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Protein

DNA polymerase IV

Gene

POL4

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Repair polymerase. Involved in gap-filling in DNA nonhomologous end joining (NHEJ) required for double-strand break repair. Seems to conduct DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases. Preferentially acts upon short gaps formed by the alignment of linear duplexes with complementary single-strand ends. Required for filling gaps that need removal of a 5'- or 3'-terminal mismatch, however lacks nuclease activities.3 Publications

Catalytic activityi

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

Cofactori

Mg2+By similarity

Enzyme regulationi

Stimulated by the interaction with the DNL4-LIF1 complex.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi367 – 3671MagnesiumBy similarity
Metal bindingi369 – 3691MagnesiumBy similarity
Metal bindingi502 – 5021MagnesiumBy similarity

GO - Molecular functioni

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

GO - Biological processi

  • double-strand break repair Source: SGD
  • double-strand break repair via nonhomologous end joining Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

DNA-directed DNA polymerase, Nucleotidyltransferase, Transferase

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-29329-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase IV (EC:2.7.7.7)
Short name:
POL IV
Gene namesi
Name:POL4
Synonyms:POLX
Ordered Locus Names:YCR014C
ORF Names:YCR14C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome III

Organism-specific databases

EuPathDBiFungiDB:YCR014C.
SGDiS000000607. POL4.

Subcellular locationi

GO - Cellular componenti

  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi247 – 2471K → R: Weakened DNA-binding. 1 Publication
Mutagenesisi248 – 2481K → R: Weakened DNA-binding. 1 Publication
Mutagenesisi367 – 3671D → E: Loss of nucleotidyl transfer. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved1 Publication
Chaini2 – 582581DNA polymerase IVPRO_0000218789Add
BLAST

Expressioni

Inductioni

During meiosis.1 Publication

Interactioni

Subunit structurei

Interacts with DNL4 subunit of the DNL4-LIF1 complex.1 Publication

Protein-protein interaction databases

BioGridi30992. 25 interactions.
DIPiDIP-4228N.
MINTiMINT-473646.

Structurei

3D structure databases

ProteinModelPortaliP25615.
SMRiP25615. Positions 195-574.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni360 – 36910Involved in ssDNA bindingBy similarity

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi472 – 4787Poly-Glu

Sequence similaritiesi

Belongs to the DNA polymerase type-X family.Curated

Phylogenomic databases

HOGENOMiHOG000057123.
InParanoidiP25615.
KOiK10981.
OMAiDFFCCKW.
OrthoDBiEOG7ZGXBS.

Family and domain databases

Gene3Di1.10.150.110. 1 hit.
3.30.210.10. 1 hit.
InterProiIPR002054. DNA-dir_DNA_pol_X.
IPR019843. DNA_pol-X_BS.
IPR010996. DNA_pol_b-like_N.
IPR028207. DNA_pol_B_palm_palm.
IPR022312. DNA_pol_X.
IPR002008. DNA_pol_X_beta-like.
IPR027421. DNA_pol_X_lyase_dom.
IPR029398. PolB_thumb.
[Graphical view]
PfamiPF14792. DNA_pol_B_palm. 1 hit.
PF14791. DNA_pol_B_thumb. 1 hit.
PF14716. HHH_8. 1 hit.
[Graphical view]
PRINTSiPR00869. DNAPOLX.
PR00870. DNAPOLXBETA.
SMARTiSM00483. POLXc. 1 hit.
[Graphical view]
SUPFAMiSSF47802. SSF47802. 1 hit.
PROSITEiPS00522. DNA_POLYMERASE_X. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P25615-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSLKGKFFAF LPNPNTSSNK FFKSILEKKG ATIVSSIQNC LQSSRKEVVI
60 70 80 90 100
LIEDSFVDSD MHLTQKDIFQ REAGLNDVDE FLGKIEQSGI QCVKTSCITK
110 120 130 140 150
WVQNDKFAFQ KDDLIKFQPS IIVISDNADD GQSSTDKESE ISTDVESERN
160 170 180 190 200
DDSNNKDMIQ ASKPLKRLLQ GDKGRASLVT DKTKYKNNEL IIGALKRLTK
210 220 230 240 250
KYEIEGEKFR ARSYRLAKQS MENCDFNVRS GEEAHTKLRN IGPSIAKKIQ
260 270 280 290 300
VILDTGVLPG LNDSVGLEDK LKYFKNCYGI GSEIAKRWNL LNFESFCVAA
310 320 330 340 350
KKDPEEFVSD WTILFGWSYY DDWLCKMSRN ECFTHLKKVQ KALRGIDPEC
360 370 380 390 400
QVELQGSYNR GYSKCGDIDL LFFKPFCNDT TELAKIMETL CIKLYKDGYI
410 420 430 440 450
HCFLQLTPNL EKLFLKRIVE RFRTAKIVGY GERKRWYSSE IIKKFFMGVK
460 470 480 490 500
LSPRELEELK EMKNDEGTLL IEEEEEEETK LKPIDQYMSL NAKDGNYCRR
510 520 530 540 550
LDFFCCKWDE LGAGRIHYTG SKEYNRWIRI LAAQKGFKLT QHGLFRNNIL
560 570 580
LESFNERRIF ELLNLKYAEP EHRNIEWEKK TA
Length:582
Mass (Da):67,527
Last modified:January 23, 2007 - v4
Checksum:i63BD59061F4864D0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X59720 Genomic DNA. Translation: CAA42331.2.
BK006937 Genomic DNA. Translation: DAA07491.1.
PIRiS19424.
RefSeqiNP_009940.2. NM_001178727.1.

