DPOD2_YEAST
ID DPOD2_YEAST Reviewed; 487 AA.
AC P46957; D6VWI1;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1995, sequence version 1.
DT 03-AUG-2022, entry version 167.
DE RecName: Full=DNA polymerase delta small subunit;
DE EC=2.7.7.7;
DE AltName: Full=Hydroxyurea-sensitive protein 2;
GN Name=POL31; Synonyms=HUS2, HYS2, SDP5; OrderedLocusNames=YJR006W;
GN ORFNames=J1427, YJR83.7;
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 [GENOMIC DNA], AND FUNCTION.
RX PubMed=7567461; DOI=10.1093/nar/23.17.3493;
RA Sugimoto K., Sakamoto Y., Takahashi O., Matsumoto K.;
RT "HYS2, an essential gene required for DNA replication in Saccharomyces
RT cerevisiae.";
RL Nucleic Acids Res. 23:3493-3500(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8641269; DOI=10.1002/j.1460-2075.1996.tb00557.x;
RA Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C.,
RA Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D.,
RA Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J.,
RA Heumann K., Hilger F., Hollenberg C.P., Huang M.-E., Jacq C.,
RA Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E.,
RA Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T.,
RA Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B.,
RA Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R.,
RA Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N.,
RA To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H.,
RA von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.;
RT "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X.";
RL EMBO J. 15:2031-2049(1996).
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 PARTIAL PROTEIN SEQUENCE, AND CHARACTERIZATION.
RX PubMed=9421503; DOI=10.1093/nar/26.2.477;
RA Hashimoto K., Nakashima N., Ohara T., Maki S., Sugino A.;
RT "The second subunit of DNA polymerase III (delta) is encoded by the HYS2
RT gene in Saccharomyces cerevisiae.";
RL Nucleic Acids Res. 26:477-485(1998).
RN [5]
RP CHARACTERIZATION.
RX PubMed=9677405; DOI=10.1074/jbc.273.31.19747;
RA Gerik K.J., Li X., Pautz A., Burgers P.M.;
RT "Characterization of the two small subunits of Saccharomyces cerevisiae DNA
RT polymerase delta.";
RL J. Biol. Chem. 273:19747-19755(1998).
RN [6]
RP COMPOSITION OF THE DNA POLYMERASE DELTA COMPLEX.
RX PubMed=11568188; DOI=10.1074/jbc.m108842200;
RA Johansson E., Majka J., Burgers P.M.;
RT "Structure of DNA polymerase delta from Saccharomyces cerevisiae.";
RL J. Biol. Chem. 276:43824-43828(2001).
RN [7]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-20, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [9]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
CC -!- FUNCTION: DNA polymerase delta (DNA polymerase III) participates in
CC chromosomal DNA replication. It is required during synthesis of the
CC leading and lagging DNA strands at the replication fork and binds at/or
CC near replication origins and moves along DNA with the replication fork.
CC It has 3'-5' proofreading exonuclease activity that correct errors
CC arising during DNA replication. It is also involved in DNA synthesis
CC during DNA repair. {ECO:0000269|PubMed:7567461}.
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 -!- SUBUNIT: DNA polymerase delta is a heterotrimer of POL3, POL32 and
CC HYS2.
CC -!- INTERACTION:
CC P46957; P15436: POL3; NbExp=6; IntAct=EBI-6080, EBI-6134;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- MISCELLANEOUS: Present with 626 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the DNA polymerase delta/II small subunit
CC family. {ECO:0000305}.
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DR EMBL; D50324; BAA08859.1; -; Genomic_DNA.
DR EMBL; X87611; CAA60928.1; -; Genomic_DNA.
DR EMBL; Z49506; CAA89528.1; -; Genomic_DNA.
DR EMBL; BK006943; DAA08797.1; -; Genomic_DNA.
DR PIR; S55194; S55194.
DR RefSeq; NP_012539.1; NM_001181663.1.
DR PDB; 6P1H; EM; 3.20 A; B=1-487.
