GENL2_ARATH
ID GENL2_ARATH Reviewed; 600 AA.
AC Q9M2Z3; B3H5Z3; Q9SMT0;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 15-JAN-2008, sequence version 2.
DT 03-AUG-2022, entry version 127.
DE RecName: Full=Single-strand DNA endonuclease 1 {ECO:0000303|PubMed:25037209};
DE Short=AtSEND1 {ECO:0000303|PubMed:25037209};
DE EC=3.1.-.-;
DE AltName: Full=Flap endonuclease GEN-like 2 {ECO:0000305};
DE Short=XPG-like endonuclease 2 {ECO:0000305};
GN Name=SEND1 {ECO:0000303|PubMed:25037209}; Synonyms=GEN2 {ECO:0000305};
GN OrderedLocusNames=At3g48900/At3g48910 {ECO:0000312|Araport:AT3G48900};
GN ORFNames=T21J18.170/T2J13.250 {ECO:0000312|EMBL:CAB62019.1,
GN ECO:0000312|EMBL:CAB87918.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP FUNCTION, AND MUTAGENESIS OF ASP-76.
RC STRAIN=cv. Columbia;
RX PubMed=25037209; DOI=10.1104/pp.114.237834;
RA Bauknecht M., Kobbe D.;
RT "AtGEN1 and AtSEND1, two paralogs in Arabidopsis, possess holliday junction
RT resolvase activity.";
RL Plant Physiol. 166:202-216(2014).
RN [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=26704385; DOI=10.1105/tpc.15.00898;
RA Olivier M., Da Ines O., Amiard S., Serra H., Goubely C., White C.I.,
RA Gallego M.E.;
RT "The structure-specific endonucleases MUS81 and SEND1 are essential for
RT telomere stability in Arabidopsis.";
RL Plant Cell 28:74-86(2016).
CC -!- FUNCTION: Endonuclease which cleaves flap structures at the junction
CC between single-stranded DNA and double-stranded DNA with a specific
CC cleavage site in the 5' overhang strand exactly one nucleotide 3' of
CC the branch point (PubMed:25037209). Structure- and sequence-specific
CC nuclease that resolves holliday junctions (HJs) by symmetrically
CC oriented incisions in two opposing strands near the junction point,
CC thus leading to ligatable products; HJs are physical links between
CC homologous DNA molecules that arise as central intermediary structures
CC during homologous recombination and repair in meiotic and somatic cells
CC (PubMed:25037209). Structure-specific nuclease with 5'-flap
CC endonuclease activity, preferentially cleaving static flaps 5' overhang
CC strand exactly one nucleotide in the 3' direction of the branch point
CC and, to lower extent, on the two neighboring positions
CC (PubMed:25037209). Also able to cleave double-stranded flap strand 1
CC one nucleotide in the 3' direction of the branch point
CC (PubMed:25037209). Together with MUS81, essential for the resolution of
CC toxic replication structures to ensure genome stability, and to
CC maintain telomere integrity and replication (PubMed:26704385).
CC {ECO:0000269|PubMed:25037209, ECO:0000269|PubMed:26704385}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:Q17RS7};
CC Note=Binds 2 magnesium ions per subunit. They probably participate in
CC the reaction catalyzed by the enzyme. May bind an additional third
CC magnesium ion after substrate binding. {ECO:0000250|UniProtKB:Q17RS7};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q17RS7}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9M2Z3-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9M2Z3-2; Sequence=VSP_040519, VSP_040520;
CC -!- DISRUPTION PHENOTYPE: Normal sensitivity to DNA damaging agents
CC (PubMed:26704385). Mild UV sensitivity in the gen1 send1 double mutant
CC (PubMed:26704385). The double mutant mus81 send1 exhibits severe
CC developmental defects (e.g. strong growth retardation and impaired leaf
CC and shoot development), increased endoreduplication, slower cell cycle
CC progression, spontaneous cell death and genome instability associated
CC with a dramatic loss of telomeric repeats (PubMed:26704385).
CC {ECO:0000269|PubMed:26704385}.
CC -!- MISCELLANEOUS: [Isoform 2]: May be due to an intron retention.
CC {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the XPG/RAD2 endonuclease family. GEN subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB62019.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to two different genes At3g48900 and At3g48910.; Evidence={ECO:0000305};
CC Sequence=CAB87918.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to two different genes At3g48900 and At3g48910.; Evidence={ECO:0000305};
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DR EMBL; AL132963; CAB87918.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL132967; CAB62019.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE78471.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE78472.1; -; Genomic_DNA.
DR EMBL; AY075628; -; NOT_ANNOTATED_CDS; mRNA.
DR PIR; T46139; T46139.
DR PIR; T49286; T49286.
DR RefSeq; NP_001118795.1; NM_001125323.2. [Q9M2Z3-1]
DR RefSeq; NP_190459.2; NM_114749.3. [Q9M2Z3-2]
DR AlphaFoldDB; Q9M2Z3; -.
DR SMR; Q9M2Z3; -.
DR STRING; 3702.AT3G48900.2; -.
DR PaxDb; Q9M2Z3; -.
DR PRIDE; Q9M2Z3; -.
DR EnsemblPlants; AT3G48900.1; AT3G48900.1; AT3G48900. [Q9M2Z3-2]
DR EnsemblPlants; AT3G48900.2; AT3G48900.2; AT3G48900. [Q9M2Z3-1]
DR GeneID; 824051; -.
