CLPR4_ARATH
ID CLPR4_ARATH Reviewed; 305 AA.
AC Q8LB10; O23548; Q8RXG1;
DT 13-NOV-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 1.
DT 25-MAY-2022, entry version 112.
DE RecName: Full=ATP-dependent Clp protease proteolytic subunit-related protein 4, chloroplastic {ECO:0000303|PubMed:11299370};
DE Short=ClpR4 {ECO:0000303|PubMed:11299370};
DE AltName: Full=Protein HAPPY ON NORFLURAZON 5 {ECO:0000303|PubMed:21208309};
DE Flags: Precursor;
GN Name=CLPR4 {ECO:0000303|PubMed:11299370};
GN Synonyms=HON5 {ECO:0000303|PubMed:21208309};
GN OrderedLocusNames=At4g17040 {ECO:0000312|Araport:AT4G17040};
GN ORFNames=dl4550c {ECO:0000312|EMBL:CAB10484.1},
GN FCAALL.413 {ECO:0000312|EMBL:CAB80975.1};
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=9461215; DOI=10.1038/35140;
RA Bevan M., Bancroft I., Bent E., Love K., Goodman H.M., Dean C.,
RA Bergkamp R., Dirkse W., van Staveren M., Stiekema W., Drost L., Ridley P.,
RA Hudson S.-A., Patel K., Murphy G., Piffanelli P., Wedler H., Wedler E.,
RA Wambutt R., Weitzenegger T., Pohl T., Terryn N., Gielen J., Villarroel R.,
RA De Clercq R., van Montagu M., Lecharny A., Aubourg S., Gy I., Kreis M.,
RA Lao N., Kavanagh T., Hempel S., Kotter P., Entian K.-D., Rieger M.,
RA Schaefer M., Funk B., Mueller-Auer S., Silvey M., James R., Monfort A.,
RA Pons A., Puigdomenech P., Douka A., Voukelatou E., Milioni D.,
RA Hatzopoulos P., Piravandi E., Obermaier B., Hilbert H., Duesterhoeft A.,
RA Moores T., Jones J.D.G., Eneva T., Palme K., Benes V., Rechmann S.,
RA Ansorge W., Cooke R., Berger C., Delseny M., Voet M., Volckaert G.,
RA Mewes H.-W., Klosterman S., Schueller C., Chalwatzis N.;
RT "Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis
RT thaliana.";
RL Nature 391:485-488(1998).
RN [2]
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 [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=11910074; DOI=10.1126/science.1071006;
RA Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA Shinagawa A., Shinozaki K.;
RT "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL Science 296:141-145(2002).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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 [6]
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 [7]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=11299370; DOI=10.1104/pp.125.4.1912;
RA Adam Z., Adamska I., Nakabayashi K., Ostersetzer O., Haussuhl K.,
RA Manuell A., Zheng B., Vallon O., Rodermel S.R., Shinozaki K., Clarke A.K.;
RT "Chloroplast and mitochondrial proteases in Arabidopsis. A proposed
RT nomenclature.";
RL Plant Physiol. 125:1912-1918(2001).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY, SUBUNIT, SUBCELLULAR LOCATION, AND
RP 3D-STRUCTURE MODELING.
RX PubMed=14593120; DOI=10.1074/jbc.m309212200;
RA Peltier J.-B., Ripoll D.R., Friso G., Rudella A., Cai Y., Ytterberg J.,
RA Giacomelli L., Pillardy J., van Wijk K.J.;
RT "Clp protease complexes from photosynthetic and non-photosynthetic plastids
RT and mitochondria of plants, their predicted three-dimensional structures,
RT and functional implications.";
RL J. Biol. Chem. 279:4768-4781(2004).
RN [9]
RP NOMENCLATURE, AND DISRUPTION PHENOTYPE.
RX DOI=10.1111/j.1399-3054.2005.00452.x;
RA Clarke A.K., MacDonald T.M., Sjoegren L.L.;
RT "The ATP-dependent Clp protease in chloroplasts of higher plants.";
RL Physiol. Plantarum 123:406-412(2005).
RN [10]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBUNIT.
