DPO4_YEAST
ID DPO4_YEAST Reviewed; 582 AA.
AC P25615; D6VR22;
DT 01-MAY-1992, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 4.
DT 03-AUG-2022, entry version 181.
DE RecName: Full=DNA polymerase IV;
DE Short=POL IV;
DE EC=2.7.7.7;
GN Name=POL4; Synonyms=POLX; OrderedLocusNames=YCR014C; ORFNames=YCR14C;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=1574125; DOI=10.1038/357038a0;
RA Oliver S.G., van der Aart Q.J.M., Agostoni-Carbone M.L., Aigle M.,
RA Alberghina L., Alexandraki D., Antoine G., Anwar R., Ballesta J.P.G.,
RA Benit P., Berben G., Bergantino E., Biteau N., Bolle P.-A.,
RA Bolotin-Fukuhara M., Brown A., Brown A.J.P., Buhler J.-M., Carcano C.,
RA Carignani G., Cederberg H., Chanet R., Contreras R., Crouzet M.,
RA Daignan-Fornier B., Defoor E., Delgado M.D., Demolder J., Doira C.,
RA Dubois E., Dujon B., Duesterhoeft A., Erdmann D., Esteban M., Fabre F.,
RA Fairhead C., Faye G., Feldmann H., Fiers W., Francingues-Gaillard M.-C.,
RA Franco L., Frontali L., Fukuhara H., Fuller L.J., Galland P., Gent M.E.,
RA Gigot D., Gilliquet V., Glansdorff N., Goffeau A., Grenson M., Grisanti P.,
RA Grivell L.A., de Haan M., Haasemann M., Hatat D., Hoenicka J.,
RA Hegemann J.H., Herbert C.J., Hilger F., Hohmann S., Hollenberg C.P.,
RA Huse K., Iborra F., Indge K.J., Isono K., Jacq C., Jacquet M., James C.M.,
RA Jauniaux J.-C., Jia Y., Jimenez A., Kelly A., Kleinhans U., Kreisl P.,
RA Lanfranchi G., Lewis C., van der Linden C.G., Lucchini G.,
RA Lutzenkirchen K., Maat M.J., Mallet L., Mannhaupt G., Martegani E.,
RA Mathieu A., Maurer C.T.C., McConnell D., McKee R.A., Messenguy F.,
RA Mewes H.-W., Molemans F., Montague M.A., Muzi Falconi M., Navas L.,
RA Newlon C.S., Noone D., Pallier C., Panzeri L., Pearson B.M., Perea J.,
RA Philippsen P., Pierard A., Planta R.J., Plevani P., Poetsch B., Pohl F.M.,
RA Purnelle B., Ramezani Rad M., Rasmussen S.W., Raynal A., Remacha M.A.,
RA Richterich P., Roberts A.B., Rodriguez F., Sanz E.,
RA Schaaff-Gerstenschlaeger I., Scherens B., Schweitzer B., Shu Y., Skala J.,
RA Slonimski P.P., Sor F., Soustelle C., Spiegelberg R., Stateva L.I.,
RA Steensma H.Y., Steiner S., Thierry A., Thireos G., Tzermia M.,
RA Urrestarazu L.A., Valle G., Vetter I., van Vliet-Reedijk J.C., Voet M.,
RA Volckaert G., Vreken P., Wang H., Warmington J.R., von Wettstein D.,
RA Wicksteed B.L., Wilson C., Wurst H., Xu G., Yoshikawa A., Zimmermann F.K.,
RA Sgouros J.G.;
RT "The complete DNA sequence of yeast chromosome III.";
RL Nature 357:38-46(1992).
RN [2]
RP SEQUENCE REVISION TO 49; 171; 451 AND 482.
RA Valles G., Volckaerts G.;
RL Submitted (JUN-2001) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 303-582.
RX PubMed=1626432; DOI=10.1002/yea.320080508;
RA Skala J., Purnelle B., Goffeau A.;
RT "The complete sequence of a 10.8 kb segment distal of SUF2 on the right arm
RT of chromosome III from Saccharomyces cerevisiae reveals seven open reading
RT frames including the RVS161, ADP1 and PGK genes.";
RL Yeast 8:409-417(1992).
RN [5]
RP CHARACTERIZATION, AND PROTEIN SEQUENCE OF 2-15.
RX PubMed=8265341; DOI=10.1093/nar/21.23.5301;
RA Prasad R., Widen S.G., Singhal R.K., Watkins J., Prakash L., Wilson S.H.;
RT "Yeast open reading frame YCR14C encodes a DNA beta-polymerase-like
RT enzyme.";
RL Nucleic Acids Res. 21:5301-5307(1993).