DR PDB; 6V8P; EM; 4.10 A; F=1-487.
DR PDB; 6V93; EM; 3.10 A; F=1-487.
DR PDB; 7KC0; EM; 3.20 A; B=1-487.
DR PDB; 7LXD; EM; 4.11 A; F=1-487.
DR PDBsum; 6P1H; -.
DR PDBsum; 6V8P; -.
DR PDBsum; 6V93; -.
DR PDBsum; 7KC0; -.
DR PDBsum; 7LXD; -.
DR AlphaFoldDB; P46957; -.
DR SMR; P46957; -.
DR BioGRID; 33762; 477.
DR ComplexPortal; CPX-2101; DNA polymerase delta complex.
DR DIP; DIP-2525N; -.
DR IntAct; P46957; 5.
DR MINT; P46957; -.
DR STRING; 4932.YJR006W; -.
DR iPTMnet; P46957; -.
DR MaxQB; P46957; -.
DR PaxDb; P46957; -.
DR PRIDE; P46957; -.
DR EnsemblFungi; YJR006W_mRNA; YJR006W; YJR006W.
DR GeneID; 853462; -.
DR KEGG; sce:YJR006W; -.
DR SGD; S000003766; POL31.
DR VEuPathDB; FungiDB:YJR006W; -.
DR eggNOG; KOG2732; Eukaryota.
DR GeneTree; ENSGT00390000006780; -.
DR HOGENOM; CLU_021763_1_0_1; -.
DR InParanoid; P46957; -.
DR OMA; DPANFML; -.
DR BioCyc; YEAST:G3O-31652-MON; -.
DR BRENDA; 2.7.7.7; 984.
DR Reactome; R-SCE-69166; Removal of the Flap Intermediate.
DR Reactome; R-SCE-69183; Processive synthesis on the lagging strand.
DR PRO; PR:P46957; -.
DR Proteomes; UP000002311; Chromosome X.
DR RNAct; P46957; protein.
DR GO; GO:0005829; C:cytosol; IDA:SGD.
DR GO; GO:0043625; C:delta DNA polymerase complex; IPI:ComplexPortal.
DR GO; GO:0042575; C:DNA polymerase complex; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IDA:SGD.
DR GO; GO:0006284; P:base-excision repair; TAS:SGD.
DR GO; GO:0006259; P:DNA metabolic process; IDA:ComplexPortal.
DR GO; GO:0043137; P:DNA replication, removal of RNA primer; IDA:SGD.
DR GO; GO:0006271; P:DNA strand elongation involved in DNA replication; IBA:GO_Central.
DR GO; GO:0006273; P:lagging strand elongation; TAS:SGD.
DR GO; GO:0006272; P:leading strand elongation; TAS:SGD.
DR GO; GO:0006298; P:mismatch repair; TAS:SGD.
DR GO; GO:0090305; P:nucleic acid phosphodiester bond hydrolysis; IEA:GOC.
DR GO; GO:0006289; P:nucleotide-excision repair; TAS:SGD.
DR GO; GO:0006301; P:postreplication repair; TAS:SGD.
DR GO; GO:0006278; P:RNA-templated DNA biosynthetic process; IDA:SGD.
DR CDD; cd07387; MPP_PolD2_C; 1.
DR InterPro; IPR007185; DNA_pol_a/d/e_bsu.
DR InterPro; IPR040663; DNA_pol_D_N.
DR InterPro; IPR024826; DNA_pol_delta/II_ssu.
DR InterPro; IPR041863; PolD2_C.
DR PANTHER; PTHR10416; PTHR10416; 1.
DR Pfam; PF18018; DNA_pol_D_N; 1.
DR Pfam; PF04042; DNA_pol_E_B; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Direct protein sequencing; DNA replication;
KW DNA-directed DNA polymerase; Nucleotidyltransferase; Nucleus;
KW Phosphoprotein; Reference proteome; Transferase.
