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

 DNA2_CHICK              Reviewed;         992 AA.
Q5ZKG3; F1NWZ9;
12-DEC-2006, integrated into UniProtKB/Swiss-Prot.
03-OCT-2012, sequence version 2.
25-OCT-2017, entry version 73.
RecName: Full=DNA replication ATP-dependent helicase/nuclease DNA2;
AltName: Full=DNA replication ATP-dependent helicase-like homolog;
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; Synonyms=DNA2L; ORFNames=RCJMB04_11a16;
Gallus gallus (Chicken).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes;
Phasianidae; Phasianinae; Gallus.
NCBI_TaxID=9031;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=CB; TISSUE=Bursa of Fabricius;
PubMed=15642098; DOI=10.1186/gb-2004-6-1-r6;
Caldwell R.B., Kierzek A.M., Arakawa H., Bezzubov Y., Zaim J.,
Fiedler P., Kutter S., Blagodatski A., Kostovska D., Koter M.,
Plachy J., Carninci P., Hayashizaki Y., Buerstedde J.-M.;
"Full-length cDNAs from chicken bursal lymphocytes to facilitate gene
function analysis.";
Genome Biol. 6:R6.1-R6.9(2005).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=Red jungle fowl;
PubMed=15592404; DOI=10.1038/nature03154;
Hillier L.W., Miller W., Birney E., Warren W., Hardison R.C.,
Ponting C.P., Bork P., Burt D.W., Groenen M.A.M., Delany M.E.,
Dodgson J.B., Chinwalla A.T., Cliften P.F., Clifton S.W.,
Delehaunty K.D., Fronick C., Fulton R.S., Graves T.A., Kremitzki C.,
Layman D., Magrini V., McPherson J.D., Miner T.L., Minx P., Nash W.E.,
Nhan M.N., Nelson J.O., Oddy L.G., Pohl C.S., Randall-Maher J.,
Smith S.M., Wallis J.W., Yang S.-P., Romanov M.N., Rondelli C.M.,
Paton B., Smith J., Morrice D., Daniels L., Tempest H.G.,
Robertson L., Masabanda J.S., Griffin D.K., Vignal A., Fillon V.,
Jacobbson L., Kerje S., Andersson L., Crooijmans R.P., Aerts J.,
van der Poel J.J., Ellegren H., Caldwell R.B., Hubbard S.J.,
Grafham D.V., Kierzek A.M., McLaren S.R., Overton I.M., Arakawa H.,
Beattie K.J., Bezzubov Y., Boardman P.E., Bonfield J.K.,
Croning M.D.R., Davies R.M., Francis M.D., Humphray S.J., Scott C.E.,
Taylor R.G., Tickle C., Brown W.R.A., Rogers J., Buerstedde J.-M.,
Wilson S.A., Stubbs L., Ovcharenko I., Gordon L., Lucas S.,
Miller M.M., Inoko H., Shiina T., Kaufman J., Salomonsen J.,
Skjoedt K., Wong G.K.-S., Wang J., Liu B., Wang J., Yu J., Yang H.,
Nefedov M., Koriabine M., Dejong P.J., Goodstadt L., Webber C.,
Dickens N.J., Letunic I., Suyama M., Torrents D., von Mering C.,
Zdobnov E.M., Makova K., Nekrutenko A., Elnitski L., Eswara P.,
King D.C., Yang S.-P., Tyekucheva S., Radakrishnan A., Harris R.S.,
Chiaromonte F., Taylor J., He J., Rijnkels M., Griffiths-Jones S.,
Ureta-Vidal A., Hoffman M.M., Severin J., Searle S.M.J., Law A.S.,
Speed D., Waddington D., Cheng Z., Tuzun E., Eichler E., Bao Z.,
Flicek P., Shteynberg D.D., Brent M.R., Bye J.M., Huckle E.J.,
Chatterji S., Dewey C., Pachter L., Kouranov A., Mourelatos Z.,
Hatzigeorgiou A.G., Paterson A.H., Ivarie R., Brandstrom M.,
Axelsson E., Backstrom N., Berlin S., Webster M.T., Pourquie O.,
Reymond A., Ucla C., Antonarakis S.E., Long M., Emerson J.J.,
Betran E., Dupanloup I., Kaessmann H., Hinrichs A.S., Bejerano G.,
Furey T.S., Harte R.A., Raney B., Siepel A., Kent W.J., Haussler D.,
Eyras E., Castelo R., Abril J.F., Castellano S., Camara F., Parra G.,
Guigo R., Bourque G., Tesler G., Pevzner P.A., Smit A., Fulton L.A.,
Mardis E.R., Wilson R.K.;
"Sequence and comparative analysis of the chicken genome provide
unique perspectives on vertebrate evolution.";
Nature 432:695-716(2004).