RN [6]
RP PROTEIN SEQUENCE OF 67-79; 138-149; 287-299; 342-356 AND 365-373, FUNCTION,
RP AND INDUCTION.
RX PubMed=8065914; DOI=10.1093/nar/22.15.3011;
RA Leem S.-H., Ropp P.A., Sugino A.;
RT "The yeast Saccharomyces cerevisiae DNA polymerase IV: possible involvement
RT in double strand break DNA repair.";
RL Nucleic Acids Res. 22:3011-3017(1994).
RN [7]
RP FUNCTION, ACTIVITY REGULATION, AND INTERACTION WITH THE DNL4-LIF1 COMPLEX.
RX PubMed=12235149; DOI=10.1074/jbc.m206861200;
RA Tseng H.-M., Tomkinson A.E.;
RT "A physical and functional interaction between yeast Pol4 and Dnl4-Lif1
RT links DNA synthesis and ligation in nonhomologous end joining.";
RL J. Biol. Chem. 277:45630-45637(2002).
RN [8]
RP FUNCTION, AND MUTAGENESIS OF LYS-247; LYS-248 AND ASP-367.
RX PubMed=10438542; DOI=10.1074/jbc.274.33.23599;
RA Wilson T.E., Lieber M.R.;
RT "Efficient processing of DNA ends during yeast nonhomologous end joining.
RT Evidence for a DNA polymerase beta (Pol4)-dependent pathway.";
RL J. Biol. Chem. 274:23599-23609(1999).
RN [9]
RP SIMILARITY TO DNA POLYMERASE TYPE-X FAMILY.
RX PubMed=1304897; DOI=10.1002/pro.5560011216;
RA Bork P., Ouzounis C., Sander C., Scharf M., Schneider R., Sonnhammer E.;
RT "Comprehensive sequence analysis of the 182 predicted open reading frames
RT of yeast chromosome III.";
RL Protein Sci. 1:1677-1690(1992).
CC -!- FUNCTION: Repair polymerase. Involved in gap-filling in DNA
CC nonhomologous end joining (NHEJ) required for double-strand break
CC repair. Seems to conduct DNA synthesis in a stepwise distributive
CC fashion rather than in a processive fashion as for other DNA
CC polymerases. Preferentially acts upon short gaps formed by the
CC alignment of linear duplexes with complementary single-strand ends.
CC Required for filling gaps that need removal of a 5'- or 3'-terminal
CC mismatch, however lacks nuclease activities.
CC {ECO:0000269|PubMed:10438542, ECO:0000269|PubMed:12235149,
CC ECO:0000269|PubMed:8065914}.
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 -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC -!- ACTIVITY REGULATION: Stimulated by the interaction with the DNL4-LIF1
CC complex. {ECO:0000269|PubMed:12235149}.
CC -!- SUBUNIT: Interacts with DNL4 subunit of the DNL4-LIF1 complex.
CC {ECO:0000269|PubMed:12235149}.
CC -!- SUBCELLULAR LOCATION: Nucleus.
CC -!- INDUCTION: During meiosis. {ECO:0000269|PubMed:8065914}.
CC -!- SIMILARITY: Belongs to the DNA polymerase type-X family. {ECO:0000305}.
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DR EMBL; X59720; CAA42331.2; -; Genomic_DNA.
DR EMBL; BK006937; DAA07491.1; -; Genomic_DNA.
DR PIR; S19424; S19424.
DR RefSeq; NP_009940.2; NM_001178727.1.
DR AlphaFoldDB; P25615; -.
DR SMR; P25615; -.
DR BioGRID; 30992; 83.
DR DIP; DIP-4228N; -.
DR IntAct; P25615; 10.
DR MINT; P25615; -.
DR STRING; 4932.YCR014C; -.
DR iPTMnet; P25615; -.
DR PaxDb; P25615; -.
DR PRIDE; P25615; -.
DR EnsemblFungi; YCR014C_mRNA; YCR014C; YCR014C.
DR GeneID; 850372; -.
DR KEGG; sce:YCR014C; -.
DR SGD; S000000607; POL4.
DR VEuPathDB; FungiDB:YCR014C; -.
DR eggNOG; KOG2534; Eukaryota.
DR GeneTree; ENSGT00940000158515; -.
DR HOGENOM; CLU_008698_3_1_1; -.
DR InParanoid; P25615; -.
