POLK_ARATH
ID POLK_ARATH Reviewed; 671 AA.
AC Q6JDV7; A0A1P8ANH5; Q56YN7; Q9LPM1;
DT 30-AUG-2017, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 137.
DE RecName: Full=DNA polymerase kappa {ECO:0000303|PubMed:15200644};
DE Short=AtPOLK {ECO:0000303|PubMed:15200644};
DE EC=2.7.7.7 {ECO:0000269|PubMed:15200644, ECO:0000269|PubMed:17550419};
GN Name=POLK {ECO:0000303|PubMed:15200644};
GN OrderedLocusNames=At1g49980 {ECO:0000312|Araport:AT1G49980};
GN ORFNames=F2J10.13 {ECO:0000312|EMBL:AAF76444.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), ALTERNATIVE SPLICING, FUNCTION,
RP MUTAGENESIS OF ASP-200; GLU-201 AND 479-ASN--LYS-671, TISSUE SPECIFICITY,
RP DEVELOPMENTAL STAGE, AND CATALYTIC ACTIVITY.
RC STRAIN=cv. Columbia;
RX PubMed=15200644; DOI=10.1111/j.1365-313x.2004.02112.x;
RA Garcia-Ortiz M.V., Ariza R.R., Hoffman P.D., Hays J.B., Roldan-Arjona T.;
RT "Arabidopsis thaliana AtPOLK encodes a DinB-like DNA polymerase that
RT extends mispaired primer termini and is highly expressed in a variety of
RT tissues.";
RL Plant J. 39:84-97(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP REVIEW ON DNA DAMAGE REPAIR.
RX PubMed=15645454; DOI=10.1002/em.20094;
RA Kunz B.A., Anderson H.J., Osmond M.J., Vonarx E.J.;
RT "Components of nucleotide excision repair and DNA damage tolerance in
RT Arabidopsis thaliana.";
RL Environ. Mol. Mutagen. 45:115-127(2005).
RN [6]
RP FUNCTION, MUTAGENESIS OF 479-ASN--LYS-671, BIOPHYSICOCHEMICAL PROPERTIES,
RP CATALYTIC ACTIVITY, AND ACTIVITY REGULATION.
RX PubMed=17550419; DOI=10.1111/j.1742-4658.2007.05868.x;
RA Garcia-Ortiz M.V., Roldan-Arjona T., Ariza R.R.;
RT "The noncatalytic C-terminus of AtPOLK Y-family DNA polymerase affects
RT synthesis fidelity, mismatch extension and translesion replication.";
RL FEBS J. 274:3340-3350(2007).
CC -!- FUNCTION: Template-directed low-fidelity DNA polymerase specifically
CC involved in DNA repair (PubMed:15200644, PubMed:17550419). Able to
CC extend primer-terminal mispairs, and to insert nucleotides opposite to
CC a single 7,8-dihydro-8-oxoGuanine (8-oxoG) lesion and moderately extend
CC from the resulting primer end, thus leading to both error-free and
CC error-prone bypass of 8-oxoG DNA lesions (PubMed:17550419). Probably
CC involved in consecutive DNA replication cycles in the absence of
CC mitosis (PubMed:15200644). Binds preferentially template-primer DNA
CC substrates or single-stranded DNA (PubMed:17550419). Plays an important
CC role in translesion synthesis, where the normal high-fidelity DNA
CC polymerases cannot proceed and DNA synthesis stalls. Depending on the
CC context, it inserts the correct base, but causes frequent base
CC transitions, transversions and frameshifts (By similarity).
CC {ECO:0000250|UniProtKB:Q9UBT6, ECO:0000269|PubMed:15200644,
CC ECO:0000269|PubMed:17550419}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) =
CC diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339,
CC Rhea:RHEA-COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560,
CC ChEBI:CHEBI:173112; EC=2.7.7.7;
CC Evidence={ECO:0000269|PubMed:15200644, ECO:0000269|PubMed:17550419};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:Q9UBT6};
CC -!- ACTIVITY REGULATION: Unable to bypass a single 1,N(6)-ethenoadenine
CC (epsilon-dA) or an abasic site lesions in DNA templates.