-!- FUNCTION: Key enzyme involved in DNA replication and DNA repair in
nucleus and mitochondrion. 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,
while the 3'-ssDNA cleavage is prevented by the presence of RPA.
Also involved in DNA replication checkpoint independently of
Okazaki fragments processing. 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 subject to debate. According to various
reports, the helicase activity is weak and its function remains
largely unclear. Helicase activity may promote the motion of DNA2
on the flap, helping the nuclease function (By similarity).
{ECO:0000250}.
-!- CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
-!- COFACTOR:
Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
Evidence={ECO:0000250};
Note=Binds 1 [4Fe-4S] cluster. {ECO:0000250};
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}. Mitochondrion
{ECO:0000250}.
-!- SIMILARITY: Belongs to the DNA2/NAM7 helicase family.
{ECO:0000305}.
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EMBL; AJ720121; CAG31780.1; -; mRNA.
EMBL; AADN02028013; -; NOT_ANNOTATED_CDS; Genomic_DNA.
RefSeq; NP_001006497.1; NM_001006497.1.
UniGene; Gga.42409; -.
SMR; Q5ZKG3; -.
STRING; 9031.ENSGALP00000006419; -.
PaxDb; Q5ZKG3; -.
Ensembl; ENSGALT00000006429; ENSGALP00000006419; ENSGALG00000004037.
GeneID; 423688; -.
KEGG; gga:423688; -.
CTD; 1763; -.
eggNOG; KOG1805; Eukaryota.
eggNOG; COG1112; LUCA.
GeneTree; ENSGT00780000122010; -.
HOGENOM; HOG000168456; -.
HOVERGEN; HBG081456; -.
InParanoid; Q5ZKG3; -.
KO; K10742; -.
Reactome; R-GGA-174437; Removal of the Flap Intermediate from the C-strand.
Reactome; R-GGA-5685938; HDR through Single Strand Annealing (SSA).
Reactome; R-GGA-5685942; HDR through Homologous Recombination (HRR).
Reactome; R-GGA-5693554; Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA).
Reactome; R-GGA-5693568; Resolution of D-loop Structures through Holliday Junction Intermediates.
Reactome; R-GGA-5693579; Homologous DNA Pairing and Strand Exchange.
Reactome; R-GGA-5693607; Processing of DNA double-strand break ends.
Reactome; R-GGA-5693616; Presynaptic phase of homologous DNA pairing and strand exchange.
Reactome; R-GGA-69166; Removal of the Flap Intermediate.
PRO; PR:Q5ZKG3; -.
Proteomes; UP000000539; Chromosome 6.
ExpressionAtlas; Q5ZKG3; baseline.
GO; GO:0005760; C:gamma DNA polymerase complex; IEA:Ensembl.
GO; GO:0042645; C:mitochondrial nucleoid; IEA:Ensembl.
GO; GO:0000784; C:nuclear chromosome, telomeric region; IEA:Ensembl.
GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
GO; GO:0043139; F:5'-3' DNA helicase activity; ISS:UniProtKB.
GO; GO:0017108; F:5'-flap endonuclease activity; ISS:UniProtKB.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0003677; F:DNA binding; ISS:UniProtKB.
GO; GO:0003678; F:DNA helicase activity; ISS:UniProtKB.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0004518; F:nuclease activity; ISS:UniProtKB.
GO; GO:0043142; F:single-stranded DNA-dependent ATPase activity; ISS:UniProtKB.
GO; GO:0016890; F:site-specific endodeoxyribonuclease activity, specific for altered base; ISS:UniProtKB.
GO; GO:0006284; P:base-excision repair; ISS:UniProtKB.
GO; GO:0000729; P:DNA double-strand break processing; ISS:UniProtKB.
GO; GO:0006260; P:DNA replication; ISS:UniProtKB.
GO; GO:0000076; P:DNA replication checkpoint; ISS:UniProtKB.
GO; GO:0033567; P:DNA replication, Okazaki fragment processing; ISS:UniProtKB.
GO; GO:0043137; P:DNA replication, removal of RNA primer; ISS:UniProtKB.
GO; GO:0043504; P:mitochondrial DNA repair; IEA:Ensembl.
GO; GO:0006264; P:mitochondrial DNA replication; ISS:UniProtKB.
