ENDO3_ARATH
ID ENDO3_ARATH Reviewed; 294 AA.
AC Q8LDW6; O65424;
DT 13-JUN-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 1.
DT 03-AUG-2022, entry version 117.
DE RecName: Full=Endonuclease 3 {ECO:0000303|PubMed:17651368};
DE Short=AtENDO3 {ECO:0000303|PubMed:17651368};
DE EC=3.1.30.1 {ECO:0000269|PubMed:23620482};
DE AltName: Full=Deoxyribonuclease ENDO3 {ECO:0000303|PubMed:17651368};
DE AltName: Full=Single-stranded-nucleate endonuclease ENDO3 {ECO:0000303|PubMed:17651368};
DE Flags: Precursor;
GN Name=ENDO3 {ECO:0000303|PubMed:17651368};
GN OrderedLocusNames=At4g21590 {ECO:0000312|Araport:AT4G21590};
GN ORFNames=F17L22.50 {ECO:0000312|EMBL:CAB36803.1},
GN F18E5.210 {ECO:0000312|EMBL:CAA18723.1};
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=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
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].
RC STRAIN=cv. Columbia;
RA Quinitio C., Chen H., Kim C.J., Shinn P., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION, GENE FAMILY, AND NOMENCLATURE.
RX PubMed=17651368; DOI=10.1111/j.1365-313x.2007.03201.x;
RA Triques K., Sturbois B., Gallais S., Dalmais M., Chauvin S., Clepet C.,
RA Aubourg S., Rameau C., Caboche M., Bendahmane A.;
RT "Characterization of Arabidopsis thaliana mismatch specific endonucleases:
RT application to mutation discovery by TILLING in pea.";
RL Plant J. 51:1116-1125(2007).
RN [6]
RP FUNCTION, MUTAGENESIS OF 280-THR--ALA-294, BIOPHYSICOCHEMICAL PROPERTIES,
RP CATALYTIC ACTIVITY, COFACTOR, PROTEOLYTIC CLEAVAGE, AND GENE FAMILY.
RX PubMed=23620482; DOI=10.1093/pcp/pct061;
RA Lesniewicz K., Karlowski W.M., Pienkowska J.R., Krzywkowski P., Poreba E.;
RT "The plant s1-like nuclease family has evolved a highly diverse range of
RT catalytic capabilities.";
RL Plant Cell Physiol. 54:1064-1078(2013).
CC -!- FUNCTION: Endonuclease that can use RNA and single-stranded DNA as
CC substrates (PubMed:23620482). In contradiction with PubMed:23620482,
CC cannot hydrolyze single-stranded DNA and does not cleave mismatches
CC (PubMed:17651368). {ECO:0000269|PubMed:17651368,
CC ECO:0000269|PubMed:23620482}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endonucleolytic cleavage to 5'-phosphomononucleotide and 5'-
CC phosphooligonucleotide end-products.; EC=3.1.30.1;
CC Evidence={ECO:0000269|PubMed:23620482};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:23620482};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:23620482};
CC Note=Binds 3 divalent metal cations (PubMed:23620482). Can use Mn(2+)
CC with a lower efficiency than Zn(2+) ions (PubMed:23620482).
CC {ECO:0000269|PubMed:23620482};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 5.5 with RNA and ssDNA as substrates.
CC {ECO:0000269|PubMed:23620482};
CC -!- SUBUNIT: Monomer. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the nuclease type I family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA18723.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB36803.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB81266.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL022603; CAA18723.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL035527; CAB36803.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161555; CAB81266.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE84477.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE84478.1; -; Genomic_DNA.
DR EMBL; BT026061; ABG48417.1; -; mRNA.
DR EMBL; AY085756; AAM62974.1; -; mRNA.
DR PIR; T05167; T05167.
DR RefSeq; NP_001078420.1; NM_001084951.2.
DR RefSeq; NP_567630.1; NM_118279.3.
DR AlphaFoldDB; Q8LDW6; -.
DR SMR; Q8LDW6; -.
DR STRING; 3702.AT4G21590.1; -.
DR PaxDb; Q8LDW6; -.
DR PRIDE; Q8LDW6; -.
DR ProteomicsDB; 222693; -.
DR EnsemblPlants; AT4G21590.1; AT4G21590.1; AT4G21590.
DR EnsemblPlants; AT4G21590.2; AT4G21590.2; AT4G21590.