Genome annotation databases

EnsemblFungiiCAA42331; CAA42331; CAA42331.
YCR014C; YCR014C; YCR014C.
GeneIDi850372.
KEGGisce:YCR014C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X59720 Genomic DNA. Translation: CAA42331.2.
BK006937 Genomic DNA. Translation: DAA07491.1.
PIRiS19424.
RefSeqiNP_009940.2. NM_001178727.1.

3D structure databases

ProteinModelPortaliP25615.
SMRiP25615. Positions 195-574.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi30992. 25 interactions.
DIPiDIP-4228N.
MINTiMINT-473646.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiCAA42331; CAA42331; CAA42331.
YCR014C; YCR014C; YCR014C.
GeneIDi850372.
KEGGisce:YCR014C.

Organism-specific databases

EuPathDBiFungiDB:YCR014C.
SGDiS000000607. POL4.

Phylogenomic databases

HOGENOMiHOG000057123.
InParanoidiP25615.
KOiK10981.
OMAiDFFCCKW.
OrthoDBiEOG7ZGXBS.

Enzyme and pathway databases

BioCyciYEAST:G3O-29329-MONOMER.

Miscellaneous databases

PROiP25615.

Family and domain databases

Gene3Di1.10.150.110. 1 hit.
3.30.210.10. 1 hit.
InterProiIPR002054. DNA-dir_DNA_pol_X.
IPR019843. DNA_pol-X_BS.
IPR010996. DNA_pol_b-like_N.
IPR028207. DNA_pol_B_palm_palm.
IPR022312. DNA_pol_X.
IPR002008. DNA_pol_X_beta-like.
IPR027421. DNA_pol_X_lyase_dom.
IPR029398. PolB_thumb.
[Graphical view]
PfamiPF14792. DNA_pol_B_palm. 1 hit.
PF14791. DNA_pol_B_thumb. 1 hit.
PF14716. HHH_8. 1 hit.
[Graphical view]
PRINTSiPR00869. DNAPOLX.
PR00870. DNAPOLXBETA.
SMARTiSM00483. POLXc. 1 hit.
[Graphical view]
SUPFAMiSSF47802. SSF47802. 1 hit.
PROSITEiPS00522. DNA_POLYMERASE_X. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The complete DNA sequence of yeast chromosome III."
    Oliver S.G., van der Aart Q.J.M., Agostoni-Carbone M.L., Aigle M., Alberghina L., Alexandraki D., Antoine G., Anwar R., Ballesta J.P.G., Benit P., Berben G., Bergantino E., Biteau N., Bolle P.-A., Bolotin-Fukuhara M., Brown A., Brown A.J.P., Buhler J.-M.
    , Carcano C., Carignani G., Cederberg H., Chanet R., Contreras R., Crouzet M., Daignan-Fornier B., Defoor E., Delgado M.D., Demolder J., Doira C., Dubois E., Dujon B., Duesterhoeft A., Erdmann D., Esteban M., Fabre F., Fairhead C., Faye G., Feldmann H., Fiers W., Francingues-Gaillard M.-C., Franco L., Frontali L., Fukuhara H., Fuller L.J., Galland P., Gent M.E., Gigot D., Gilliquet V., Glansdorff N., Goffeau A., Grenson M., Grisanti P., Grivell L.A., de Haan M., Haasemann M., Hatat D., Hoenicka J., Hegemann J.H., Herbert C.J., Hilger F., Hohmann S., Hollenberg C.P., Huse K., Iborra F., Indge K.J., Isono K., Jacq C., Jacquet M., James C.M., Jauniaux J.-C., Jia Y., Jimenez A., Kelly A., Kleinhans U., Kreisl P., Lanfranchi G., Lewis C., van der Linden C.G., Lucchini G., Lutzenkirchen K., Maat M.J., Mallet L., Mannhaupt G., Martegani E., Mathieu A., Maurer C.T.C., McConnell D., McKee R.A., Messenguy F., Mewes H.