DNA2_YEAST
ID DNA2_YEAST Reviewed; 1522 AA.
AC P38859; D3DLB3;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 189.
DE RecName: Full=DNA replication ATP-dependent helicase/nuclease DNA2;
DE Includes:
DE RecName: Full=DNA replication nuclease DNA2;
DE EC=3.1.-.-;
DE Includes:
DE RecName: Full=DNA replication ATP-dependent helicase DNA2;
DE EC=3.6.4.12;
GN Name=DNA2; OrderedLocusNames=YHR164C;
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=8091229; DOI=10.1126/science.8091229;
RA Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Dover J., Du Z.,
RA Favello A., Fulton L., Gattung S., Geisel C., Kirsten J., Kucaba T.,
RA Hillier L.W., Jier M., Johnston L., Langston Y., Latreille P., Louis E.J.,
RA Macri C., Mardis E., Menezes S., Mouser L., Nhan M., Rifkin L., Riles L.,
RA St Peter H., Trevaskis E., Vaughan K., Vignati D., Wilcox L., Wohldman P.,
RA Waterston R., Wilson R., Vaudin M.;
RT "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome
RT VIII.";
RL Science 265:2077-2082(1994).
RN [2]
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 [3]
RP CHARACTERIZATION.
RX PubMed=7644470; DOI=10.1073/pnas.92.17.7642;
RA Budd M.E., Campbell J.L.;
RT "A yeast gene required for DNA replication encodes a protein with homology
RT to DNA helicases.";
RL Proc. Natl. Acad. Sci. U.S.A. 92:7642-7646(1995).
RN [4]
RP FUNCTION.
RX PubMed=9756935; DOI=10.1074/jbc.273.41.26880;
RA Bae S.H., Choi E., Lee K.H., Park J.S., Lee S.H., Seo Y.S.;
RT "Dna2 of Saccharomyces cerevisiae possesses a single-stranded DNA-specific
RT endonuclease activity that is able to act on double-stranded DNA in the
RT presence of ATP.";
RL J. Biol. Chem. 273:26880-26890(1998).
RN [5]
RP FUNCTION.
RX PubMed=15448135; DOI=10.1074/jbc.m409231200;
RA Kao H.I., Campbell J.L., Bambara R.A.;
RT "Dna2p helicase/nuclease is a tracking protein, like FEN1, for flap
RT cleavage during Okazaki fragment maturation.";
RL J. Biol. Chem. 279:50840-50849(2004).
RN [6]
RP FUNCTION.
RX PubMed=18805091; DOI=10.1016/j.cell.2008.08.037;
RA Zhu Z., Chung W.H., Shim E.Y., Lee S.E., Ira G.;
RT "Sgs1 helicase and two nucleases Dna2 and Exo1 resect DNA double-strand
RT break ends.";
RL Cell 134:981-994(2008).
RN [7]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-962, 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 [8]
RP FUNCTION, AND MUTAGENESIS OF GLU-675 AND LYS-677.
RX PubMed=20929864; DOI=10.1074/jbc.m110.165191;
RA Balakrishnan L., Polaczek P., Pokharel S., Campbell J.L., Bambara R.A.;
RT "Dna2 exhibits a unique strand end-dependent helicase function.";
RL J. Biol. Chem. 285:38861-38868(2010).
RN [9]
RP FUNCTION.
RX PubMed=20811461; DOI=10.1038/nature09355;
RA Cejka P., Cannavo E., Polaczek P., Masuda-Sasa T., Pokharel S.,
RA Campbell J.L., Kowalczykowski S.C.;
RT "DNA end resection by Dna2-Sgs1-RPA and its stimulation by Top3-Rmi1 and
RT Mre11-Rad50-Xrs2.";
RL Nature 467:112-116(2010).
RN [10]
RP FUNCTION, PHOSPHORYLATION AT THR-4; SER-17 AND SER-237, AND MUTAGENESIS OF
RP THR-4; SER-17 AND SER-237.