FT CHAIN 1..487
FT /note="DNA polymerase delta small subunit"
FT /id="PRO_0000096174"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0007744|PubMed:22814378"
FT MOD_RES 20
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT CONFLICT 156
FT /note="L -> H (in Ref. 1; BAA08859)"
FT /evidence="ECO:0000305"
FT CONFLICT 465
FT /note="S -> N (in Ref. 1; BAA08859)"
FT /evidence="ECO:0000305"
FT HELIX 1..9
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 19..21
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 33..36
FT /evidence="ECO:0007829|PDB:6V93"
FT TURN 44..46
FT /evidence="ECO:0007829|PDB:6V93"
FT HELIX 53..75
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 83..86
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 98..100
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 106..109
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 113..115
FT /evidence="ECO:0007829|PDB:6P1H"
FT HELIX 116..124
FT /evidence="ECO:0007829|PDB:6V93"
FT HELIX 133..137
FT /evidence="ECO:0007829|PDB:6V93"
FT TURN 139..141
FT /evidence="ECO:0007829|PDB:6P1H"
FT STRAND 147..152
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 154..157
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 158..160
FT /evidence="ECO:0007829|PDB:7KC0"
FT TURN 161..163
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 172..177
FT /evidence="ECO:0007829|PDB:6P1H"
FT STRAND 181..185
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 186..191
FT /evidence="ECO:0007829|PDB:7KC0"
FT STRAND 207..209
FT /evidence="ECO:0007829|PDB:7KC0"
FT STRAND 213..217
FT /evidence="ECO:0007829|PDB:6V93"
FT HELIX 228..240
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 243..245
FT /evidence="ECO:0007829|PDB:6V93"
FT HELIX 248..251
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 254..259
FT /evidence="ECO:0007829|PDB:6V93"
FT TURN 268..270
FT /evidence="ECO:0007829|PDB:6P1H"
FT HELIX 273..290
FT /evidence="ECO:0007829|PDB:6V93"
FT TURN 291..293
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 294..298
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 302..306
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 308..311
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 317..320
FT /evidence="ECO:0007829|PDB:6V93"
FT HELIX 322..324
FT /evidence="ECO:0007829|PDB:6V93"
FT TURN 325..327
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 328..331
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 334..338
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 341..347
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 350..355
FT /evidence="ECO:0007829|PDB:6V93"
FT HELIX 358..363
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 385..387
FT /evidence="ECO:0007829|PDB:6P1H"
FT HELIX 392..404
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 405..408
FT /evidence="ECO:0007829|PDB:6P1H"
FT HELIX 412..415
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 422..424
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 426..428
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 434..443
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 445..449
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 456..462
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 464..467
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 469..477
FT /evidence="ECO:0007829|PDB:6V93"
FT STRAND 480..485
FT /evidence="ECO:0007829|PDB:6V93"
SQ SEQUENCE 487 AA; 55296 MW; F9E200BFE97A2C07 CRC64;
MDALLTKFNE DRSLQDENLS QPRTRVRIVD DNLYNKSNPF QLCYKKRDYG SQYYHIYQYR
LKTFRERVLK ECDKRWDAGF TLNGQLVLKK DKVLDIQGNQ PCWCVGSIYC EMKYKPNVLD
EVINDTYGAP DLTKSYTDKE GGSDEIMLED ESGRVLLVGD FIRSTPFITG VVVGILGMEA
EAGTFQVLDI CYPTPLPQNP FPAPIATCPT RGKIALVSGL NLNNTSPDRL LRLEILREFL
MGRINNKIDD ISLIGRLLIC GNSVDFDIKS VNKDELMISL TEFSKFLHNI LPSISVDIMP
GTNDPSDKSL PQQPFHKSLF DKSLESYFNG SNKEILNLVT NPYEFSYNGV DVLAVSGKNI
NDICKYVIPS NDNGESENKV EEGESNDFKD DIEHRLDLME CTMKWQNIAP TAPDTLWCYP
YTDKDPFVLD KWPHVYIVAN QPYFGTRVVE IGGKNIKIIS VPEFSSTGMI ILLDLETLEA
ETVKIDI
