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DNA replication ATP-dependent helicase/nuclease DNA2 [Includes: DNA replication nuclease DNA2 (EC 3.1.-.-); DNA replication ATP-dependent helicase DNA2 (EC 3.6.4.12)]

 DNA2_YEAST              Reviewed;        1522 AA.
P38859; D3DLB3;
01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
01-FEB-1995, sequence version 1.
22-NOV-2017, entry version 159.
RecName: Full=DNA replication ATP-dependent helicase/nuclease DNA2;
Includes:
RecName: Full=DNA replication nuclease DNA2;
EC=3.1.-.-;
Includes:
RecName: Full=DNA replication ATP-dependent helicase DNA2;
EC=3.6.4.12;
Name=DNA2; OrderedLocusNames=YHR164C;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=8091229; DOI=10.1126/science.8091229;
Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Dover J.,
Du Z., Favello A., Fulton L., Gattung S., Geisel C., Kirsten J.,
Kucaba T., Hillier L.W., Jier M., Johnston L., Langston Y.,
Latreille P., Louis E.J., Macri C., Mardis E., Menezes S., Mouser L.,
Nhan M., Rifkin L., Riles L., St Peter H., Trevaskis E., Vaughan K.,
Vignati D., Wilcox L., Wohldman P., Waterston R., Wilson R.,
Vaudin M.;
"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome
VIII.";
Science 265:2077-2082(1994).
[2]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[3]
CHARACTERIZATION.
PubMed=7644470; DOI=10.1073/pnas.92.17.7642;
Budd M.E., Campbell J.L.;
"A yeast gene required for DNA replication encodes a protein with
homology to DNA helicases.";
Proc. Natl. Acad. Sci. U.S.A. 92:7642-7646(1995).
[4]
FUNCTION.
PubMed=9756935; DOI=10.1074/jbc.273.41.26880;
Bae S.H., Choi E., Lee K.H., Park J.S., Lee S.H., Seo Y.S.;
"Dna2 of Saccharomyces cerevisiae possesses a single-stranded DNA-
specific endonuclease activity that is able to act on double-stranded
DNA in the presence of ATP.";
J. Biol. Chem. 273:26880-26890(1998).
[5]
FUNCTION.
PubMed=15448135; DOI=10.1074/jbc.M409231200;
Kao H.I., Campbell J.L., Bambara R.A.;
"Dna2p helicase/nuclease is a tracking protein, like FEN1, for flap
cleavage during Okazaki fragment maturation.";
J. Biol. Chem. 279:50840-50849(2004).
[6]
FUNCTION.
PubMed=18805091; DOI=10.1016/j.cell.2008.08.037;
Zhu Z., Chung W.H., Shim E.Y., Lee S.E., Ira G.;
"Sgs1 helicase and two nucleases Dna2 and Exo1 resect DNA double-
strand break ends.";
Cell 134:981-994(2008).
[7]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-962, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=18407956; DOI=10.1074/mcp.M700468-MCP200;
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
"A multidimensional chromatography technology for in-depth
phosphoproteome analysis.";
Mol. Cell. Proteomics 7:1389-1396(2008).
[8]
FUNCTION, AND MUTAGENESIS OF GLU-675 AND LYS-677.
PubMed=20929864; DOI=10.1074/jbc.M110.165191;
Balakrishnan L., Polaczek P., Pokharel S., Campbell J.L.,
Bambara R.A.;
"Dna2 exhibits a unique strand end-dependent helicase function.";
J. Biol. Chem. 285:38861-38868(2010).
[9]
FUNCTION.
PubMed=20811461; DOI=10.1038/nature09355;
Cejka P., Cannavo E., Polaczek P., Masuda-Sasa T., Pokharel S.,
Campbell J.L., Kowalczykowski S.C.;
"DNA end resection by Dna2-Sgs1-RPA and its stimulation by Top3-Rmi1
and Mre11-Rad50-Xrs2.";
Nature 467:112-116(2010).
[10]
FUNCTION, PHOSPHORYLATION AT THR-4; SER-17 AND SER-237, AND
MUTAGENESIS OF THR-4; SER-17 AND SER-237.
PubMed=21841787; DOI=10.1038/nsmb.2105;
Chen X., Niu H., Chung W.H., Zhu Z., Papusha A., Shim E.Y., Lee S.E.,
Sung P., Ira G.;
"Cell cycle regulation of DNA double-strand break end resection by
Cdk1-dependent Dna2 phosphorylation.";
Nat. Struct. Mol. Biol. 18:1015-1019(2011).
[11]
COFACTOR, IRON-SULFUR-BINDING, AND MUTAGENESIS OF PRO-504; CYS-519;
CYS-768; CYS-771 AND CYS-777.
PubMed=22684504; DOI=10.1093/nar/gks534;
Pokharel S., Campbell J.L.;
"Cross talk between the nuclease and helicase activities of Dna2: role
of an essential iron-sulfur cluster domain.";
Nucleic Acids Res. 40:7821-7830(2012).
-!- FUNCTION: Key enzyme involved in DNA replication and DNA repair.