CC {ECO:0000269|PubMed:17550419}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=52.6 uM for dATP (with cytosine as template)
CC {ECO:0000269|PubMed:17550419};
CC KM=12.51 uM for dGTP (with cytosine as template)
CC {ECO:0000269|PubMed:17550419};
CC KM=83.3 uM for dTTP (with cytosine as template)
CC {ECO:0000269|PubMed:17550419};
CC KM=156.8 uM for dCTP (with cytosine as template)
CC {ECO:0000269|PubMed:17550419};
CC KM=2.61 uM for dATP (with thymine as template)
CC {ECO:0000269|PubMed:17550419};
CC KM=62.29 uM for dCTP (with thymine as template)
CC {ECO:0000269|PubMed:17550419};
CC KM=4.7 uM for dTTP (with adenine as template)
CC {ECO:0000269|PubMed:17550419};
CC KM=100.41 uM for dCTP (with adenine as template)
CC {ECO:0000269|PubMed:17550419};
CC KM=29.16 uM for dTTP (with guanine as template)
CC {ECO:0000269|PubMed:17550419};
CC KM=7.76 uM for dCTP (with guanine as template)
CC {ECO:0000269|PubMed:17550419};
CC Note=With cytosine as template, kcat is 0.024 min(-1) with dATP as
CC substrate, kcat is 0.125 min(-1) with dGTP as substrate, kcat is
CC 0.057 min(-1) with dATTP as substrate and kcat is 0.0038 min(-1) with
CC dCTP as substrate. With thymine as template, kcat is 0.157 min(-1)
CC with dATP as substrate and kcat is 0.038 min(-1) with dCTP as
CC substrate. With adenine as template, kcat is 0.207 min(-1) with dTTP
CC as substrate and kcat is 0.045 min(-1) with dCTP as substrate. With
CC guanine as template, kcat is 0.022 min(-1) with dTTP as substrate and
CC kcat is 0.061 min(-1) with dCTP as substrate.
CC {ECO:0000269|PubMed:17550419};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q9UBT6,
CC ECO:0000255|PROSITE-ProRule:PRU00768}. Note=Detected throughout the
CC nucleus and at replication foci. {ECO:0000250|UniProtKB:Q9UBT6}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Comment=Additional isoforms seem to exist.
CC {ECO:0000269|PubMed:15200644, ECO:0000312|Araport:AT1G49980};
CC Name=1; Synonyms=AtPOLKa {ECO:0000303|PubMed:15200644};
CC IsoId=Q6JDV7-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q6JDV7-2; Sequence=VSP_059052;
CC Name=3;
CC IsoId=Q6JDV7-3; Sequence=VSP_059053;
CC -!- TISSUE SPECIFICITY: Expressed in roots, leaves, stems, flowers and
CC siliques. Present in endoreduplicating cells.
CC {ECO:0000269|PubMed:15200644}.
CC -!- DEVELOPMENTAL STAGE: In young seedlings, strongly expressed in
CC cotyledons, and, at lower levels, in the hypocotyl adjacent region.
CC Later confined to cotyledons vascular tissues and observed in leaf
CC primordia and young growing leaves. Accumulates in the basal part of
CC trichomes. In mature flowers, present in sepals, stamen filaments and
CC stigma. Accumulates progressively in maturating siliques.
CC {ECO:0000269|PubMed:15200644}.
CC -!- DOMAIN: The C-terminal region negatively affects catalytic efficiency
CC for correct nucleotide insertion, thus decreasing the fidelity of the
CC enzyme. {ECO:0000269|PubMed:17550419}.