RX PubMed=21841787; DOI=10.1038/nsmb.2105;
RA Chen X., Niu H., Chung W.H., Zhu Z., Papusha A., Shim E.Y., Lee S.E.,
RA Sung P., Ira G.;
RT "Cell cycle regulation of DNA double-strand break end resection by Cdk1-
RT dependent Dna2 phosphorylation.";
RL Nat. Struct. Mol. Biol. 18:1015-1019(2011).
RN [11]
RP COFACTOR, IRON-SULFUR-BINDING, AND MUTAGENESIS OF PRO-504; CYS-519;
RP CYS-768; CYS-771 AND CYS-777.
RX PubMed=22684504; DOI=10.1093/nar/gks534;
RA Pokharel S., Campbell J.L.;
RT "Cross talk between the nuclease and helicase activities of Dna2: role of
RT an essential iron-sulfur cluster domain.";
RL Nucleic Acids Res. 40:7821-7830(2012).
CC -!- FUNCTION: Key enzyme involved in DNA replication and DNA repair.
CC Involved in Okazaki fragments processing by cleaving long flaps that
CC escape FEN1: flaps that are longer than 27 nucleotides are coated by
CC replication protein A complex (RPA), leading to recruit DNA2 which
CC cleaves the flap until it is too short to bind RPA and becomes a
CC substrate for FEN1. Also involved in 5'-end resection of DNA during
CC double-strand break (DSB) repair by mediating the cleavage of 5'-ssDNA.
CC Possesses different enzymatic activities, such as single-stranded DNA
CC (ssDNA)-dependent ATPase, 5'-3' helicase and endonuclease activities.
CC While the ATPase and endonuclease activities are well-defined and play
CC a key role in Okazaki fragments processing and DSB repair, the 5'-3'
CC DNA helicase activity is atypical: it cannot load onto its tracking
CC strand internally and has an absolute free 5'-end requirement. Helicase
CC activity may promote the motion of DNA2 on the flap, helping the
CC nuclease function. {ECO:0000269|PubMed:15448135,
CC ECO:0000269|PubMed:18805091, ECO:0000269|PubMed:20811461,
CC ECO:0000269|PubMed:20929864, ECO:0000269|PubMed:21841787,
CC ECO:0000269|PubMed:9756935}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.12;
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000269|PubMed:22684504};
CC Note=Binds 1 [4Fe-4S] cluster. {ECO:0000269|PubMed:22684504};
CC -!- INTERACTION:
CC P38859; P26793: RAD27; NbExp=3; IntAct=EBI-5973, EBI-14693;
CC P38859; P22336: RFA1; NbExp=3; IntAct=EBI-5973, EBI-14971;
CC -!- SUBCELLULAR LOCATION: Nucleus. Chromosome. Note=Recruited to double-
CC strand. break (DSB) sites following phosphorylation at Ser-17 and Ser-
CC 237.
CC -!- PTM: Phosphorylated at Ser-17 and Ser-237 by CDK1 in response to DNA
CC damage, leading to promote recruitment to double-strand break (DSB)
CC sites and DNA resection. {ECO:0000269|PubMed:21841787}.
CC -!- SIMILARITY: Belongs to the DNA2/NAM7 helicase family. {ECO:0000305}.
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DR EMBL; U00027; AAB68010.1; -; Genomic_DNA.
DR EMBL; BK006934; DAA06857.1; -; Genomic_DNA.
DR PIR; S48904; S48904.
DR RefSeq; NP_012034.1; NM_001179295.1.
DR PDB; 5HOG; X-ray; 3.09 A; D/E=207-223.
DR PDBsum; 5HOG; -.
DR AlphaFoldDB; P38859; -.
DR SMR; P38859; -.
DR BioGRID; 36598; 571.
DR DIP; DIP-2324N; -.
DR IntAct; P38859; 11.
DR MINT; P38859; -.
DR STRING; 4932.YHR164C; -.
DR iPTMnet; P38859; -.
