ID GENL2_ORYSJ Reviewed; 641 AA.
AC Q8W5R1; B9FYM5;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 27-MAR-2024, entry version 113.
DE RecName: Full=Single-strand DNA endonuclease 1 {ECO:0000303|PubMed:12602891};
DE Short=OsSEND-1 {ECO:0000303|PubMed:12602891};
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:12602891}; Synonyms=GEN2;
GN OrderedLocusNames=Os08g0101600 {ECO:0000305}, LOC_Os08g01130 {ECO:0000305};
GN ORFNames=B1147B12.17, OsJ_25722 {ECO:0000312|EMBL:EEE67892.1};
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, COFACTOR, TISSUE SPECIFICITY, AND
RP INDUCTION.
RC STRAIN=cv. Nipponbare;
RX PubMed=12602891; DOI=10.1023/a:1020789314722;
RA Furukawa T., Kimura S., Ishibashi T., Mori Y., Hashimoto J., Sakaguchi K.;
RT "OsSEND-1: a new RAD2 nuclease family member in higher plants.";
RL Plant Mol. Biol. 51:59-70(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
CC -!- FUNCTION: Single-stranded DNA endonuclease activity in vitro
CC (PubMed:12602891). May not be active as double-stranded DNA
CC endonuclease (PubMed:12602891). Endonuclease which cleaves flap
CC structures at the junction between single-stranded DNA and double-
CC stranded DNA with a specific cleavage site in the 5' overhang strand
CC exactly one nucleotide 3' of the branch point (By similarity).
CC Structure- and sequence-specific nuclease that resolves holliday
CC junctions (HJs) by symmetrically oriented incisions in two opposing
CC strands near the junction point, thus leading to ligatable products;
CC HJs are physical links between homologous DNA molecules that arise as
CC central intermediary structures during homologous recombination and
CC repair in meiotic and somatic cells (By similarity). Probably involved
CC in the resolution of toxic replication structures to ensure genome
CC stability, and to maintain telomere integrity and replication (By
CC similarity). {ECO:0000250|UniProtKB:Q9M2Z3,
CC ECO:0000269|PubMed:12602891}.
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:0000305}.
CC -!- TISSUE SPECIFICITY: Highly expressed in shoot apical meristem (SAM) and
CC young leaves. Expressed in roots, flag leaf and panicles.
CC {ECO:0000269|PubMed:12602891}.
CC -!- INDUCTION: By the DNA-damaging agents methyl methanesulfonate (MMS),
CC H(2)O(2) and UV. Down-regulated by sucrose starvation and the cell
CC cycle inhibitors aphidicolin, hydroxyurea and colchicine.
CC {ECO:0000269|PubMed:12602891}.
CC -!- SIMILARITY: Belongs to the XPG/RAD2 endonuclease family. GEN subfamily.
CC {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AB074260; BAB72003.1; -; mRNA.
DR EMBL; AP008214; BAF22676.1; -; Genomic_DNA.
DR EMBL; AP014964; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CM000145; EEE67892.1; -; Genomic_DNA.
DR RefSeq; XP_015650609.1; XM_015795123.1.
DR AlphaFoldDB; Q8W5R1; -.
DR SMR; Q8W5R1; -.
DR STRING; 39947.Q8W5R1; -.
DR PaxDb; 39947-Q8W5R1; -.
DR EnsemblPlants; Os08t0101600-02; Os08t0101600-02; Os08g0101600.
DR GeneID; 4344420; -.
DR Gramene; Os08t0101600-02; Os08t0101600-02; Os08g0101600.
DR KEGG; osa:4344420; -.
DR eggNOG; KOG2519; Eukaryota.
DR InParanoid; Q8W5R1; -.
DR OrthoDB; 26655at2759; -.
DR Proteomes; UP000000763; Chromosome 8.
DR Proteomes; UP000007752; Chromosome 8.
DR Proteomes; UP000059680; Chromosome 8.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0017108; F:5'-flap endonuclease activity; IBA:GO_Central.
DR GO; GO:0008821; F:crossover junction DNA endonuclease activity; IEA:EnsemblPlants.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
DR GO; GO:0000723; P:telomere maintenance; IEA:EnsemblPlants.
