CLPP3_ARATH
ID CLPP3_ARATH Reviewed; 309 AA.
AC Q9SXJ6; O82421; Q94JY6;
DT 13-NOV-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 137.
DE RecName: Full=ATP-dependent Clp protease proteolytic subunit 3, chloroplastic {ECO:0000303|PubMed:11299370};
DE EC=3.4.21.92;
DE AltName: Full=Endopeptidase ClpP3 {ECO:0000303|PubMed:11299370};
DE Short=nClpP3;
DE AltName: Full=nClpP4;
DE Flags: Precursor;
GN Name=CLPP3 {ECO:0000303|PubMed:11299370}; Synonyms=CLP, NCLPP3, NCLPP4;
GN OrderedLocusNames=At1g66670 {ECO:0000312|Araport:AT1G66670};
GN ORFNames=F4N21.19 {ECO:0000312|EMBL:AAG60075.1},
GN T12I7.12 {ECO:0000312|EMBL:AAG51173.1};
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].
RX AGRICOLA=IND22014948; DOI=10.1007/s004970050128;
RA Letham D.L.D., Nasrallah J.B.;
RT "A ClpP homolog linked to the Brassica self-incompatibility (S) locus.";
RL Sex. Plant Reprod. 11:117-119(1998).
RN [2]
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 [3]
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 [4]
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 [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 PROTEIN SEQUENCE OF 238-260, 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 [8]
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 [9]
RP SUBCELLULAR LOCATION, INDUCTION, AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia; TISSUE=Seedling;
RX PubMed=11982939; DOI=10.1034/j.1399-3054.2002.1140113.x;
RA Zheng B., Halperin T., Hruskova-Heidingsfeldova O., Adam Z., Clarke A.K.;
RT "Characterization of chloroplast Clp proteins in Arabidopsis: localization,
RT tissue specificity and stress responses.";
RL Physiol. Plantarum 114:92-101(2002).
RN [10]
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 [11]
RP NOMENCLATURE.
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 [12]
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 [13]
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 [14]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-194, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
RN [15]
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 [16]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT VAL-71, CLEAVAGE OF TRANSIT PEPTIDE
RP [LARGE SCALE ANALYSIS] AFTER SER-70, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
RN [17]
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).
RN [18]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=23548781; DOI=10.1104/pp.113.215699;
RA Kim J., Olinares P.D., Oh S.H., Ghisaura S., Poliakov A., Ponnala L.,
RA van Wijk K.J.;
RT "Modified Clp protease complex in the ClpP3 null mutant and consequences
RT for chloroplast development and function in Arabidopsis.";
RL Plant Physiol. 162:157-179(2013).
RN [19]
RP INTERACTION WITH CHIP, AND UBIQUITINATION.
RX PubMed=26085677; DOI=10.1093/jxb/erv286;
RA Wei J., Qiu X., Chen L., Hu W., Hu R., Chen J., Sun L., Li L., Zhang H.,
RA Lv Z., Shen G.;
RT "The E3 ligase AtCHIP positively regulates Clp proteolytic subunit
RT homeostasis.";
RL J. Exp. Bot. 66:5809-5820(2015).
CC -!- FUNCTION: Cleaves peptides in various proteins in a process that
CC requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a
CC major role in the degradation of misfolded proteins (By similarity). In
CC the absence of CLPP3, modified ClpPR core(s) could be formed, albeit at
CC strongly reduced levels (PubMed:23548781). {ECO:0000250,
CC ECO:0000269|PubMed:23548781}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Hydrolysis of proteins to small peptides in the presence of
CC ATP and magnesium. alpha-casein is the usual test substrate. In the
CC absence of ATP, only oligopeptides shorter than five residues are
CC hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec, and Leu-Tyr-Leu-|-Tyr-
CC Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also
CC occurs).; EC=3.4.21.92;
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). 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). Interacts with CHIP
CC (PubMed:26085677). {ECO:0000269|PubMed:11278690,
CC ECO:0000269|PubMed:14593120, ECO:0000269|PubMed:16766689,
CC ECO:0000269|PubMed:16980539, ECO:0000269|PubMed:21712416,
CC ECO:0000269|PubMed:26085677}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma
CC {ECO:0000269|PubMed:11982939, ECO:0000269|PubMed:14593120}.
CC -!- TISSUE SPECIFICITY: Mostly expressed in leaves. Also detected in stems,
CC and to a lower extent, in roots (at protein level).
CC {ECO:0000269|PubMed:11982939}.
CC -!- INDUCTION: Repressed in darkness. Accumulates during leaf senescence.
CC Induced during cold acclimation (at protein level).
CC {ECO:0000269|PubMed:10427773, ECO:0000269|PubMed:11982939}.
