CLPR2_ARATH
ID CLPR2_ARATH Reviewed; 279 AA.
AC Q9XJ36; Q93ZD4;
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 2, chloroplastic {ECO:0000303|PubMed:11299370};
DE Short=ClpR2 {ECO:0000303|PubMed:11299370};
DE Short=nClpP2;
DE Flags: Precursor;
GN Name=CLPR2 {ECO:0000303|PubMed:11299370}; Synonyms=NCLPP2;
GN OrderedLocusNames=At1g12410 {ECO:0000312|Araport:AT1G12410};
GN ORFNames=F5O11.13 {ECO:0000312|EMBL:AAF79635.1};
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], 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 81-96 AND 99-129, SUBUNIT, AND IDENTIFICATION BY MASS
RP 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 FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, AND TISSUE SPECIFICITY.
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.
RC STRAIN=cv. Columbia;
RX PubMed=16461379; DOI=10.1104/pp.105.076083;
RA Ytterberg A.J., Peltier J.-B., van Wijk K.J.;
RT "Protein profiling of plastoglobules in chloroplasts and chromoplasts. A
RT surprising site for differential accumulation of metabolic enzymes.";
RL Plant Physiol. 140:984-997(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 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 integrity. Involved
CC in the regulation of plastoglobules formation.
CC {ECO:0000269|PubMed:16461379, ECO:0000269|PubMed:16766689}.
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: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:11278690,
CC ECO:0000269|PubMed:14593120, ECO:0000269|PubMed:16980539,
CC ECO:0000269|PubMed:21712416}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:14593120}.
CC -!- TISSUE SPECIFICITY: Expressed at least in leaves and roots.
CC {ECO:0000269|PubMed:16766689}.
CC -!- INDUCTION: Repressed in darkness. {ECO:0000269|PubMed:10427773}.
CC -!- DISRUPTION PHENOTYPE: Embryo lethal (Ref.8). 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.8}.
CC -!- SIMILARITY: Belongs to the peptidase S14 family. {ECO:0000305}.
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DR EMBL; AB022327; BAA82066.1; -; mRNA.
DR EMBL; AC025416; AAF79635.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE28876.1; -; Genomic_DNA.
DR EMBL; AY057617; AAL14412.1; -; mRNA.
DR EMBL; AY062770; AAL32848.1; -; mRNA.
DR EMBL; AY081641; AAM10203.1; -; mRNA.
DR PIR; T52454; T52454.
DR RefSeq; NP_563907.1; NM_101113.4.
DR AlphaFoldDB; Q9XJ36; -.
DR SMR; Q9XJ36; -.
DR BioGRID; 23037; 7.
DR IntAct; Q9XJ36; 2.
DR STRING; 3702.AT1G12410.1; -.
DR PaxDb; Q9XJ36; -.
DR PRIDE; Q9XJ36; -.
DR ProteomicsDB; 246660; -.
DR EnsemblPlants; AT1G12410.1; AT1G12410.1; AT1G12410.
DR GeneID; 837797; -.
DR Gramene; AT1G12410.1; AT1G12410.1; AT1G12410.
DR KEGG; ath:AT1G12410; -.
DR Araport; AT1G12410; -.
DR TAIR; locus:2034625; AT1G12410.
DR eggNOG; KOG0840; Eukaryota.
DR HOGENOM; CLU_058707_2_2_1; -.
DR InParanoid; Q9XJ36; -.
DR OMA; GHRFAMP; -.
DR OrthoDB; 1274502at2759; -.
DR PhylomeDB; Q9XJ36; -.
DR PRO; PR:Q9XJ36; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9XJ36; baseline and differential.
DR Genevisible; Q9XJ36; 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:0005576; C:extracellular region; HDA: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:0009658; P:chloroplast organization; IMP:TAIR.
DR GO; GO:0006515; P:protein quality control for misfolded or incompletely synthesized proteins; IBA:GO_Central.
DR CDD; cd07017; S14_ClpP_2; 1.
DR HAMAP; MF_00444; ClpP; 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..54
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 55..279
FT /note="ATP-dependent Clp protease proteolytic subunit-
FT related protein 2, chloroplastic"
FT /id="PRO_0000308983"
FT CONFLICT 126
FT /note="D -> G (in Ref. 4; AAL14412)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 279 AA; 31209 MW; DAD1CFDDD3478308 CRC64;
MAVSFNTTLH QPSLSPSCSI KLYSGLKPQS ASFLASGYQN LNKEFYGRVY KSLQSGTGKA
SRSRVKMMPI GTPRVPYRNR EEGTWQWVDI WNALYRERVI FIGQNIDEEF SNQILATMLY
LDTLDDSRRI YMYLNGPGGD LTPSLAIYDT MKSLKSPVGT HCVGLAYNLA GFLLAAGEKG
HRFAMPLSRI ALQSPAGAAR GQADDIQNEA KELSRIRDYL FNELAKNTGQ PAERVFKDLS
RVKRFNAEEA IEYGLIDKIV RPPRIKEDAP RQDESAGLG