DR MaxQB; P38859; -.
DR PaxDb; P38859; -.
DR PRIDE; P38859; -.
DR TopDownProteomics; P38859; -.
DR EnsemblFungi; YHR164C_mRNA; YHR164C; YHR164C.
DR GeneID; 856569; -.
DR KEGG; sce:YHR164C; -.
DR SGD; S000001207; DNA2.
DR VEuPathDB; FungiDB:YHR164C; -.
DR eggNOG; KOG1805; Eukaryota.
DR GeneTree; ENSGT00940000165719; -.
DR HOGENOM; CLU_001666_2_1_1; -.
DR InParanoid; P38859; -.
DR OMA; NYCEAAI; -.
DR BioCyc; YEAST:G3O-31198-MON; -.
DR Reactome; R-SCE-69166; Removal of the Flap Intermediate.
DR PRO; PR:P38859; -.
DR Proteomes; UP000002311; Chromosome VIII.
DR RNAct; P38859; protein.
DR GO; GO:0000781; C:chromosome, telomeric region; IDA:SGD.
DR GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR GO; GO:0005829; C:cytosol; TAS:Reactome.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0035861; C:site of double-strand break; IDA:UniProtKB.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:UniProtKB.
DR GO; GO:0043139; F:5'-3' DNA helicase activity; IDA:UniProtKB.
DR GO; GO:0017108; F:5'-flap endonuclease activity; IDA:SGD.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003678; F:DNA helicase activity; IDA:SGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004518; F:nuclease activity; IDA:UniProtKB.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0000014; F:single-stranded DNA endodeoxyribonuclease activity; IDA:SGD.
DR GO; GO:0017116; F:single-stranded DNA helicase activity; IDA:UniProtKB.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; IDA:UniProtKB.
DR GO; GO:0000729; P:DNA double-strand break processing; IMP:UniProtKB.
DR GO; GO:0006281; P:DNA repair; IMP:SGD.
DR GO; GO:0033567; P:DNA replication, Okazaki fragment processing; IEA:InterPro.
DR GO; GO:0006261; P:DNA-templated DNA replication; IDA:SGD.
DR GO; GO:0006273; P:lagging strand elongation; IMP:SGD.
DR GO; GO:0000706; P:meiotic DNA double-strand break processing; IGI:SGD.
DR GO; GO:0071932; P:replication fork reversal; IBA:GO_Central.
DR GO; GO:0000723; P:telomere maintenance; IMP:SGD.
DR CDD; cd18808; SF1_C_Upf1; 1.
DR Gene3D; 3.40.50.300; -; 3.
DR Gene3D; 3.90.320.10; -; 1.
DR InterPro; IPR026851; Dna2.
DR InterPro; IPR045055; DNA2/NAM7-like.
DR InterPro; IPR041679; DNA2/NAM7-like_C.
DR InterPro; IPR041677; DNA2/NAM7_AAA_11.
DR InterPro; IPR014808; DNA_replication_fac_Dna2_N.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR011604; PDDEXK-like_dom_sf.
DR PANTHER; PTHR10887; PTHR10887; 1.
DR PANTHER; PTHR10887:SF433; PTHR10887:SF433; 1.
DR Pfam; PF13086; AAA_11; 2.
DR Pfam; PF13087; AAA_12; 1.
DR Pfam; PF08696; Dna2; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
PE 1: Evidence at protein level;
KW 3D-structure; 4Fe-4S; ATP-binding; Chromosome; DNA damage; DNA repair;
KW DNA replication; DNA-binding; Helicase; Hydrolase; Iron; Iron-sulfur;
KW Metal-binding; Multifunctional enzyme; Nuclease; Nucleotide-binding;
KW Nucleus; Phosphoprotein; Reference proteome.
