CLPR1_ARATH
ID CLPR1_ARATH Reviewed; 387 AA.
AC Q9XJ35;
DT 13-NOV-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 25-MAY-2022, entry version 124.
DE RecName: Full=ATP-dependent Clp protease proteolytic subunit-related protein 1, chloroplastic {ECO:0000303|PubMed:11299370};
DE Short=ClpR1 {ECO:0000303|PubMed:11299370};
DE AltName: Full=Protein SUPPRESSOR OF VARIEGATION 2 {ECO:0000303|PubMed:18599582};
DE AltName: Full=nClpP5;
DE Flags: Precursor;
GN Name=CLPR1 {ECO:0000303|PubMed:11299370};
GN Synonyms=NCLPP5, SVR2 {ECO:0000303|PubMed:18599582};
GN OrderedLocusNames=At1g49970 {ECO:0000312|Araport:AT1G49970};
GN ORFNames=F2J10.14 {ECO:0000312|EMBL:AAF76446.1};
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 [MRNA], SUBCELLULAR LOCATION, AND INDUCTION.
RC STRAIN=cv. Columbia;
RX PubMed=10427773; DOI=10.1093/oxfordjournals.pcp.a029571;
RA Nakabayashi K., Ito M., Kiyosue T., Shinozaki K., Watanabe A.;
RT "Identification of clp genes expressed in senescing Arabidopsis leaves.";
RL Plant Cell Physiol. 40:504-514(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
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=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 [5]
RP PROTEIN SEQUENCE OF 167-180 AND 304-318, SUBUNIT, AND IDENTIFICATION BY
RP MASS SPECTROMETRY.
RX PubMed=11278690; DOI=10.1074/jbc.m010503200;
RA Peltier J.-B., Ytterberg J., Liberles D.A., Roepstorff P., van Wijk K.J.;
RT "Identification of a 350-kDa ClpP protease complex with 10 different Clp
RT isoforms in chloroplasts of Arabidopsis thaliana.";
RL J. Biol. Chem. 276:16318-16327(2001).
RN [6]
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 [7]
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 [8]
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 [9]
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 [10]
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 [11]
RP FUNCTION.
RX PubMed=17009084; DOI=10.1007/s11103-006-9074-2;
RA Koussevitzky S., Stanne T.M., Peto C.A., Giap T., Sjoegren L.L.E., Zhao Y.,
RA Clarke A.K., Chory J.;
RT "An Arabidopsis thaliana virescent mutant reveals a role for ClpR1 in
RT plastid development.";
RL Plant Mol. Biol. 63:85-96(2007).
RN [12]
RP FUNCTION.
RX PubMed=18599582; DOI=10.1105/tpc.107.054965;
RA Yu F., Liu X., Alsheikh M., Park S., Rodermel S.;
RT "Mutations in SUPPRESSOR OF VARIEGATION1, a factor required for normal
RT chloroplast translation, suppress var2-mediated leaf variegation in
RT Arabidopsis.";
RL Plant Cell 20:1786-1804(2008).
RN [13]
RP DISRUPTION PHENOTYPE.
RX PubMed=18754756; DOI=10.1042/bj20081146;
RA Stanne T.M., Sjoegren L.L., Koussevitzky S., Clarke A.K.;
RT "Identification of new protein substrates for the chloroplast ATP-dependent
RT Clp protease supports its constitutive role in Arabidopsis.";
RL Biochem. J. 417:257-268(2009).
RN [14]
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 [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: Required for chloroplast development and differentiation.
CC {ECO:0000269|PubMed:17009084, ECO:0000269|PubMed:18599582}.
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:11278690, PubMed:14593120, PubMed:16766689,
CC PubMed:16980539). The core complex is organized in two heptameric
CC rings, one containing CLPP3,4,5,6 in a 1:2:3:1 ratio and the other
CC CLPP1 and CLPR1,2,3,4 in a 3:1:1:1:1 ratio (PubMed:21712416).
CC {ECO:0000269|PubMed:11278690, ECO:0000269|PubMed:14593120,
CC ECO:0000269|PubMed:16766689, ECO:0000269|PubMed:16980539,
CC ECO:0000269|PubMed:21712416}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma
CC {ECO:0000269|PubMed:10427773, ECO:0000269|PubMed:14593120}.