DR Gramene; AT3G48900.1; AT3G48900.1; AT3G48900. [Q9M2Z3-2]
DR Gramene; AT3G48900.2; AT3G48900.2; AT3G48900. [Q9M2Z3-1]
DR KEGG; ath:AT3G48900; -.
DR Araport; AT3G48900; -.
DR TAIR; locus:2099463; AT3G48900.
DR eggNOG; KOG2519; Eukaryota.
DR HOGENOM; CLU_013777_2_1_1; -.
DR InParanoid; Q9M2Z3; -.
DR OMA; QEKACEI; -.
DR OrthoDB; 1094524at2759; -.
DR PhylomeDB; Q9M2Z3; -.
DR PRO; PR:Q9M2Z3; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9M2Z3; baseline and differential.
DR Genevisible; Q9M2Z3; AT.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0017108; F:5'-flap endonuclease activity; IDA:UniProtKB.
DR GO; GO:0008821; F:crossover junction endodeoxyribonuclease activity; IDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006281; P:DNA repair; IMP:UniProtKB.
DR GO; GO:0000723; P:telomere maintenance; IMP:UniProtKB.
DR GO; GO:0009650; P:UV protection; IGI:UniProtKB.
DR InterPro; IPR036279; 5-3_exonuclease_C_sf.
DR InterPro; IPR016197; Chromo-like_dom_sf.
DR InterPro; IPR000953; Chromo/chromo_shadow_dom.
DR InterPro; IPR029060; PIN-like_dom_sf.
DR InterPro; IPR006086; XPG-I_dom.
DR InterPro; IPR006084; XPG/Rad2.
DR InterPro; IPR006085; XPG_DNA_repair_N.
DR PANTHER; PTHR11081; PTHR11081; 1.
DR Pfam; PF00867; XPG_I; 1.
DR Pfam; PF00752; XPG_N; 1.
DR PRINTS; PR00853; XPGRADSUPER.
DR SMART; SM00484; XPGI; 1.
DR SMART; SM00485; XPGN; 1.
DR SUPFAM; SSF47807; SSF47807; 1.
DR SUPFAM; SSF54160; SSF54160; 1.
DR SUPFAM; SSF88723; SSF88723; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; DNA damage; DNA repair; Endonuclease; Hydrolase;
KW Magnesium; Metal-binding; Nuclease; Nucleus; Reference proteome.
FT CHAIN 1..600
FT /note="Single-strand DNA endonuclease 1"
FT /id="PRO_0000315624"
FT REGION 1..97
FT /note="N-domain"
FT REGION 2..97
FT /note="XPG-N domain"
FT /evidence="ECO:0000250|UniProtKB:Q17RS7"
FT REGION 130..219
FT /note="I-domain"
FT REGION 130..218
FT /note="I-domain"
FT /evidence="ECO:0000250|UniProtKB:Q9LPD2"
FT REGION 130..215
FT /note="XPG-I domain"
FT /evidence="ECO:0000250|UniProtKB:Q17RS7"
FT REGION 215..353
FT /note="5'-3' exonuclease domain"
FT /evidence="ECO:0000250|UniProtKB:Q17RS7"
FT REGION 433..458
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 30
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P39748"
FT BINDING 76
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q17RS7"
FT BINDING 142
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q17RS7"
FT BINDING 144
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q58839"
FT BINDING 163
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9UQ84"
FT BINDING 165
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9UQ84"
FT BINDING 215
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q58839"
FT VAR_SEQ 1..64
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_040519"
FT VAR_SEQ 65..96
FT /note="IALNCSIILVSDGAIPGIKVPTYKRRLKARFE -> MMSNVALVVSSLHMMA
FT SFWIVFFDFVLYWFSQ (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_040520"
FT MUTAGEN 76
FT /note="D->A: Impaired nuclease activity."
FT /evidence="ECO:0000269|PubMed:25037209"
SQ SEQUENCE 600 AA; 68181 MW; C5CF269D0BA83581 CRC64;
MGVKYLWDVL EPCKKTFPLD HLQNKRVCVD LSCWMVELHK VNKSYCATKE KVYLRGFFHR
LRALIALNCS IILVSDGAIP GIKVPTYKRR LKARFEIADD GVEPSKETSL KRNMGSEFSC
IIKEAKVIAS TLGILCLDGI EEAEAQCALL NSESLCDACF SFDSDIFLFG AKTVYREICL
GEGGYVVCYE MDDIKKKLGL GRNSLIALAL LLGSDYSQGV RGLRQEKACE LVRSIGDNVI
LEKVASEGLS FAEKPRKSKK QVRPSVCSKK GTLPLVVING NNRDPERLEE IKQVIDAFMN
PKCHQADSNT VSRALAEFSF QRTKLQEICH QFFEWPPEKT DEYILPKVAE RNLRRFANLQ
SRSTEVEVNL PLHKPQMPEK CPVSEIIKTR KVQGRECFEV SWNDLEGLES SIVPADLVER
ACPEKIIEFK EKMAAKKKKP KPKQKQKETS SPTKSSSLVE LSLELQHLDL NSTSLVSRST
LEEAEQENEQ QNSKKHDYLR LIDSPDRENC NNAWSNRDRL GVGMSSFPLY PETEVIDLIS
PCPEARSRSV SRSYQEQKSH DHQLETVIEL SDSETDDEEH CKKARELRIF LQNIRKDIIL
