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 27-MAR-2024, entry version 197. 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}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- 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; 575. DR DIP; DIP-2324N; -. DR IntAct; P38859; 11. DR MINT; P38859; -. DR STRING; 4932.YHR164C; -. DR iPTMnet; P38859; -. DR MaxQB; P38859; -. DR PaxDb; 4932-YHR164C; -. DR PeptideAtlas; P38859; -. DR TopDownProteomics; P38859; -. DR EnsemblFungi; YHR164C_mRNA; YHR164C; YHR164C. DR GeneID; 856569; -. DR KEGG; sce:YHR164C; -. DR AGR; SGD:S000001207; -. 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 OrthoDB; 170190at2759; -. DR BioCyc; YEAST:G3O-31198-MONOMER; -. DR BioGRID-ORCS; 856569; 3 hits in 10 CRISPR screens. 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:DNA damage response; 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: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; cd18041; DEXXQc_DNA2; 1. DR CDD; cd18808; SF1_C_Upf1; 1. DR Gene3D; 3.90.320.10; -; 1. DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 3. DR InterPro; IPR026851; Dna2/JHS1_DEXXQ-box. 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 InterPro; IPR047187; SF1_C_Upf1. DR PANTHER; PTHR10887:SF433; DNA REPLICATION ATP-DEPENDENT HELICASE_NUCLEASE DNA2; 1. DR PANTHER; PTHR10887; DNA2/NAM7 HELICASE FAMILY; 1. DR Pfam; PF13086; AAA_11; 2. DR Pfam; PF13087; AAA_12; 1. DR Pfam; PF08696; Dna2; 1. DR SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 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 //