CC -!- SIMILARITY: Belongs to the DNA polymerase type-Y family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF76444.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AY508701; AAS91582.1; -; mRNA.
DR EMBL; AC015445; AAF76444.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE32503.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM58190.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM58192.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM58193.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM58196.1; -; Genomic_DNA.
DR EMBL; AK221284; BAD93992.1; -; mRNA.
DR PIR; C96536; C96536.
DR RefSeq; NP_001320644.1; NM_001333412.1. [Q6JDV7-3]
DR RefSeq; NP_001320646.1; NM_001333409.1. [Q6JDV7-3]
DR RefSeq; NP_001320647.1; NM_001333410.1. [Q6JDV7-3]
DR RefSeq; NP_001320650.1; NM_001333413.1. [Q6JDV7-3]
DR RefSeq; NP_175420.3; NM_103886.4. [Q6JDV7-1]
DR AlphaFoldDB; Q6JDV7; -.
DR SMR; Q6JDV7; -.
DR STRING; 3702.AT1G49980.1; -.
DR PaxDb; Q6JDV7; -.
DR PRIDE; Q6JDV7; -.
DR EnsemblPlants; AT1G49980.1; AT1G49980.1; AT1G49980. [Q6JDV7-1]
DR EnsemblPlants; AT1G49980.4; AT1G49980.4; AT1G49980. [Q6JDV7-3]
DR EnsemblPlants; AT1G49980.5; AT1G49980.5; AT1G49980. [Q6JDV7-3]
DR EnsemblPlants; AT1G49980.7; AT1G49980.7; AT1G49980. [Q6JDV7-3]
DR EnsemblPlants; AT1G49980.8; AT1G49980.8; AT1G49980. [Q6JDV7-3]
DR GeneID; 841422; -.
DR Gramene; AT1G49980.1; AT1G49980.1; AT1G49980. [Q6JDV7-1]
DR Gramene; AT1G49980.4; AT1G49980.4; AT1G49980. [Q6JDV7-3]
DR Gramene; AT1G49980.5; AT1G49980.5; AT1G49980. [Q6JDV7-3]
DR Gramene; AT1G49980.7; AT1G49980.7; AT1G49980. [Q6JDV7-3]
DR Gramene; AT1G49980.8; AT1G49980.8; AT1G49980. [Q6JDV7-3]
DR KEGG; ath:AT1G49980; -.
DR Araport; AT1G49980; -.
DR TAIR; locus:2031050; AT1G49980.
DR eggNOG; KOG2094; Eukaryota.
DR HOGENOM; CLU_012348_11_1_1; -.
DR InParanoid; Q6JDV7; -.
DR OrthoDB; 878533at2759; -.
DR PhylomeDB; Q6JDV7; -.
DR PRO; PR:Q6JDV7; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q6JDV7; baseline and differential.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0003684; F:damaged DNA binding; IEA:InterPro.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003697; F:single-stranded DNA binding; IDA:UniProtKB.
DR GO; GO:0006281; P:DNA repair; IDA:UniProtKB.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR GO; GO:0042276; P:error-prone translesion synthesis; IBA:GO_Central.
DR CDD; cd03586; PolY_Pol_IV_kappa; 1.
DR Gene3D; 3.30.1490.100; -; 1.
DR Gene3D; 3.30.70.270; -; 1.
DR HAMAP; MF_01113; DNApol_IV; 1.
DR InterPro; IPR043502; DNA/RNA_pol_sf.
DR InterPro; IPR036775; DNA_pol_Y-fam_lit_finger_sf.
DR InterPro; IPR017961; DNA_pol_Y-fam_little_finger.
DR InterPro; IPR022880; DNApol_IV.
DR InterPro; IPR043128; Rev_trsase/Diguanyl_cyclase.
DR InterPro; IPR041298; UBZ3.
DR InterPro; IPR001126; UmuC.
DR Pfam; PF00817; IMS; 1.
DR Pfam; PF11799; IMS_C; 1.
