P38859 (DNA2_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA replication ATP-dependent helicase/nuclease DNA2

Including the following 2 domains:

1. DNA replication nuclease DNA2
   EC=3.1.-.-
2. DNA replication ATP-dependent helicase DNA2
   EC=3.6.4.12

Gene names

Name:	DNA2
Ordered Locus Names:	YHR164C

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	1522 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

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. Ref.4 Ref.5 Ref.8 Ref.9 Ref.10 Ref.11
Catalytic activity	ATP + H2O = ADP + phosphate.
Cofactor	Binds 1 4Fe-4S cluster. Ref.12
Subcellular location	Nucleus. Chromosome. Note: Recruited to double-strand. break (DSB) sites following phosphorylation at Ser-17 and Ser-237.
Post-translational modification	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. Ref.11
Sequence similarities	Belongs to the DNA2/NAM7 helicase family.

Ontologies

Keywords
Biological process	DNA damage DNA repair DNA replication
Cellular component	Chromosome Nucleus
Ligand	4Fe-4S ATP-binding DNA-binding Iron Iron-sulfur Metal-binding Nucleotide-binding
Molecular function	Helicase Hydrolase Nuclease
PTM	Phosphoprotein
Technical term	Complete proteome Multifunctional enzyme Reference proteome
Gene Ontology (GO)
Biological_process	DNA replication, Okazaki fragment processing Inferred from electronic annotation. Source: InterPro DNA strand renaturation Inferred from direct assay PubMed 17032657. Source: SGD lagging strand elongation Inferred from mutant phenotype PubMed 10101169PubMed 10330154. Source: SGD meiotic DNA double-strand break processing Inferred from genetic interaction PubMed 20150422. Source: SGD replicative cell aging Inferred from mutant phenotype PubMed 12024027. Source: SGD telomere maintenance Inferred from mutant phenotype PubMed 12024033. Source: SGD
Cellular_component	cytoplasm Inferred from direct assay PubMed 19520826. Source: SGD nuclear chromosome, telomeric region Inferred from direct assay PubMed 12024033. Source: SGD site of double-strand break Inferred from direct assay Ref.11. Source: UniProtKB
Molecular_function	4 iron, 4 sulfur cluster binding Inferred from direct assay Ref.12. Source: UniProtKB 5'-3' DNA helicase activity Inferred from direct assay Ref.9. Source: UniProtKB 5'-flap endonuclease activity Inferred from direct assay Ref.5. Source: SGD ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATP-dependent DNA helicase activity Inferred from direct assay Ref.3. Source: SGD DNA binding Inferred from electronic annotation. Source: UniProtKB-KW metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW single-stranded DNA specific endodeoxyribonuclease activity Inferred from direct assay Ref.4. Source: SGD single-stranded DNA-dependent ATPase activity Inferred from direct assay Ref.12. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
RAD27	P26793	3	EBI-5973,EBI-14693

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1522	1522	DNA replication ATP-dependent helicase/nuclease DNA2		PRO_0000080711
Regions
	Nucleotide binding	1074 – 1081	8	ATP By similarity
	Region	450 – 900	451	Nuclease activity
	Region	901 – 1522	622	Helicase activity
Sites
	Metal binding	519	1	Iron-sulfur (4Fe-4S)
	Metal binding	768	1	Iron-sulfur (4Fe-4S)
	Metal binding	771	1	Iron-sulfur (4Fe-4S)
	Metal binding	777	1	Iron-sulfur (4Fe-4S)
Amino acid modifications
	Modified residue	4	1	Phosphothreonine Ref.11
	Modified residue	17	1	Phosphoserine; by CDK1 Ref.11
	Modified residue	236	1	Phosphoserine Ref.6 Ref.7
	Modified residue	237	1	Phosphoserine; by CDK1 Ref.6 Ref.7 Ref.11
	Modified residue	962	1	Phosphothreonine Ref.7
Experimental info
	Mutagenesis	4	1	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. Ref.11
	Mutagenesis	17	1	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. Ref.11
	Mutagenesis	17	1	S → D: Mimics phosphorylation; restores nuclear localization and recruitment at double-strand. break (DSB) sites following DNA damage; when associated with D-237. Ref.11
	Mutagenesis	237	1	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. Ref.11
	Mutagenesis	237	1	S → D: Mimics phosphorylation; restores nuclear localization and recruitment at double-strand. break (DSB) sites following DNA damage; when associated with D-17. Ref.11
	Mutagenesis	504	1	P → S in dna2-1; temperature-sensitive mutant unable to grow at 37 degrees Celsius, probably due to abolition of iron-sulfur-binding. Ref.12
	Mutagenesis	519	1	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. Ref.12
	Mutagenesis	675	1	E → A: Nuclease dead mutant. No helicase activity when the 5'-end of the substrate is blocked. Ref.9
	Mutagenesis	677	1	K → R: Nuclease dead mutant. No helicase activity when the 5'-end of the substrate is blocked. Ref.9
	Mutagenesis	768	1	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. Ref.12
	Mutagenesis	771	1	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. Ref.12
	Mutagenesis	777	1	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. Ref.12