RX PubMed=16766689; DOI=10.1105/tpc.106.042861;
RA Rudella A., Friso G., Alonso J.M., Ecker J.R., van Wijk K.J.;
RT "Downregulation of ClpR2 leads to reduced accumulation of the ClpPRS
RT protease complex and defects in chloroplast biogenesis in Arabidopsis.";
RL Plant Cell 18:1704-1721(2006).
RN [11]
RP SUBUNIT.
RX PubMed=16980539; DOI=10.1105/tpc.106.044594;
RA Sjoegren L.L.E., Stanne T.M., Zheng B., Sutinen S., Clarke A.K.;
RT "Structural and functional insights into the chloroplast ATP-dependent Clp
RT protease in Arabidopsis.";
RL Plant Cell 18:2635-2649(2006).
RN [12]
RP DISRUPTION PHENOTYPE.
RX PubMed=19525416; DOI=10.1105/tpc.108.063784;
RA Kim J., Rudella A., Ramirez Rodriguez V., Zybailov B., Olinares P.D.,
RA van Wijk K.J.;
RT "Subunits of the plastid ClpPR protease complex have differential
RT contributions to embryogenesis, plastid biogenesis, and plant development
RT in Arabidopsis.";
RL Plant Cell 21:1669-1692(2009).
RN [13]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBUNIT.
RX PubMed=21712416; DOI=10.1105/tpc.111.086454;
RA Olinares P.D., Kim J., Davis J.I., van Wijk K.J.;
RT "Subunit stoichiometry, evolution, and functional implications of an
RT asymmetric plant plastid ClpP/R protease complex in Arabidopsis.";
RL Plant Cell 23:2348-2361(2011).
RN [14]
RP FUNCTION.
RX PubMed=21208309; DOI=10.1111/j.1365-313x.2010.04454.x;
RA Saini G., Meskauskiene R., Pijacka W., Roszak P., Sjoegren L.L.,
RA Clarke A.K., Straus M., Apel K.;
RT "'happy on norflurazon' (hon) mutations implicate perturbance of plastid
RT homeostasis with activating stress acclimatization and changing nuclear
RT gene expression in norflurazon-treated seedlings.";
RL Plant J. 65:690-702(2011).
RN [15]
RP REVIEW.
RX PubMed=22085372; DOI=10.1111/j.1399-3054.2011.01541.x;
RA Clarke A.K.;
RT "The chloroplast ATP-dependent Clp protease in vascular plants - new
RT dimensions and future challenges.";
RL Physiol. Plantarum 145:235-244(2012).
CC -!- FUNCTION: Involved in plastid protein homeostasis.
CC {ECO:0000269|PubMed:21208309}.
CC -!- SUBUNIT: Component of the chloroplastic Clp protease core complex which
CC consist of at least 16 proteins: CLPP4 (3 copies), CLPP5 (3 copies),
CC CLPR4 (2 copies), ClpP1 (1 copy), CLPP6 (1 copy), CLPR2 (1 copy), CLPT1
CC (1 copy), CLPT2 (1 copy) and 3 copies of CLPP3 and/or CLPR1 and/or
CC CLPR3 (PubMed:14593120, PubMed:16766689, PubMed:16980539). The core
CC complex is organized in two heptameric rings, one containing
CC CLPP3,4,5,6 in a 1:2:3:1 ratio and the other CLPP1 and CLPR1,2,3,4 in a
CC 3:1:1:1:1 ratio (PubMed:21712416). {ECO:0000269|PubMed:14593120,
CC ECO:0000269|PubMed:16766689, ECO:0000269|PubMed:16980539,
CC ECO:0000269|PubMed:21712416}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:14593120}.
CC -!- DISRUPTION PHENOTYPE: Embryo lethal (Ref.9). Delayed embryogenesis and
CC albino embryos, with seedling development blocked in the cotyledon
CC stage (PubMed:19525416). Under heterotrophic growth conditions,
CC seedlings develop into small albino to virescent seedlings
CC (PubMed:19525416). {ECO:0000269|PubMed:19525416, ECO:0000303|Ref.9}.
CC -!- SIMILARITY: Belongs to the peptidase S14 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB10484.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB80975.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; Z97342; CAB10484.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161545; CAB80975.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE83842.1; -; Genomic_DNA.
