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P38859

- DNA2_YEAST

UniProt

P38859 - DNA2_YEAST

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Protein

DNA replication ATP-dependent helicase/nuclease DNA2

Gene
DNA2, YHR164C
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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.6 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.

Cofactori

Binds 1 4Fe-4S cluster.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi519 – 5191Iron-sulfur (4Fe-4S)
Metal bindingi768 – 7681Iron-sulfur (4Fe-4S)
Metal bindingi771 – 7711Iron-sulfur (4Fe-4S)
Metal bindingi777 – 7771Iron-sulfur (4Fe-4S)

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi1074 – 10818ATP By similarity

GO - Molecular functioni

  1. 4 iron, 4 sulfur cluster binding Source: UniProtKB
  2. 5'-3' DNA helicase activity Source: UniProtKB
  3. 5'-flap endonuclease activity Source: SGD
  4. ATP binding Source: UniProtKB-KW
  5. ATP-dependent DNA helicase activity Source: SGD
  6. DNA binding Source: UniProtKB-KW
  7. metal ion binding Source: UniProtKB-KW
  8. nuclease activity Source: UniProtKB
  9. protein binding Source: UniProtKB
  10. single-stranded DNA-dependent ATPase activity Source: UniProtKB
  11. single-stranded DNA endodeoxyribonuclease activity Source: SGD

GO - Biological processi

  1. ATP catabolic process Source: GOC
  2. cellular response to DNA damage stimulus Source: UniProtKB
  3. DNA catabolic process, endonucleolytic Source: GOC
  4. DNA-dependent DNA replication Source: SGD
  5. DNA double-strand break processing Source: UniProtKB
  6. DNA duplex unwinding Source: GOC
  7. DNA repair Source: SGD
  8. DNA replication, Okazaki fragment processing Source: InterPro
  9. DNA strand renaturation Source: SGD
  10. lagging strand elongation Source: SGD
  11. meiotic DNA double-strand break processing Source: SGD
  12. replicative cell aging Source: SGD
  13. telomere maintenance Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase, Nuclease

Keywords - Biological processi

DNA damage, DNA repair, DNA replication

Keywords - Ligandi

4Fe-4S, ATP-binding, DNA-binding, Iron, Iron-sulfur, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-31198-MONOMER.
ReactomeiREACT_188901. Cytosolic iron-sulfur cluster assembly.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA replication ATP-dependent helicase/nuclease DNA2
Including the following 2 domains:
DNA replication nuclease DNA2 (EC:3.1.-.-)
DNA replication ATP-dependent helicase DNA2 (EC:3.6.4.12)
Gene namesi
Name:DNA2
Ordered Locus Names:YHR164C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome VIII

Organism-specific databases

CYGDiYHR164c.
SGDiS000001207. DNA2.

Subcellular locationi

Nucleus. Chromosome
Note: Recruited to double-strand. break (DSB) sites following phosphorylation at Ser-17 and Ser-237.

GO - Cellular componenti

  1. cytoplasm Source: SGD
  2. cytosol Source: Reactome
  3. nuclear chromosome, telomeric region Source: SGD
  4. nucleus Source: UniProtKB
  5. site of double-strand break Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi4 – 41T → 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. 1 Publication
Mutagenesisi17 – 171S → 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. 1 Publication
Mutagenesisi17 – 171S → D: Mimics phosphorylation; restores nuclear localization and recruitment at double-strand. break (DSB) sites following DNA damage; when associated with D-237. 1 Publication
Mutagenesisi237 – 2371S → 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. 1 Publication
Mutagenesisi237 – 2371S → D: Mimics phosphorylation; restores nuclear localization and recruitment at double-strand. break (DSB) sites following DNA damage; when associated with D-17. 1 Publication
Mutagenesisi504 – 5041P → S in dna2-1; temperature-sensitive mutant unable to grow at 37 degrees Celsius, probably due to abolition of iron-sulfur-binding. 1 Publication
Mutagenesisi519 – 5191C → 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. 1 Publication
Mutagenesisi675 – 6751E → A: Nuclease dead mutant. No helicase activity when the 5'-end of the substrate is blocked. 1 Publication
Mutagenesisi677 – 6771K → R: Nuclease dead mutant. No helicase activity when the 5'-end of the substrate is blocked. 1 Publication
Mutagenesisi768 – 7681C → 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. 1 Publication
Mutagenesisi771 – 7711C → 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. 1 Publication
Mutagenesisi777 – 7771C → 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. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 15221522DNA replication ATP-dependent helicase/nuclease DNA2PRO_0000080711Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei4 – 41Phosphothreonine1 Publication
Modified residuei17 – 171Phosphoserine; by CDK11 Publication
Modified residuei237 – 2371Phosphoserine; by CDK11 Publication
Modified residuei962 – 9621Phosphothreonine1 Publication

Post-translational modificationi

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.1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP38859.
PaxDbiP38859.