-W., Molemans F., Montague M.A., Muzi Falconi M., Navas L., Newlon C.S., Noone D., Pallier C., Panzeri L., Pearson B.M., Perea J., Philippsen P., Pierard A., Planta R.J., Plevani P., Poetsch B., Pohl F.M., Purnelle B., Ramezani Rad M., Rasmussen S.W., Raynal A., Remacha M.A., Richterich P., Roberts A.B., Rodriguez F., Sanz E., Schaaff-Gerstenschlaeger I., Scherens B., Schweitzer B., Shu Y., Skala J., Slonimski P.P., Sor F., Soustelle C., Spiegelberg R., Stateva L.I., Steensma H.Y., Steiner S., Thierry A., Thireos G., Tzermia M., Urrestarazu L.A., Valle G., Vetter I., van Vliet-Reedijk J.C., Voet M., Volckaert G., Vreken P., Wang H., Warmington J.R., von Wettstein D., Wicksteed B.L., Wilson C., Wurst H., Xu G., Yoshikawa A., Zimmermann F.K., Sgouros J.G.
    Nature 357:38-46(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Valles G., Volckaerts G.
    Submitted (JUN-2001) to the EMBL/GenBank/DDBJ databases
    Cited for: SEQUENCE REVISION TO 49; 171; 451 AND 482.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. "The complete sequence of a 10.8 kb segment distal of SUF2 on the right arm of chromosome III from Saccharomyces cerevisiae reveals seven open reading frames including the RVS161, ADP1 and PGK genes."
    Skala J., Purnelle B., Goffeau A.
    Yeast 8:409-417(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 303-582.
  5. "Yeast open reading frame YCR14C encodes a DNA beta-polymerase-like enzyme."
    Prasad R., Widen S.G., Singhal R.K., Watkins J., Prakash L., Wilson S.H.
    Nucleic Acids Res. 21:5301-5307(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION, PROTEIN SEQUENCE OF 2-15.
  6. "The yeast Saccharomyces cerevisiae DNA polymerase IV: possible involvement in double strand break DNA repair."
    Leem S.-H., Ropp P.A., Sugino A.
    Nucleic Acids Res. 22:3011-3017(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 67-79; 138-149; 287-299; 342-356 AND 365-373, FUNCTION, INDUCTION.
  7. "A physical and functional interaction between yeast Pol4 and Dnl4-Lif1 links DNA synthesis and ligation in nonhomologous end joining."
    Tseng H.-M., Tomkinson A.E.
    J. Biol. Chem. 277:45630-45637(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, ENZYME REGULATION, INTERACTION WITH THE DNL4-LIF1 COMPLEX.
  8. "Efficient processing of DNA ends during yeast nonhomologous end joining. Evidence for a DNA polymerase beta (Pol4)-dependent pathway."
    Wilson T.E., Lieber M.R.
    J. Biol. Chem. 274:23599-23609(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, MUTAGENESIS OF LYS-247; LYS-248 AND ASP-367.
  9. "Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III."
    Bork P., Ouzounis C., Sander C., Scharf M., Schneider R., Sonnhammer E.
    Protein Sci. 1:1677-1690(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: SIMILARITY TO DNA POLYMERASE TYPE-X FAMILY.

Entry informationi

Entry nameiDPO4_YEAST
AccessioniPrimary (citable) accession number: P25615
Secondary accession number(s): D6VR22
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: January 23, 2007
Last modified: July 6, 2016
This is version 142 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome III
    Yeast (Saccharomyces cerevisiae) chromosome III: entries and gene names

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.