DR EMBL; AK117499; BAC42162.1; -; mRNA.
DR EMBL; AY081275; AAL91164.1; -; mRNA.
DR EMBL; BT000050; AAN15369.1; -; mRNA.
DR EMBL; AY087492; AAM65035.1; -; mRNA.
DR PIR; G71438; G71438.
DR RefSeq; NP_567521.1; NM_117808.3.
DR AlphaFoldDB; Q8LB10; -.
DR SMR; Q8LB10; -.
DR BioGRID; 12705; 6.
DR IntAct; Q8LB10; 2.
DR STRING; 3702.AT4G17040.1; -.
DR MEROPS; S14.001; -.
DR PaxDb; Q8LB10; -.
DR PRIDE; Q8LB10; -.
DR ProteomicsDB; 241042; -.
DR EnsemblPlants; AT4G17040.1; AT4G17040.1; AT4G17040.
DR GeneID; 827412; -.
DR Gramene; AT4G17040.1; AT4G17040.1; AT4G17040.
DR KEGG; ath:AT4G17040; -.
DR Araport; AT4G17040; -.
DR TAIR; locus:2130449; AT4G17040.
DR eggNOG; KOG0840; Eukaryota.
DR HOGENOM; CLU_058707_5_1_1; -.
DR InParanoid; Q8LB10; -.
DR OMA; ICDTINY; -.
DR OrthoDB; 1274502at2759; -.
DR PhylomeDB; Q8LB10; -.
DR PRO; PR:Q8LB10; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q8LB10; baseline and differential.
DR Genevisible; Q8LB10; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009941; C:chloroplast envelope; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0009368; C:endopeptidase Clp complex; IBA:GO_Central.
DR GO; GO:0009536; C:plastid; HDA:TAIR.
DR GO; GO:0009532; C:plastid stroma; IDA:TAIR.
DR GO; GO:0004176; F:ATP-dependent peptidase activity; IBA:GO_Central.
DR GO; GO:0051117; F:ATPase binding; IBA:GO_Central.
DR GO; GO:0004252; F:serine-type endopeptidase activity; IBA:GO_Central.
DR GO; GO:0006515; P:protein quality control for misfolded or incompletely synthesized proteins; IBA:GO_Central.
DR GO; GO:0010468; P:regulation of gene expression; IMP:TAIR.
DR GO; GO:0000302; P:response to reactive oxygen species; IMP:TAIR.
DR CDD; cd07017; S14_ClpP_2; 1.
DR InterPro; IPR001907; ClpP.
DR InterPro; IPR029045; ClpP/crotonase-like_dom_sf.
DR InterPro; IPR023562; ClpP/TepA.
DR PANTHER; PTHR10381; PTHR10381; 1.
DR Pfam; PF00574; CLP_protease; 1.
DR PRINTS; PR00127; CLPPROTEASEP.
DR SUPFAM; SSF52096; SSF52096; 1.
PE 1: Evidence at protein level;
KW Chloroplast; Plastid; Reference proteome; Transit peptide.
FT TRANSIT 1..68
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 69..305
FT /note="ATP-dependent Clp protease proteolytic subunit-
FT related protein 4, chloroplastic"
FT /id="PRO_0000308985"
FT CONFLICT 143
FT /note="E -> K (in Ref. 5; AAL91164/AAN15369)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 305 AA; 33440 MW; 7902D9ECF220B92F CRC64;
MEVAAATATS FTTLRARTSA IIPSSTRNLR SKPRFSSSSS LRASLSNGFL SPYTGGSISS
DLCGAKLRAE SLNPLNFSSS KPKRGVVTMV IPFSKGSAHE QPPPDLASYL FKNRIVYLGM
SLVPSVTELI LAEFLYLQYE DEEKPIYLYI NSTGTTKNGE KLGYDTEAFA IYDVMGYVKP
PIFTLCVGNA WGEAALLLTA GAKGNRSALP SSTIMIKQPI ARFQGQATDV EIARKEIKHI
KTEMVKLYSK HIGKSPEQIE ADMKRPKYFS PTEAVEYGII DKVVYNERGS QDRGVVSDLK
KAQLI