Expressioni

Gene expression databases

GenevestigatoriP38859.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
RAD27P267933EBI-5973,EBI-14693

Protein-protein interaction databases

BioGridi36598. 76 interactions.
DIPiDIP-2324N.
IntActiP38859. 8 interactions.
MINTiMINT-620090.
STRINGi4932.YHR164C.

Structurei

3D structure databases

ProteinModelPortaliP38859.
SMRiP38859. Positions 1049-1466.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni450 – 900451Nuclease activityAdd
BLAST
Regioni901 – 1522622Helicase activityAdd
BLAST

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG1112.
GeneTreeiENSGT00550000074852.
HOGENOMiHOG000112234.
KOiK10742.
OMAiMTLYRAQ.
OrthoDBiEOG7FZ06K.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR026851. Dna2.
IPR014808. DNA_replication_fac_Dna2_N.
IPR027417. P-loop_NTPase.
[Graphical view]
PANTHERiPTHR10887:SF14. PTHR10887:SF14. 1 hit.
PfamiPF08696. Dna2. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.

Sequencei

Sequence statusi: Complete.

P38859-1 [UniParc]FASTAAdd to Basket

« Hide

MPGTPQKNKR SASISVSPAK KTEEKEIIQN DSKAILSKQT KRKKKYAFAP     50
INNLNGKNTK VSNASVLKSI AVSQVRNTSR TKDINKAVSK SVKQLPNSQV 100
KPKREMSNLS RHHDFTQDED GPMEEVIWKY SPLQRDMSDK TTSAAEYSDD 150
YEDVQNPSST PIVPNRLKTV LSFTNIQVPN ADVNQLIQEN GNEQVRPKPA 200
EISTRESLRN IDDILDDIEG DLTIKPTITK FSDLPSSPIK APNVEKKAEV 250
NAEEVDKMDS TGDSNDGDDS LIDILTQKYV EKRKSESQIT IQGNTNQKSG 300
AQESCGKNDN TKSRGEIEDH ENVDNQAKTG NAFYENEEDS NCQRIKKNEK 350
IEYNSSDEFS DDSLIELLNE TQTQVEPNTI EQDLDKVEKM VSDDLRIATD 400
STLSAYALRA KSGAPRDGVV RLVIVSLRSV ELPKIGTQKI LECIDGKGEQ 450
SSVVVRHPWV YLEFEVGDVI HIIEGKNIEN KRLLSDDKNP KTQLANDNLL 500
VLNPDVLFSA TSVGSSVGCL RRSILQMQFQ DPRGEPSLVM TLGNIVHELL 550
QDSIKYKLSH NKISMEIIIQ KLDSLLETYS FSIIICNEEI QYVKELVMKE 600
HAENILYFVN KFVSKSNYGC YTSISGTRRT QPISISNVID IEENIWSPIY 650
GLKGFLDATV EANVENNKKH IVPLEVKTGK SRSVSYEVQG LIYTLLLNDR 700
YEIPIEFFLL YFTRDKNMTK FPSVLHSIKH ILMSRNRMSM NFKHQLQEVF 750
GQAQSRFELP PLLRDSSCDS CFIKESCMVL NKLLEDGTPE ESGLVEGEFE 800
ILTNHLSQNL ANYKEFFTKY NDLITKEESS ITCVNKELFL LDGSTRESRS 850
GRCLSGLVVS EVVEHEKTEG AYIYCFSRRR NDNNSQSMLS SQIAANDFVI 900
ISDEEGHFCL CQGRVQFINP AKIGISVKRK LLNNRLLDKE KGVTTIQSVV 950
ESELEQSSLI ATQNLVTYRI DKNDIQQSLS LARFNLLSLF LPAVSPGVDI 1000
VDERSKLCRK TKRSDGGNEI LRSLLVDNRA PKFRDANDDP VIPYKLSKDT 1050
TLNLNQKEAI DKVMRAEDYA LILGMPGTGK TTVIAEIIKI LVSEGKRVLL 1100
TSYTHSAVDN ILIKLRNTNI SIMRLGMKHK VHPDTQKYVP NYASVKSYND 1150
YLSKINSTSV VATTCLGIND ILFTLNEKDF DYVILDEASQ ISMPVALGPL 1200
RYGNRFIMVG DHYQLPPLVK NDAARLGGLE ESLFKTFCEK HPESVAELTL 1250
QYRMCGDIVT LSNFLIYDNK LKCGNNEVFA QSLELPMPEA LSRYRNESAN 1300
SKQWLEDILE PTRKVVFLNY DNCPDIIEQS EKDNITNHGE AELTLQCVEG 1350
MLLSGVPCED IGVMTLYRAQ LRLLKKIFNK NVYDGLEILT ADQFQGRDKK 1400
CIIISMVRRN SQLNGGALLK ELRRVNVAMT RAKSKLIIIG SKSTIGSVPE 1450
IKSFVNLLEE RNWVYTMCKD ALYKYKFPDR SNAIDEARKG CGKRTGAKPI 1500
TSKSKFVSDK PIIKEILQEY ES 1522
Length:1,522
Mass (Da):171,694
Last modified:February 1, 1995 - v1
Checksum:i213A0458A6C69D78
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U00027 Genomic DNA. Translation: AAB68010.1.
BK006934 Genomic DNA. Translation: DAA06857.1.
PIRiS48904.
RefSeqiNP_012034.1. NM_001179295.1.