DR GeneID; 828245; -.
DR Gramene; AT4G21590.1; AT4G21590.1; AT4G21590.
DR Gramene; AT4G21590.2; AT4G21590.2; AT4G21590.
DR KEGG; ath:AT4G21590; -.
DR Araport; AT4G21590; -.
DR TAIR; locus:2119687; AT4G21590.
DR eggNOG; ENOG502QRXU; Eukaryota.
DR HOGENOM; CLU_044365_3_0_1; -.
DR InParanoid; Q8LDW6; -.
DR OMA; MHCARIA; -.
DR OrthoDB; 1114699at2759; -.
DR PhylomeDB; Q8LDW6; -.
DR BRENDA; 3.1.30.1; 399.
DR PRO; PR:Q8LDW6; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q8LDW6; baseline and differential.
DR Genevisible; Q8LDW6; AT.
DR GO; GO:0004519; F:endonuclease activity; IDA:UniProtKB.
DR GO; GO:0004521; F:endoribonuclease activity; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
DR GO; GO:0000014; F:single-stranded DNA endodeoxyribonuclease activity; IDA:UniProtKB.
DR GO; GO:0006308; P:DNA catabolic process; IEA:InterPro.
DR GO; GO:0090502; P:RNA phosphodiester bond hydrolysis, endonucleolytic; IDA:UniProtKB.
DR CDD; cd11010; S1-P1_nuclease; 1.
DR Gene3D; 1.10.575.10; -; 1.
DR InterPro; IPR008947; PLipase_C/P1_nuclease_dom_sf.
DR InterPro; IPR003154; S1/P1nuclease.
DR PANTHER; PTHR33146; PTHR33146; 1.
DR Pfam; PF02265; S1-P1_nuclease; 1.
DR SUPFAM; SSF48537; SSF48537; 1.
PE 1: Evidence at protein level;
KW Disulfide bond; Endonuclease; Glycoprotein; Hydrolase; Manganese;
KW Metal-binding; Nuclease; Reference proteome; Signal; Zinc.
FT SIGNAL 1..24
FT /evidence="ECO:0000255"
FT CHAIN 25..278
FT /note="Endonuclease 3"
FT /id="PRO_0000417621"
FT PROPEP 279..294
FT /note="Removed in mature form"
FT /evidence="ECO:0000269|PubMed:23620482"
FT /id="PRO_0000445542"
FT REGION 142..191
FT /note="Substrate binding"
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT BINDING 25..30
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT BINDING 25
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT BINDING 30
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT BINDING 69..75
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT BINDING 69
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT BINDING 84..87
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P24289"
FT BINDING 84
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT BINDING 94..99
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P24289"
FT BINDING 113
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT BINDING 131
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT BINDING 142
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT BINDING 146
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT BINDING 146
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT BINDING 152
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT BINDING 176
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT BINDING 180
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT SITE 69
FT /note="Important for catalytic activity"
FT /evidence="ECO:0000250|UniProtKB:P24021"
FT SITE 72
FT /note="Important for catalytic activity"
FT /evidence="ECO:0000250|UniProtKB:P24289"
FT CARBOHYD 113
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT CARBOHYD 132
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT CARBOHYD 193
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT CARBOHYD 224
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT CARBOHYD 247
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT DISULFID 34..65
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT DISULFID 93..241
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT DISULFID 101..106
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT DISULFID 221..228
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT MUTAGEN 280..294
FT /note="Missing: Loss of activity."
FT /evidence="ECO:0000269|PubMed:23620482"
SQ SEQUENCE 294 AA; 33424 MW; 02B3F246DFCA4939 CRC64;
MGWSLRMWIV SILVLTQLVN GALCWGDAGH YAVCKIAQSY FEEDTVVAVK KLLPESANGE
LAAVCSWPDE IKKLPQWRWT SALHFADTPD YKCNYEYSRD CPKDWCVTGA IFNYTNQLMS
TSENSQSIVH YNLTEALMFL SHYMGDIHQP LHEGFIGDLG GNKIKVHWYN QETNLHRVWD
DMIIESALET YYNSSLPRMI HELQAKLKNG WSNDVPSWES CQLNQTACPN PYASESIDLA
CKYAYRNATA GTTLGDYYFV SRLPVVEKRL AQGGIRLAGT LNRIFSAKRK LARA