DR GO; GO:0009650; P:UV protection; IEA:EnsemblPlants.
DR CDD; cd09900; H3TH_XPG-like; 1.
DR CDD; cd09869; PIN_GEN1; 1.
DR Gene3D; 1.10.150.20; 5' to 3' exonuclease, C-terminal subdomain; 1.
DR Gene3D; 3.40.50.1010; 5'-nuclease; 1.
DR InterPro; IPR036279; 5-3_exonuclease_C_sf.
DR InterPro; IPR008918; HhH2.
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:SF54; FI23547P1; 1.
DR PANTHER; PTHR11081; FLAP ENDONUCLEASE FAMILY MEMBER; 1.
DR Pfam; PF00867; XPG_I; 1.
DR Pfam; PF00752; XPG_N; 1.
DR PRINTS; PR00853; XPGRADSUPER.
DR SMART; SM00279; HhH2; 1.
DR SMART; SM00484; XPGI; 1.
DR SMART; SM00485; XPGN; 1.
DR SUPFAM; SSF47807; 5' to 3' exonuclease, C-terminal subdomain; 1.
DR SUPFAM; SSF88723; PIN domain-like; 1.
PE 2: Evidence at transcript level;
KW DNA damage; DNA repair; Endonuclease; Hydrolase; Magnesium; Metal-binding;
KW Nuclease; Nucleus; Reference proteome.
FT CHAIN 1..641
FT /note="Single-strand DNA endonuclease 1"
FT /id="PRO_0000315625"
FT REGION 1..90
FT /note="N-domain"
FT REGION 2..97
FT /note="XPG-N domain"
FT /evidence="ECO:0000250|UniProtKB:Q17RS7"
FT REGION 132..221
FT /note="I-domain"
FT REGION 132..220
FT /note="I-domain"
FT /evidence="ECO:0000250|UniProtKB:Q9LPD2"
FT REGION 132..217
FT /note="XPG-I domain"
FT /evidence="ECO:0000250|UniProtKB:Q17RS7"
FT REGION 217..350
FT /note="5'-3' exonuclease domain"
FT /evidence="ECO:0000250|UniProtKB:Q17RS7"
FT REGION 428..448
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 572..615
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 144
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q17RS7"
FT BINDING 146
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q58839"
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 167
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9UQ84"
FT BINDING 217
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q58839"
SQ SEQUENCE 641 AA; 69918 MW; 6FECE8642BEA981A CRC64;
MGVKNLWDIL ESCKKKLPLH HLQNKKVCVD LSCWLVQMYS ANRSPAFAKD KVYLKNLFHR
IRALLALNCT LLFVTDGAIP SLKLATYRRR LGSISHAAKE SDQPNSHPSI SLRRNKGSEF
SCMIKEAKRL GMALGIPCLD GLEEAEAQCA SLDLESLCDG CFTSDSDAFL FGARTVYRDV
FIGEGGYVIC YEMEDIEKTL GFGRNSLISL AVLLGSDYSN GVNGFGPETA CRLVKSVGDN
LILDQILSNG VKATRKCKGK NSGNKVDDMC PKASSCEVGM TQDSDGQFRD VINAYLEPKC
HSPDSEAVQR VCGQHPFLRP QLQKICEEYF DWSPEKTDQY ILPKIAEREL RRFSDLRSAS
SALGIKPLLS EIPVPCPVLA IVKQRKVHGN ECYEVSWRNI EGLQVSVVPG DLVKSACPEK
ITEFLEKKGE EKKQKRRARP KKSGQAAVKD VDEQLQELLL GIEADSGGIL GATASVCQTL
TAAYTVAVED VVDLSSPSPP LRKLSKSQKK MMAEDVNVAG MNMNKMESES SFSTQSSTSD
VDNQLIDLSS PLAGGDNGMK GGRRALADIS NVGSHSTETD GGGGGGGGVA SVGHGTTIDL
SSPSPAIGDR SRVHHDDDDV IHERKARDLR MFLDSIRNEL Y
//