Sequences

	Sequence		Length	Mass (Da)
	P38859 [UniParc]. Last modified February 1, 1995. Version 1. Checksum: 213A0458A6C69D78	FASTA	1,522	171,694
	10 20 30 40 50 60 MPGTPQKNKR SASISVSPAK KTEEKEIIQN DSKAILSKQT KRKKKYAFAP INNLNGKNTK 70 80 90 100 110 120 VSNASVLKSI AVSQVRNTSR TKDINKAVSK SVKQLPNSQV KPKREMSNLS RHHDFTQDED 130 140 150 160 170 180 GPMEEVIWKY SPLQRDMSDK TTSAAEYSDD YEDVQNPSST PIVPNRLKTV LSFTNIQVPN 190 200 210 220 230 240 ADVNQLIQEN GNEQVRPKPA EISTRESLRN IDDILDDIEG DLTIKPTITK FSDLPSSPIK 250 260 270 280 290 300 APNVEKKAEV NAEEVDKMDS TGDSNDGDDS LIDILTQKYV EKRKSESQIT IQGNTNQKSG 310 320 330 340 350 360 AQESCGKNDN TKSRGEIEDH ENVDNQAKTG NAFYENEEDS NCQRIKKNEK IEYNSSDEFS 370 380 390 400 410 420 DDSLIELLNE TQTQVEPNTI EQDLDKVEKM VSDDLRIATD STLSAYALRA KSGAPRDGVV 430 440 450 460 470 480 RLVIVSLRSV ELPKIGTQKI LECIDGKGEQ SSVVVRHPWV YLEFEVGDVI HIIEGKNIEN 490 500 510 520 530 540 KRLLSDDKNP KTQLANDNLL VLNPDVLFSA TSVGSSVGCL RRSILQMQFQ DPRGEPSLVM 550 560 570 580 590 600 TLGNIVHELL QDSIKYKLSH NKISMEIIIQ KLDSLLETYS FSIIICNEEI QYVKELVMKE 610 620 630 640 650 660 HAENILYFVN KFVSKSNYGC YTSISGTRRT QPISISNVID IEENIWSPIY GLKGFLDATV 670 680 690 700 710 720 EANVENNKKH IVPLEVKTGK SRSVSYEVQG LIYTLLLNDR YEIPIEFFLL YFTRDKNMTK 730 740 750 760 770 780 FPSVLHSIKH ILMSRNRMSM NFKHQLQEVF GQAQSRFELP PLLRDSSCDS CFIKESCMVL 790 800 810 820 830 840 NKLLEDGTPE ESGLVEGEFE ILTNHLSQNL ANYKEFFTKY NDLITKEESS ITCVNKELFL 850 860 870 880 890 900 LDGSTRESRS GRCLSGLVVS EVVEHEKTEG AYIYCFSRRR NDNNSQSMLS SQIAANDFVI 910 920 930 940 950 960 ISDEEGHFCL CQGRVQFINP AKIGISVKRK LLNNRLLDKE KGVTTIQSVV ESELEQSSLI 970 980 990 1000 1010 1020 ATQNLVTYRI DKNDIQQSLS LARFNLLSLF LPAVSPGVDI VDERSKLCRK TKRSDGGNEI 1030 1040 1050 1060 1070 1080 LRSLLVDNRA PKFRDANDDP VIPYKLSKDT TLNLNQKEAI DKVMRAEDYA LILGMPGTGK 1090 1100 1110 1120 1130 1140 TTVIAEIIKI LVSEGKRVLL TSYTHSAVDN ILIKLRNTNI SIMRLGMKHK VHPDTQKYVP 1150 1160 1170 1180 1190 1200 NYASVKSYND YLSKINSTSV VATTCLGIND ILFTLNEKDF DYVILDEASQ ISMPVALGPL 1210 1220 1230 1240 1250 1260 RYGNRFIMVG DHYQLPPLVK NDAARLGGLE ESLFKTFCEK HPESVAELTL QYRMCGDIVT 1270 1280 1290 1300 1310 1320 LSNFLIYDNK LKCGNNEVFA QSLELPMPEA LSRYRNESAN SKQWLEDILE PTRKVVFLNY 1330 1340 1350 1360 1370 1380 DNCPDIIEQS EKDNITNHGE AELTLQCVEG MLLSGVPCED IGVMTLYRAQ LRLLKKIFNK 1390 1400 1410 1420 1430 1440 NVYDGLEILT ADQFQGRDKK CIIISMVRRN SQLNGGALLK ELRRVNVAMT RAKSKLIIIG 1450 1460 1470 1480 1490 1500 SKSTIGSVPE IKSFVNLLEE RNWVYTMCKD ALYKYKFPDR SNAIDEARKG CGKRTGAKPI 1510 1520 TSKSKFVSDK PIIKEILQEY ES