FT CHAIN 1..1522
FT /note="DNA replication ATP-dependent helicase/nuclease
FT DNA2"
FT /id="PRO_0000080711"
FT REGION 1..29
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 77..119
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 140..160
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 239..270
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 283..330
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 450..900
FT /note="Nuclease activity"
FT REGION 901..1522
FT /note="Helicase activity"
FT COMPBIAS 1..18
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 77..104
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 105..119
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 246..264
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 286..308
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 309..325
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 519
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT BINDING 768
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT BINDING 771
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT BINDING 777
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT BINDING 1074..1081
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT MOD_RES 4
FT /note="Phosphothreonine"
FT /evidence="ECO:0000269|PubMed:21841787"
FT MOD_RES 17
FT /note="Phosphoserine; by CDK1"
FT /evidence="ECO:0000269|PubMed:21841787"
FT MOD_RES 237
FT /note="Phosphoserine; by CDK1"
FT /evidence="ECO:0000269|PubMed:21841787"
FT MOD_RES 962
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT MUTAGEN 4
FT /note="T->A: Abolishes phosphorylation by CDK1, leading to
FT a poor recruitment at double-strand. break (DSB) sites
FT following DNA damage; when associated with A-17 and A-237."
FT /evidence="ECO:0000269|PubMed:21841787"
FT MUTAGEN 17
FT /note="S->A: Abolishes phosphorylation by CDK1, leading to
FT a poor recruitment at double-strand. break (DSB) sites
FT following DNA damage; when associated with A-4 and A-237."
FT /evidence="ECO:0000269|PubMed:21841787"
FT MUTAGEN 17
FT /note="S->D: Mimics phosphorylation; restores nuclear
FT localization and recruitment at double-strand. break (DSB)
FT sites following DNA damage; when associated with D-237."
FT /evidence="ECO:0000269|PubMed:21841787"
FT MUTAGEN 237
FT /note="S->A: Abolishes phosphorylation by CDK1, leading to
FT a poor recruitment at double-strand. break (DSB) sites
FT following DNA damage; when associated with A-4 and A-17."
FT /evidence="ECO:0000269|PubMed:21841787"
FT MUTAGEN 237
FT /note="S->D: Mimics phosphorylation; restores nuclear
FT localization and recruitment at double-strand. break (DSB)
FT sites following DNA damage; when associated with D-17."
FT /evidence="ECO:0000269|PubMed:21841787"
FT MUTAGEN 504
FT /note="P->S: In dna2-1; temperature-sensitive mutant unable
FT to grow at 37 degrees Celsius, probably due to abolition of
FT iron-sulfur-binding."
FT /evidence="ECO:0000269|PubMed:22684504"
FT MUTAGEN 519
FT /note="C->A: Abolishes iron-sulfur-binding; when associated
FT with A-768; A-771 and A-777. Impaired nuclease and ATPase
FT activities; when associated with A-768."
FT /evidence="ECO:0000269|PubMed:22684504"
FT MUTAGEN 675
FT /note="E->A: Nuclease dead mutant. No helicase activity
FT when the 5'-end of the substrate is blocked."
FT /evidence="ECO:0000269|PubMed:20929864"
FT MUTAGEN 677
FT /note="K->R: Nuclease dead mutant. No helicase activity
FT when the 5'-end of the substrate is blocked."
FT /evidence="ECO:0000269|PubMed:20929864"
FT MUTAGEN 768
FT /note="C->A: Abolishes iron-sulfur-binding; when associated
FT with A-519; A-771 and A-777. Impaired nuclease and ATPase
FT activities; when associated with A-519."
FT /evidence="ECO:0000269|PubMed:22684504"
FT MUTAGEN 771
FT /note="C->A: Abolishes iron-sulfur-binding; when associated
FT with A-519; A-768 and A-777. Impaired nuclease and ATPase
FT activities; when associated with A-777."
FT /evidence="ECO:0000269|PubMed:22684504"
FT MUTAGEN 777
FT /note="C->A: Abolishes iron-sulfur-binding; when associated
FT with A-519; A-768 and A-771. Impaired nuclease and ATPase
FT activities; when associated with A-771."