DR Pfam; PF18439; zf_UBZ; 1.
DR SUPFAM; SSF100879; SSF100879; 1.
DR SUPFAM; SSF56672; SSF56672; 1.
DR PROSITE; PS50173; UMUC; 1.
DR PROSITE; PS51907; ZF_UBZ3; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; DNA damage; DNA repair; DNA replication; DNA-binding;
KW DNA-directed DNA polymerase; Magnesium; Metal-binding; Mutator protein;
KW Nucleotidyltransferase; Nucleus; Reference proteome; Transferase; Zinc;
KW Zinc-finger.
FT CHAIN 1..671
FT /note="DNA polymerase kappa"
FT /id="PRO_0000441249"
FT DOMAIN 105..285
FT /note="UmuC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00216"
FT ZN_FING 576..613
FT /note="UBZ3-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01255"
FT REGION 607..671
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 625..632
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT COMPBIAS 609..625
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 626..653
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 655..671
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 201
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00216"
FT BINDING 109
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00216"
FT BINDING 200
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00216"
FT BINDING 583
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01255"
FT BINDING 586
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01255"
FT BINDING 601
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01255"
FT BINDING 605
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01255"
FT SITE 114
FT /note="Substrate discrimination"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00216"
FT VAR_SEQ 1..269
FT /note="Missing (in isoform 2)"
FT /id="VSP_059052"
FT VAR_SEQ 666..671
FT /note="Missing (in isoform 3)"
FT /id="VSP_059053"
FT MUTAGEN 200
FT /note="D->A: Loss of DNA polymerase kappa activity."
FT /evidence="ECO:0000269|PubMed:15200644"
FT MUTAGEN 201
FT /note="E->A: Loss of DNA polymerase kappa activity."
FT /evidence="ECO:0000269|PubMed:15200644"
FT MUTAGEN 479..671
FT /note="Missing: Increased DNA polymerase kappa activity and
FT processivity leading to enhanced catalytic efficiency and
FT fidelity, due to a greater ability to insert the correct
FT nucleotide."
FT /evidence="ECO:0000269|PubMed:15200644,
FT ECO:0000269|PubMed:17550419"
SQ SEQUENCE 671 AA; 75252 MW; 45FE9D4A3460ABEB CRC64;
MDNGESSSTN NSSRPWESYN TVFTNAKAGM EGVDKEKVQR VVYEMSKGSK YFQNEERKEA
LMKQKIEHMR DRCAKLSSLD LSNYQKVVDK RILELEATRD LSRIWLHVDM DAFYAAVETL
SDPSIKGKPM AVGGLSMIST ANYEARKFGV RAAMPGFIAR KLCPDLIFVP VDFTKYTHYS
DLTRKVFRNY DPHFIAGSLD EAYLDITEVC RERGLSGGEI AEELRSSVYS ETGLTCSAGV
AANRLLAKVC SDINKPNGQF VLQNDRSTVM TFVSFLPVRK IGGIGKVTEH ILKDALGIKT
CEEMVQKGSL LYALFSQSSA DFFLSVGLGL GGTNTPQVRS RKSISSERTF AATGDERLLY
SKLDELAEML SHDMKKEGLT ARTLTLKLKT ASFEIRSRAV SLQRYTCSSD DILKHATKLL
KAELPVSVRL IGLRMSQFVE EIRNSDPSQG TITKFIVQKD SSRQAQDLDD NDSFDLDANK
NCLSNDESGN VSFGSHETSS AHLKDVVEYE ERSQIDSGKV IPNQECMKKE ERLQILEGDS
LLKKYKECKP DTSHSMNDNS NATEAVSVFP QTEPLYWIDG YKCVLCGIEL PPSFVEERQE
HSDFHLAQRL QNEETGSSSS TTPSKRRILG KEKVNSKPKK QKPDQKDSSK HIPIHAFFTK
SNQNSNETQR K