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII." 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. Science 265:2077-2082(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[2]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[3]	"A yeast gene required for DNA replication encodes a protein with homology to DNA helicases." Budd M.E., Campbell J.L. Proc. Natl. Acad. Sci. U.S.A. 92:7642-7646(1995) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION.
[4]	"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." Bae S.H., Choi E., Lee K.H., Park J.S., Lee S.H., Seo Y.S. J. Biol. Chem. 273:26880-26890(1998) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[5]	"Dna2p helicase/nuclease is a tracking protein, like FEN1, for flap cleavage during Okazaki fragment maturation." Kao H.I., Campbell J.L., Bambara R.A. J. Biol. Chem. 279:50840-50849(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[6]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-236 AND SER-237, MASS SPECTROMETRY.
[7]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-236; SER-237 AND THR-962, MASS SPECTROMETRY.
[8]	"Sgs1 helicase and two nucleases Dna2 and Exo1 resect DNA double-strand break ends." Zhu Z., Chung W.H., Shim E.Y., Lee S.E., Ira G. Cell 134:981-994(2008) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[9]	"Dna2 exhibits a unique strand end-dependent helicase function." Balakrishnan L., Polaczek P., Pokharel S., Campbell J.L., Bambara R.A. J. Biol. Chem. 285:38861-38868(2010) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF GLU-675 AND LYS-677.
[10]	"DNA end resection by Dna2-Sgs1-RPA and its stimulation by Top3-Rmi1 and Mre11-Rad50-Xrs2." Cejka P., Cannavo E., Polaczek P., Masuda-Sasa T., Pokharel S., Campbell J.L., Kowalczykowski S.C. Nature 467:112-116(2010) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[11]	"Cell cycle regulation of DNA double-strand break end resection by Cdk1-dependent Dna2 phosphorylation." Chen X., Niu H., Chung W.H., Zhu Z., Papusha A., Shim E.Y., Lee S.E., Sung P., Ira G. Nat. Struct. Mol. Biol. 18:1015-1019(2011) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, PHOSPHORYLATION AT THR-4; SER-17 AND SER-237, MUTAGENESIS OF THR-4; SER-17 AND SER-237.
[12]	"Cross talk between the nuclease and helicase activities of Dna2: role of an essential iron-sulfur cluster domain." Pokharel S., Campbell J.L. Nucleic Acids Res. 40:7821-7830(2012) [PubMed] [Europe PMC] [Abstract] Cited for: COFACTOR, IRON-SULFUR-BINDING, MUTAGENESIS OF PRO-504; CYS-519; CYS-768; CYS-771 AND CYS-777.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U00027 Genomic DNA. Translation: AAB68010.1. BK006934 Genomic DNA. Translation: DAA06857.1.
PIR	S48904.
RefSeq	NP_012034.1. NM_001179295.1.
3D structure databases
ProteinModelPortal	P38859.
SMR	P38859. Positions 1049-1466.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-2324N.
IntAct	P38859. 8 interactions.
MINT	MINT-620090.
STRING	4932.YHR164C.
Proteomic databases
PaxDb	P38859.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YHR164C; YHR164C; YHR164C.
GeneID	856569.
KEGG	sce:YHR164C.
Organism-specific databases
CYGD	YHR164c.
SGD	S000001207. DNA2.
Phylogenomic databases
eggNOG	COG1112.
GeneTree	ENSGT00550000074852.
HOGENOM	HOG000112234.
KO	K10742.
OMA	GLARYNI.
OrthoDB	EOG47H8Z4.
Gene expression databases
Genevestigator	P38859.
GermOnline	YHR164C. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR026851. Dna2. IPR014808. DNA_replication_fac_Dna2_N. [Graphical view]
PANTHER	PTHR10887:SF14. PTHR10887:SF14. 1 hit.
Pfam	PF08696. Dna2. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	982411.

Entry information

Entry name

DNA2_YEAST

Accession

Primary (citable) accession number: P38859
Secondary accession number(s): D3DLB3

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	February 1, 1995
Last modified:	May 1, 2013
This is version 113 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program