Involved in Okazaki fragments processing by cleaving long flaps
that escape FEN1: flaps that are longer than 27 nucleotides are
coated by replication protein A complex (RPA), leading to recruit
DNA2 which cleaves the flap until it is too short to bind RPA and
becomes a substrate for FEN1. Also involved in 5'-end resection of
DNA during double-strand break (DSB) repair by mediating the
cleavage of 5'-ssDNA. Possesses different enzymatic activities,
such as single-stranded DNA (ssDNA)-dependent ATPase, 5'-3'
helicase and endonuclease activities. While the ATPase and
endonuclease activities are well-defined and play a key role in
Okazaki fragments processing and DSB repair, the 5'-3' DNA
helicase activity is atypical: it cannot load onto its tracking
strand internally and has an absolute free 5'-end requirement.
Helicase activity may promote the motion of DNA2 on the flap,
helping the nuclease function. {ECO:0000269|PubMed:15448135,
ECO:0000269|PubMed:18805091, ECO:0000269|PubMed:20811461,
ECO:0000269|PubMed:20929864, ECO:0000269|PubMed:21841787,
ECO:0000269|PubMed:9756935}.
-!- CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
-!- COFACTOR:
Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
Evidence={ECO:0000269|PubMed:22684504};
Note=Binds 1 [4Fe-4S] cluster. {ECO:0000269|PubMed:22684504};
-!- INTERACTION:
P26793:RAD27; NbExp=3; IntAct=EBI-5973, EBI-14693;
P22336:RFA1; NbExp=3; IntAct=EBI-5973, EBI-14971;
-!- SUBCELLULAR LOCATION: Nucleus. Chromosome. Note=Recruited to
double-strand. break (DSB) sites following phosphorylation at Ser-
17 and Ser-237.
-!- PTM: Phosphorylated at Ser-17 and Ser-237 by CDK1 in response to
DNA damage, leading to promote recruitment to double-strand break
(DSB) sites and DNA resection. {ECO:0000269|PubMed:21841787}.
-!- SIMILARITY: Belongs to the DNA2/NAM7 helicase family.
{ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; U00027; AAB68010.1; -; Genomic_DNA.
EMBL; BK006934; DAA06857.1; -; Genomic_DNA.
PIR; S48904; S48904.
RefSeq; NP_012034.1; NM_001179295.1.
PDB; 5HOG; X-ray; 3.09 A; D/E=207-223.
PDBsum; 5HOG; -.
ProteinModelPortal; P38859; -.
SMR; P38859; -.
BioGrid; 36598; 567.
DIP; DIP-2324N; -.
IntAct; P38859; 11.
MINT; MINT-620090; -.
STRING; 4932.YHR164C; -.
iPTMnet; P38859; -.
MaxQB; P38859; -.
PRIDE; P38859; -.
TopDownProteomics; P38859; -.
EnsemblFungi; YHR164C; YHR164C; YHR164C.
GeneID; 856569; -.
KEGG; sce:YHR164C; -.
EuPathDB; FungiDB:YHR164C; -.
SGD; S000001207; DNA2.
GeneTree; ENSGT00780000122010; -.
HOGENOM; HOG000112234; -.
InParanoid; P38859; -.
KO; K10742; -.
OMA; DIEENLW; -.
OrthoDB; EOG092C07AQ; -.
BioCyc; YEAST:G3O-31198-MONOMER; -.
Reactome; R-SCE-2564818; Cytosolic iron-sulfur cluster assembly (yeast).
Reactome; R-SCE-69166; Removal of the Flap Intermediate.
PRO; PR:P38859; -.
Proteomes; UP000002311; Chromosome VIII.
GO; GO:0005737; C:cytoplasm; IDA:SGD.
GO; GO:0005829; C:cytosol; TAS:Reactome.
GO; GO:0000784; C:nuclear chromosome, telomeric region; IDA:SGD.
GO; GO:0005634; C:nucleus; IDA:UniProtKB.
GO; GO:0035861; C:site of double-strand break; IDA:UniProtKB.
GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:UniProtKB.
GO; GO:0043139; F:5'-3' DNA helicase activity; IDA:UniProtKB.
GO; GO:0017108; F:5'-flap endonuclease activity; IDA:SGD.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0004003; F:ATP-dependent DNA helicase activity; IDA:SGD.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0004518; F:nuclease activity; IDA:UniProtKB.
GO; GO:0000014; F:single-stranded DNA endodeoxyribonuclease activity; IDA:SGD.
GO; GO:0043142; F:single-stranded DNA-dependent ATPase activity; IDA:UniProtKB.
GO; GO:0006974; P:cellular response to DNA damage stimulus; IDA:UniProtKB.
GO; GO:0000729; P:DNA double-strand break processing; IMP:UniProtKB.
GO; GO:0006281; P:DNA repair; IMP:SGD.
GO; GO:0033567; P:DNA replication, Okazaki fragment processing; IEA:InterPro.
GO; GO:0000733; P:DNA strand renaturation; IDA:SGD.
GO; GO:0006261; P:DNA-dependent DNA replication; IDA:SGD.