DR OMA; DFFCCKW; -.
DR BioCyc; YEAST:G3O-29329-MON; -.
DR PRO; PR:P25615; -.
DR Proteomes; UP000002311; Chromosome III.
DR RNAct; P25615; protein.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IDA:SGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006302; P:double-strand break repair; IDA:SGD.
DR GO; GO:0006303; P:double-strand break repair via nonhomologous end joining; IDA:SGD.
DR CDD; cd00141; NT_POLXc; 1.
DR Gene3D; 1.10.150.110; -; 1.
DR Gene3D; 3.30.210.10; -; 1.
DR Gene3D; 3.30.460.10; -; 1.
DR InterPro; IPR002054; DNA-dir_DNA_pol_X.
DR InterPro; IPR019843; DNA_pol-X_BS.
DR InterPro; IPR010996; DNA_pol_b-like_N.
DR InterPro; IPR028207; DNA_pol_B_palm_palm.
DR InterPro; IPR027421; DNA_pol_lamdba_lyase_dom_sf.
DR InterPro; IPR037160; DNA_Pol_thumb_sf.
DR InterPro; IPR022312; DNA_pol_X.
DR InterPro; IPR002008; DNA_pol_X_beta-like.
DR InterPro; IPR043519; NT_sf.
DR InterPro; IPR029398; PolB_thumb.
DR PANTHER; PTHR11276; PTHR11276; 1.
DR Pfam; PF14792; DNA_pol_B_palm; 1.
DR Pfam; PF14791; DNA_pol_B_thumb; 1.
DR Pfam; PF14716; HHH_8; 1.
DR PRINTS; PR00869; DNAPOLX.
DR PRINTS; PR00870; DNAPOLXBETA.
DR SMART; SM00483; POLXc; 1.
DR SUPFAM; SSF47802; SSF47802; 1.
DR SUPFAM; SSF81301; SSF81301; 1.
DR PROSITE; PS00522; DNA_POLYMERASE_X; 1.
PE 1: Evidence at protein level;
KW Direct protein sequencing; DNA damage; DNA repair;
KW DNA-directed DNA polymerase; Magnesium; Metal-binding;
KW Nucleotidyltransferase; Nucleus; Reference proteome; Transferase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:8265341"
FT CHAIN 2..582
FT /note="DNA polymerase IV"
FT /id="PRO_0000218789"
FT REGION 127..161
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 360..369
FT /note="Involved in ssDNA binding"
FT /evidence="ECO:0000250"
FT COMPBIAS 131..156
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 367
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 369
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 502
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT MUTAGEN 247
FT /note="K->R: Weakened DNA-binding."
FT /evidence="ECO:0000269|PubMed:10438542"
FT MUTAGEN 248
FT /note="K->R: Weakened DNA-binding."
FT /evidence="ECO:0000269|PubMed:10438542"
FT MUTAGEN 367
FT /note="D->E: Loss of nucleotidyl transfer."
FT /evidence="ECO:0000269|PubMed:10438542"
SQ SEQUENCE 582 AA; 67527 MW; 63BD59061F4864D0 CRC64;
MSLKGKFFAF LPNPNTSSNK FFKSILEKKG ATIVSSIQNC LQSSRKEVVI LIEDSFVDSD
MHLTQKDIFQ REAGLNDVDE FLGKIEQSGI QCVKTSCITK WVQNDKFAFQ KDDLIKFQPS
IIVISDNADD GQSSTDKESE ISTDVESERN DDSNNKDMIQ ASKPLKRLLQ GDKGRASLVT
DKTKYKNNEL IIGALKRLTK KYEIEGEKFR ARSYRLAKQS MENCDFNVRS GEEAHTKLRN
IGPSIAKKIQ VILDTGVLPG LNDSVGLEDK LKYFKNCYGI GSEIAKRWNL LNFESFCVAA
KKDPEEFVSD WTILFGWSYY DDWLCKMSRN ECFTHLKKVQ KALRGIDPEC QVELQGSYNR
GYSKCGDIDL LFFKPFCNDT TELAKIMETL CIKLYKDGYI HCFLQLTPNL EKLFLKRIVE
RFRTAKIVGY GERKRWYSSE IIKKFFMGVK LSPRELEELK EMKNDEGTLL IEEEEEEETK
LKPIDQYMSL NAKDGNYCRR LDFFCCKWDE LGAGRIHYTG SKEYNRWIRI LAAQKGFKLT
QHGLFRNNIL LESFNERRIF ELLNLKYAEP EHRNIEWEKK TA
