMU-5685942. HDR through Homologous Recombination (HRR).
R-MMU-5696397. Gap-filling DNA repair synthesis and ligation in GG-NER.
R-MMU-5696400. Dual Incision in GG-NER.
R-MMU-6782135. Dual incision in TC-NER.
R-MMU-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.

Miscellaneous databases

PROiQ9QUG2.
SOURCEiSearch...

Gene expression databases

BgeeiQ9QUG2.
CleanExiMM_POLK.
ExpressionAtlasiQ9QUG2. baseline and differential.
GenevisibleiQ9QUG2. MM.

Family and domain databases

Gene3Di3.30.1490.100. 1 hit.
HAMAPiMF_01113. DNApol_IV.
InterProiIPR017061. DNA_pol_eta/kappa.
IPR017961. DNA_pol_Y-fam_little_finger.
IPR022880. DNApol_IV.
IPR001126. UmuC.
IPR006642. Znf_Rad18_put.
[Graphical view]
PfamiPF00817. IMS. 1 hit.
PF11799. IMS_C. 1 hit.
[Graphical view]
PIRSFiPIRSF036603. DPol_eta. 1 hit.
SMARTiSM00734. ZnF_Rad18. 2 hits.
[Graphical view]
SUPFAMiSSF100879. SSF100879. 1 hit.
PROSITEiPS50173. UMUC. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Mutation enhancement by DINB1, a mammalian homologue of the Escherichia coli mutagenesis protein dinB."
    Ogi T., Kato T. Jr., Kato R., Ohmori H.
    Genes Cells 4:607-618(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY.
    Strain: BALB/cJ.
    Tissue: Testis.
  2. "Human and mouse homologs of Escherichia coli DinB (DNA polymerase IV), members of the UmuC/DinB superfamily."
    Gerlach V.L., Aravind L., Gotway G., Schultz R.A., Koonin E.V., Friedberg E.C.
    Proc. Natl. Acad. Sci. U.S.A. 96:11922-11927(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
    Tissue: Testis.
  3. "Pol kappa protects mammalian cells against the lethal and mutagenic effects of benzo[a]pyrene."
    Ogi T., Shinkai Y., Tanaka K., Ohmori H.
    Proc. Natl. Acad. Sci. U.S.A. 99:15548-15553(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
  4. "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] (ISOFORM 2), VARIANTS GLY-544; ALA-550; GLN-606; SER-692; SER-710; ALA-736 AND GLU-747.
    Strain: C3H/He.
    Tissue: Osteoblast.
  5. "Mouse Rev1 protein interacts with multiple DNA polymerases involved in translesion DNA synthesis."
    Guo C., Fischhaber P.L., Luk-Paszyc M.J., Masuda Y., Zhou J., Kamiya K., Kisker C., Friedberg E.C.
    EMBO J. 22:6621-6630(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH REV1.

Entry informationi

Entry nameiPOLK_MOUSE
AccessioniPrimary (citable) accession number: Q9QUG2
Secondary accession number(s): Q7TPY7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 15, 2005
Last sequence update: May 1, 2000
Last modified: June 8, 2016
This is version 118 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.