Genome annotation databases

EnsemblFungiiYHR164C; YHR164C; YHR164C.
GeneIDi856569.
KEGGisce:YHR164C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U00027 Genomic DNA. Translation: AAB68010.1 .
BK006934 Genomic DNA. Translation: DAA06857.1 .
PIRi S48904.
RefSeqi NP_012034.1. NM_001179295.1.

3D structure databases

ProteinModelPortali P38859.
SMRi P38859. Positions 1049-1466.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 36598. 76 interactions.
DIPi DIP-2324N.
IntActi P38859. 8 interactions.
MINTi MINT-620090.
STRINGi 4932.YHR164C.

Proteomic databases

MaxQBi P38859.
PaxDbi P38859.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YHR164C ; YHR164C ; YHR164C .
GeneIDi 856569.
KEGGi sce:YHR164C.

Organism-specific databases

CYGDi YHR164c.
SGDi S000001207. DNA2.

Phylogenomic databases

eggNOGi COG1112.
GeneTreei ENSGT00550000074852.
HOGENOMi HOG000112234.
KOi K10742.
OMAi MTLYRAQ.
OrthoDBi EOG7FZ06K.

Enzyme and pathway databases

BioCyci YEAST:G3O-31198-MONOMER.
Reactomei REACT_188901. Cytosolic iron-sulfur cluster assembly.

Miscellaneous databases

NextBioi 982411.
PROi P38859.

Gene expression databases

Genevestigatori P38859.

Family and domain databases

Gene3Di 3.40.50.300. 2 hits.
InterProi IPR026851. Dna2.
IPR014808. DNA_replication_fac_Dna2_N.
IPR027417. P-loop_NTPase.
[Graphical view ]
PANTHERi PTHR10887:SF14. PTHR10887:SF14. 1 hit.
Pfami PF08696. Dna2. 1 hit.
[Graphical view ]
SUPFAMi SSF52540. SSF52540. 2 hits.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. 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. "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.
  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 THR-962, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  8. Cited for: FUNCTION, MUTAGENESIS OF GLU-675 AND LYS-677.
  9. "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.
  10. "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.
  11. "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.

Entry informationi

Entry nameiDNA2_YEAST
AccessioniPrimary (citable) accession number: P38859
Secondary accession number(s): D3DLB3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: September 3, 2014
This is version 125 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Multifunctional enzyme, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome VIII
    Yeast (Saccharomyces cerevisiae) chromosome VIII: entries and gene names

External Data

Dasty 3

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