CC -!- PTM: Ubiquitinated in vitro by CHIP. {ECO:0000269|PubMed:26085677}.
CC -!- DISRUPTION PHENOTYPE: Delayed embryo development and seedling
CC lethality. Can be rescued by adding sugars to the growth medium.
CC -!- SIMILARITY: Belongs to the peptidase S14 family. {ECO:0000305}.
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DR EMBL; AF032123; AAC35489.1; -; mRNA.
DR EMBL; AB022328; BAA82067.1; -; mRNA.
DR EMBL; AC013288; AAG60075.1; -; Genomic_DNA.
DR EMBL; AC079285; AAG51173.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE34543.1; -; Genomic_DNA.
DR EMBL; AF370528; AAK48955.1; -; mRNA.
DR EMBL; AY072526; AAL66941.1; -; mRNA.
DR EMBL; AY087349; AAM64899.1; -; mRNA.
DR PIR; T52041; T52041.
DR PIR; T52453; T52453.
DR RefSeq; NP_564880.1; NM_105338.4.
DR AlphaFoldDB; Q9SXJ6; -.
DR SMR; Q9SXJ6; -.
DR BioGRID; 28206; 8.
DR IntAct; Q9SXJ6; 1.
DR STRING; 3702.AT1G66670.1; -.
DR MEROPS; S14.A03; -.
DR iPTMnet; Q9SXJ6; -.
DR PaxDb; Q9SXJ6; -.
DR PRIDE; Q9SXJ6; -.
DR ProteomicsDB; 246590; -.
DR EnsemblPlants; AT1G66670.1; AT1G66670.1; AT1G66670.
DR GeneID; 842985; -.
DR Gramene; AT1G66670.1; AT1G66670.1; AT1G66670.
DR KEGG; ath:AT1G66670; -.
DR Araport; AT1G66670; -.
DR TAIR; locus:2033344; AT1G66670.
DR eggNOG; KOG0840; Eukaryota.
DR HOGENOM; CLU_058707_1_0_1; -.
DR InParanoid; Q9SXJ6; -.
DR OMA; WMPRFEE; -.
DR OrthoDB; 1274502at2759; -.
DR PhylomeDB; Q9SXJ6; -.
DR PRO; PR:Q9SXJ6; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9SXJ6; baseline and differential.
DR Genevisible; Q9SXJ6; 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: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 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 InterPro; IPR033135; ClpP_His_AS.
DR InterPro; IPR018215; ClpP_Ser_AS.
DR PANTHER; PTHR10381; PTHR10381; 1.
DR Pfam; PF00574; CLP_protease; 1.
DR PRINTS; PR00127; CLPPROTEASEP.
DR SUPFAM; SSF52096; SSF52096; 1.
DR PROSITE; PS00382; CLP_PROTEASE_HIS; 1.
DR PROSITE; PS00381; CLP_PROTEASE_SER; 1.
PE 1: Evidence at protein level;
KW Acetylation; Chloroplast; Direct protein sequencing; Hydrolase;
KW Phosphoprotein; Plastid; Protease; Reference proteome; Serine protease;
KW Transit peptide; Ubl conjugation.
FT TRANSIT 1..70
FT /note="Chloroplast"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CHAIN 71..309
FT /note="ATP-dependent Clp protease proteolytic subunit 3,
FT chloroplastic"
FT /id="PRO_0000308978"
FT REGION 290..309
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 164
FT /note="Nucleophile"
FT /evidence="ECO:0000250"
FT ACT_SITE 189
FT /evidence="ECO:0000250"
FT MOD_RES 71
FT /note="N-acetylvaline"
FT /evidence="ECO:0007744|PubMed:22223895"
FT MOD_RES 194
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:19376835"
FT CONFLICT 1..4
FT /note="MEMS -> NSARG (in Ref. 1; AAC35489)"
FT /evidence="ECO:0000305"
FT CONFLICT 289
FT /note="K -> E (in Ref. 5; AAK48955/AAL66941)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 309 AA; 33925 MW; 0D2D0D3D1118AA0D CRC64;
MEMSLRLASS STSNPICLLN PGKNLNFPIR NHRIPKTSKP FCVRSSMSLS KPPRQTLSSN
WDVSSFSIDS VAQSPSRLPS FEELDTTNML LRQRIVFLGS QVDDMTADLV ISQLLLLDAE
DSERDITLFI NSPGGSITAG MGIYDAMKQC KADVSTVCLG LAASMGAFLL ASGSKGKRYC
MPNSKVMIHQ PLGTAGGKAT EMSIRIREMM YHKIKLNKIF SRITGKPESE IESDTDRDNF
LNPWEAKEYG LIDAVIDDGK PGLIAPIGDG TPPPKTKVWD LWKVEGTKKD NTNLPSERSM
TQNGYAAIE
