ENDO4_ARATH
ID ENDO4_ARATH Reviewed; 299 AA.
AC F4JJL0;
DT 13-JUN-2012, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 68.
DE RecName: Full=Endonuclease 4 {ECO:0000303|PubMed:17651368};
DE Short=AtENDO4 {ECO:0000303|PubMed:17651368};
DE EC=3.1.30.1 {ECO:0000269|PubMed:23620482};
DE AltName: Full=Deoxyribonuclease ENDO4 {ECO:0000303|PubMed:17651368};
DE AltName: Full=Single-stranded-nucleate endonuclease ENDO4 {ECO:0000303|PubMed:17651368};
DE Flags: Precursor;
GN Name=ENDO4 {ECO:0000303|PubMed:17651368};
GN OrderedLocusNames=At4g21585 {ECO:0000312|Araport:AT4G21585};
GN ORFNames=F18E5 {ECO:0000312|EMBL:AL022603};
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 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 [4]
RP FUNCTION, MUTAGENESIS OF 284-ALA--SER-299, 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 single-stranded RNA and 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=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:23620482};
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000269|PubMed:23620482};
CC Note=Binds 3 divalent metal cations. {ECO:0000269|PubMed:23620482};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 8 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}.
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DR EMBL; AL022603; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CP002687; AEE84476.1; -; Genomic_DNA.
DR EMBL; CP002687; ANM66198.1; -; Genomic_DNA.
DR RefSeq; NP_001328107.1; NM_001341503.1.
DR RefSeq; NP_680734.1; NM_148368.2.
DR AlphaFoldDB; F4JJL0; -.
DR SMR; F4JJL0; -.
DR STRING; 3702.AT4G21585.1; -.
DR PaxDb; F4JJL0; -.
DR PRIDE; F4JJL0; -.
DR ProteomicsDB; 222716; -.
DR EnsemblPlants; AT4G21585.1; AT4G21585.1; AT4G21585.
DR EnsemblPlants; AT4G21585.4; AT4G21585.4; AT4G21585.
DR GeneID; 828244; -.
DR Gramene; AT4G21585.1; AT4G21585.1; AT4G21585.
DR Gramene; AT4G21585.4; AT4G21585.4; AT4G21585.
DR KEGG; ath:AT4G21585; -.
DR Araport; AT4G21585; -.
DR TAIR; locus:504955531; AT4G21585.
DR eggNOG; ENOG502QRXU; Eukaryota.
DR HOGENOM; CLU_044365_3_0_1; -.
DR InParanoid; F4JJL0; -.
DR OMA; WDTSIPN; -.
DR PhylomeDB; F4JJL0; -.
DR BRENDA; 3.1.30.2; 399.
DR PRO; PR:F4JJL0; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; F4JJL0; baseline and differential.
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 Calcium; Disulfide bond; Endonuclease; Glycoprotein; Hydrolase; Manganese;
KW Metal-binding; Nuclease; Reference proteome; Signal.
FT SIGNAL 1..24
FT /evidence="ECO:0000255"
FT CHAIN 25..283
FT /note="Endonuclease 4"
FT /id="PRO_0000417622"
FT PROPEP 284..299
FT /note="Removed in mature form"
FT /evidence="ECO:0000269|PubMed:23620482"
FT /id="PRO_0000445543"
FT REGION 147..196
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 118
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT BINDING 136
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT BINDING 147
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT BINDING 151
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT BINDING 151
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT BINDING 157
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT BINDING 181
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT BINDING 185
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 118
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT CARBOHYD 137
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT CARBOHYD 198
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT CARBOHYD 211
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT CARBOHYD 229
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..246
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT DISULFID 101..111
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT DISULFID 226..233
FT /evidence="ECO:0000250|UniProtKB:Q9C9G4"
FT MUTAGEN 284..299
FT /note="Missing: Loss of activity."
FT /evidence="ECO:0000269|PubMed:23620482"
SQ SEQUENCE 299 AA; 34204 MW; 6F51DC9B188B88D5 CRC64;
MSSSLRQWFA RVLVLTQLIN GALCWGKEGH YTVCKIAESY FEEETVAAVK KLLPKSADGD
LASVCSWPDE IKHHWQWRWT SPLHYVDTPD YRCNYEYCRD CHDTHKNQDR CVTGAIFNYT
MQLMSASENS DTIVHYNLTE ALMFLSHFIG DIHQPLHVGF LGDEGGNTIT VRWYRRKTNL
HHVWDNMIIE SALKTYYNKS LPLMIEALQA NLTNDWSNDV PLWESCQLNQ TACPNPYASE
SINLACKYAY RNATPGTTLG DDYFLSRLPI VEKRLAQGGI RLAATLNRIF SSKPKHAGS