GO; GO:1902990; P:mitotic telomere maintenance via semi-conservative replication; IEA:Ensembl.
GO; GO:0045740; P:positive regulation of DNA replication; ISS:UniProtKB.
InterPro; IPR026851; Dna2.
InterPro; IPR014808; DNA_replication_fac_Dna2_N.
InterPro; IPR027417; P-loop_NTPase.
PANTHER; PTHR10887:SF14; PTHR10887:SF14; 1.
Pfam; PF08696; Dna2; 1.
SUPFAM; SSF52540; SSF52540; 2.
2: Evidence at transcript level;
4Fe-4S; ATP-binding; Complete proteome; DNA damage; DNA repair;
DNA replication; DNA-binding; Endonuclease; Helicase; Hydrolase; Iron;
Iron-sulfur; Metal-binding; Mitochondrion; Multifunctional enzyme;
Nuclease; Nucleotide-binding; Nucleus; Reference proteome.
CHAIN 1 992 DNA replication ATP-dependent
helicase/nuclease DNA2.
/FTId=PRO_0000263605.
NP_BIND 617 624 ATP. {ECO:0000255}.
REGION 51 488 Nuclease activity. {ECO:0000250}.
REGION 489 992 Helicase activity. {ECO:0000250}.
METAL 106 106 Iron-sulfur (4Fe-4S). {ECO:0000250}.
METAL 362 362 Iron-sulfur (4Fe-4S). {ECO:0000250}.
METAL 365 365 Iron-sulfur (4Fe-4S). {ECO:0000250}.
METAL 371 371 Iron-sulfur (4Fe-4S). {ECO:0000250}.
CONFLICT 578 578 S -> T (in Ref. 1; CAG31780).
{ECO:0000305}.
CONFLICT 931 931 K -> E (in Ref. 1; CAG31780).
{ECO:0000305}.
CONFLICT 980 980 P -> A (in Ref. 1; CAG31780).
{ECO:0000305}.
SEQUENCE 992 AA; 111679 MW; 34A62421494C2E6C CRC64;
MADPSNAALR SGLNNRYRVL EVRVVRGEGR DPEKHLAVSS DPSLGDTELC VLQNGWESVP
VVPGDIVHLE GDCSSGTWVI NEQSGYLILY PDLLLSGTTI SSSIRCMRKA VLSERFRGSE
CGSRQTLVGT ILHEIFQQSV TNNLSPEKVE ELAKKIVYGQ KYLKEMYHLK LKQTEIMQEI
EEYLPSFFKW TEDFVRNPAN QNKMQLKLPS ENKTGDCSST VEIVDILDIE ENIWSPRFGL
KGKIDVTARV KIHRQGGIQS RIMPLELKSG KESNSVEHRS QVILYTLLNL ERRVDPEAGF
LLYLKTGTMY PVTGTRMDRR ELIKLRNQVA FYLMHSTYKS AVGRQQSQLA ALPPLIDDSQ
ACKYCSQIHN CFLYSRAVEE RMASVSFPPA LIPIIEKETQ HLKPSHLEYF SLWYLMLTLE
MQSGDSKKGY KNIWMIPSLE REKAGDCVGN MIRVDQVQEV SEGQYLHSFQ RKNGAVPGAN
LLVGDRVVVS GEENGLLGLA TGYVREISAT KISCLLGRNL SKLPESTTFR LDHEEGDCSI
GVPFENLSKL MKDSPVSEKL RNLIIDFHKP RFIQHLSSVL PPEAKEAVAS ILKGLNKPQK
QAMKQVLLSR DYTLIVGMPG TGKTTTICAL VRILSACGFS VLLTSFTHTA VDNILLKLAK
FKVGFLRLGR AQKVHPDIRK FTEEEICRSK SIKSVTDLEE LYNSQPVVAT ACMGINHPIF
VQKQFDFCIV DEASQISQPI CLGPLFCSKR FVLVGDHQQL PPLVQNSEAR DLGMSESLFK
RLEQNQNAVV QLTVQYRMNS KIMSLSNKLV YEGKLECGSE KVSNATANLP NLKMLKLEFA
DASKTWLKEV LEPDKPVCFL NTEKAGCRPS DIGIISPYRH QLKVITDLMA RLKENRVEVN
TIDKYQGRDK SIIIVSFVRN SNDENLGALL KDWRRLNVAI TRAKHKLIMV GCVPSLRRYP
PLEKLLCHLQ SEAMIFNLPP GAHESIHKCN IL


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