GO; GO:0006273; P:lagging strand elongation; IMP:SGD.
GO; GO:0000706; P:meiotic DNA double-strand break processing; IGI:SGD.
GO; GO:0001302; P:replicative cell aging; IMP:SGD.
GO; GO:0044281; P:small molecule metabolic process; TAS:Reactome.
GO; GO:0000723; P:telomere maintenance; IMP:SGD.
InterPro; IPR026851; Dna2.
InterPro; IPR014808; DNA_replication_fac_Dna2_N.
InterPro; IPR027417; P-loop_NTPase.
PANTHER; PTHR10887:SF14; PTHR10887:SF14; 2.
Pfam; PF08696; Dna2; 1.
SUPFAM; SSF52540; SSF52540; 2.
1: Evidence at protein level;
3D-structure; 4Fe-4S; ATP-binding; Chromosome; Complete proteome;
DNA damage; DNA repair; DNA replication; DNA-binding; Helicase;
Hydrolase; Iron; Iron-sulfur; Metal-binding; Multifunctional enzyme;
Nuclease; Nucleotide-binding; Nucleus; Phosphoprotein;
Reference proteome.
CHAIN 1 1522 DNA replication ATP-dependent
helicase/nuclease DNA2.
/FTId=PRO_0000080711.
NP_BIND 1074 1081 ATP. {ECO:0000250}.
REGION 450 900 Nuclease activity.
REGION 901 1522 Helicase activity.
METAL 519 519 Iron-sulfur (4Fe-4S).
METAL 768 768 Iron-sulfur (4Fe-4S).
METAL 771 771 Iron-sulfur (4Fe-4S).
METAL 777 777 Iron-sulfur (4Fe-4S).
MOD_RES 4 4 Phosphothreonine.
{ECO:0000269|PubMed:21841787}.
MOD_RES 17 17 Phosphoserine; by CDK1.
{ECO:0000269|PubMed:21841787}.
MOD_RES 237 237 Phosphoserine; by CDK1.
{ECO:0000269|PubMed:21841787}.
MOD_RES 962 962 Phosphothreonine.
{ECO:0000244|PubMed:18407956}.
MUTAGEN 4 4 T->A: Abolishes phosphorylation by CDK1,
leading to a poor recruitment at double-
strand. break (DSB) sites following DNA
damage; when associated with A-17 and A-
237. {ECO:0000269|PubMed:21841787}.
MUTAGEN 17 17 S->A: Abolishes phosphorylation by CDK1,
leading to a poor recruitment at double-
strand. break (DSB) sites following DNA
damage; when associated with A-4 and A-
237. {ECO:0000269|PubMed:21841787}.
MUTAGEN 17 17 S->D: Mimics phosphorylation; restores
nuclear localization and recruitment at
double-strand. break (DSB) sites
following DNA damage; when associated
with D-237.
{ECO:0000269|PubMed:21841787}.
MUTAGEN 237 237 S->A: Abolishes phosphorylation by CDK1,
leading to a poor recruitment at double-
strand. break (DSB) sites following DNA
damage; when associated with A-4 and A-
17. {ECO:0000269|PubMed:21841787}.
MUTAGEN 237 237 S->D: Mimics phosphorylation; restores
nuclear localization and recruitment at
double-strand. break (DSB) sites
following DNA damage; when associated
with D-17. {ECO:0000269|PubMed:21841787}.
MUTAGEN 504 504 P->S: In dna2-1; temperature-sensitive
mutant unable to grow at 37 degrees
Celsius, probably due to abolition of
iron-sulfur-binding.
{ECO:0000269|PubMed:22684504}.
MUTAGEN 519 519 C->A: Abolishes iron-sulfur-binding; when
associated with A-768; A-771 and A-777.
Impaired nuclease and ATPase activities;
when associated with A-768.
{ECO:0000269|PubMed:22684504}.
MUTAGEN 675 675 E->A: Nuclease dead mutant. No helicase
activity when the 5'-end of the substrate
is blocked.
{ECO:0000269|PubMed:20929864}.
MUTAGEN 677 677 K->R: Nuclease dead mutant. No helicase
activity when the 5'-end of the substrate
is blocked.
{ECO:0000269|PubMed:20929864}.
MUTAGEN 768 768 C->A: Abolishes iron-sulfur-binding; when
associated with A-519; A-771 and A-777.
Impaired nuclease and ATPase activities;
when associated with A-519.
{ECO:0000269|PubMed:22684504}.
MUTAGEN 771 771 C->A: Abolishes iron-sulfur-binding; when
associated with A-519; A-768 and A-777.
Impaired nuclease and ATPase activities;
when associated with A-777.
{ECO:0000269|PubMed:22684504}.
MUTAGEN 777 777 C->A: Abolishes iron-sulfur-binding; when
associated with A-519; A-768 and A-771.
Impaired nuclease and ATPase activities;
when associated with A-771.
{ECO:0000269|PubMed:22684504}.
HELIX 212 215 {ECO:0000244|PDB:5HOG}.
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


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