FT /evidence="ECO:0000269|PubMed:22684504"
FT HELIX 212..215
FT /evidence="ECO:0007829|PDB:5HOG"
SQ SEQUENCE 1522 AA; 171694 MW; 213A0458A6C69D78 CRC64;
MPGTPQKNKR SASISVSPAK KTEEKEIIQN DSKAILSKQT KRKKKYAFAP INNLNGKNTK
VSNASVLKSI AVSQVRNTSR TKDINKAVSK SVKQLPNSQV KPKREMSNLS RHHDFTQDED
GPMEEVIWKY SPLQRDMSDK TTSAAEYSDD YEDVQNPSST PIVPNRLKTV LSFTNIQVPN
ADVNQLIQEN GNEQVRPKPA EISTRESLRN IDDILDDIEG DLTIKPTITK FSDLPSSPIK
APNVEKKAEV NAEEVDKMDS TGDSNDGDDS LIDILTQKYV EKRKSESQIT IQGNTNQKSG
AQESCGKNDN TKSRGEIEDH ENVDNQAKTG NAFYENEEDS NCQRIKKNEK IEYNSSDEFS
DDSLIELLNE TQTQVEPNTI EQDLDKVEKM VSDDLRIATD STLSAYALRA KSGAPRDGVV
RLVIVSLRSV ELPKIGTQKI LECIDGKGEQ SSVVVRHPWV YLEFEVGDVI HIIEGKNIEN
KRLLSDDKNP KTQLANDNLL VLNPDVLFSA TSVGSSVGCL RRSILQMQFQ DPRGEPSLVM
TLGNIVHELL QDSIKYKLSH NKISMEIIIQ KLDSLLETYS FSIIICNEEI QYVKELVMKE
HAENILYFVN KFVSKSNYGC YTSISGTRRT QPISISNVID IEENIWSPIY GLKGFLDATV
EANVENNKKH IVPLEVKTGK SRSVSYEVQG LIYTLLLNDR YEIPIEFFLL YFTRDKNMTK
FPSVLHSIKH ILMSRNRMSM NFKHQLQEVF GQAQSRFELP PLLRDSSCDS CFIKESCMVL
NKLLEDGTPE ESGLVEGEFE ILTNHLSQNL ANYKEFFTKY NDLITKEESS ITCVNKELFL
LDGSTRESRS GRCLSGLVVS EVVEHEKTEG AYIYCFSRRR NDNNSQSMLS SQIAANDFVI
ISDEEGHFCL CQGRVQFINP AKIGISVKRK LLNNRLLDKE KGVTTIQSVV ESELEQSSLI
ATQNLVTYRI DKNDIQQSLS LARFNLLSLF LPAVSPGVDI VDERSKLCRK TKRSDGGNEI
LRSLLVDNRA PKFRDANDDP VIPYKLSKDT TLNLNQKEAI DKVMRAEDYA LILGMPGTGK
TTVIAEIIKI LVSEGKRVLL TSYTHSAVDN ILIKLRNTNI SIMRLGMKHK VHPDTQKYVP
NYASVKSYND YLSKINSTSV VATTCLGIND ILFTLNEKDF DYVILDEASQ ISMPVALGPL
RYGNRFIMVG DHYQLPPLVK NDAARLGGLE ESLFKTFCEK HPESVAELTL QYRMCGDIVT
LSNFLIYDNK LKCGNNEVFA QSLELPMPEA LSRYRNESAN SKQWLEDILE PTRKVVFLNY
DNCPDIIEQS EKDNITNHGE AELTLQCVEG MLLSGVPCED IGVMTLYRAQ LRLLKKIFNK
NVYDGLEILT ADQFQGRDKK CIIISMVRRN SQLNGGALLK ELRRVNVAMT RAKSKLIIIG
SKSTIGSVPE IKSFVNLLEE RNWVYTMCKD ALYKYKFPDR SNAIDEARKG CGKRTGAKPI
TSKSKFVSDK PIIKEILQEY ES