CC -!- INDUCTION: Repressed in darkness. Accumulates during leaf senescence.
CC {ECO:0000269|PubMed:10427773}.
CC -!- DISRUPTION PHENOTYPE: Variegated leaf phenotype (Ref.8). Slow-growth
CC phenotype, with chlorotic leaves during early development
CC (PubMed:17009084, PubMed:18754756). {ECO:0000269|PubMed:17009084,
CC ECO:0000269|PubMed:18754756, ECO:0000303|Ref.8}.
CC -!- SIMILARITY: Belongs to the peptidase S14 family. {ECO:0000305}.
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DR EMBL; AB022330; BAA82069.1; -; mRNA.
DR EMBL; AC015445; AAF76446.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE32501.1; -; Genomic_DNA.
DR EMBL; AY045677; AAK74035.1; -; mRNA.
DR EMBL; BT000572; AAN18141.1; -; mRNA.
DR PIR; T52451; T52451.
DR RefSeq; NP_564560.1; NM_103884.4.
DR AlphaFoldDB; Q9XJ35; -.
DR SMR; Q9XJ35; -.
DR BioGRID; 26645; 7.
DR IntAct; Q9XJ35; 1.
DR STRING; 3702.AT1G49970.1; -.
DR iPTMnet; Q9XJ35; -.
DR PaxDb; Q9XJ35; -.
DR PRIDE; Q9XJ35; -.
DR ProteomicsDB; 246592; -.
DR EnsemblPlants; AT1G49970.1; AT1G49970.1; AT1G49970.
DR GeneID; 841420; -.
DR Gramene; AT1G49970.1; AT1G49970.1; AT1G49970.
DR KEGG; ath:AT1G49970; -.
DR Araport; AT1G49970; -.
DR TAIR; locus:2031070; AT1G49970.
DR eggNOG; KOG0840; Eukaryota.
DR HOGENOM; CLU_051940_0_0_1; -.
DR OMA; GPAKYSM; -.
DR OrthoDB; 1274502at2759; -.
DR PhylomeDB; Q9XJ35; -.
DR PRO; PR:Q9XJ35; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9XJ35; baseline and differential.
DR Genevisible; Q9XJ35; 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:0009534; C:chloroplast thylakoid; IDA:TAIR.
DR GO; GO:0009840; C:chloroplastic endopeptidase Clp complex; IDA:TAIR.
DR GO; GO:0009368; C:endopeptidase Clp complex; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; 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:0003723; F:RNA binding; IDA:UniProtKB.
DR GO; GO:0004252; F:serine-type endopeptidase activity; IBA:GO_Central.
DR GO; GO:0009658; P:chloroplast organization; IMP:UniProtKB.
DR GO; GO:0006515; P:protein quality control for misfolded or incompletely synthesized proteins; IBA:GO_Central.
DR GO; GO:0006396; P:RNA processing; IDA:UniProtKB.
DR GO; GO:0006364; P:rRNA processing; IMP:UniProtKB.
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; Direct protein sequencing; Plastid; Reference proteome;
KW Transit peptide.
FT TRANSIT 1..41
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 42..387
FT /note="ATP-dependent Clp protease proteolytic subunit-
FT related protein 1, chloroplastic"
FT /id="PRO_0000308982"
FT REGION 355..387
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 387 AA; 42627 MW; 9422999CF20FA1FC CRC64;
MATALVSPLT SQLNHEAVCS KFVLPKSPFM SGSKLFSSNM PCSTVPRRTR RSHCFASAKD
MSFDHIPKQF RGDNLKDGVM QNFKNVPQYF YGLNSAQMDM FMTEDSPVRR QAEKVTEESI
SSRNNYLNNG GIWSMSGMNA ADARRYSMSV QMYRGGGGGG GSERPRTAPP DLPSLLLDAR
ICYLGMPIVP AVTELLVAQF MWLDYDNPTK PIYLYINSPG TQNEKMETVG SETEAYAIAD
TISYCKSDVY TINCGMAFGQ AAMLLSLGKK GYRAVQPHSS TKLYLPKVNR SSGAAIDMWI
KAKELDANTE YYIELLAKGT GKSKEQINED IKRPKYLQAQ AAIDYGIADK IADSQDSSFE
KRDYDGTLAQ RAMRPGGGSP AAPAGLR
