CLPP5_ARATH
ID CLPP5_ARATH Reviewed; 298 AA.
AC Q9S834;
DT 13-NOV-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 133.
DE RecName: Full=ATP-dependent Clp protease proteolytic subunit 5, chloroplastic {ECO:0000303|PubMed:11299370};
DE EC=3.4.21.92;
DE AltName: Full=Endopeptidase ClpP5 {ECO:0000303|PubMed:11299370};
DE Short=nClpP5;
DE AltName: Full=nClpP1;
DE Flags: Precursor;
GN Name=CLPP5 {ECO:0000303|PubMed:11299370}; Synonyms=NCLPP1, NCLPP5;
GN OrderedLocusNames=At1g02560 {ECO:0000312|Araport:AT1G02560};
GN ORFNames=T14P4.12 {ECO:0000312|EMBL:AAG10637.1};
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 [MRNA], TISSUE SPECIFICITY, INDUCTION, AND SUBCELLULAR
RP LOCATION.
RC STRAIN=cv. Columbia; TISSUE=Hypocotyl;
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 [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;
RA Kim C.J., Chen H., Shinn P., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (MAR-2006) to the EMBL/GenBank/DDBJ databases.
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 112-123; 243-273 AND 277-290, SUBUNIT, AND
RP IDENTIFICATION BY 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 [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 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 [10]
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 [11]
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 [12]
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 [13]
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 [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 ACETYLATION [LARGE SCALE ANALYSIS] AT GLY-101, CLEAVAGE OF TRANSIT PEPTIDE
RP [LARGE SCALE ANALYSIS] AFTER GLN-100, 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 [16]
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 [17]
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).
CC {ECO:0000250}.
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,
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). Interacts
CC with CHIP (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|Ref.5}.
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. Induced by high light stress and
CC 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: Embryo lethal. {ECO:0000269|PubMed:19525416}.
CC -!- SIMILARITY: Belongs to the peptidase S14 family. {ECO:0000305}.
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DR EMBL; AB022326; BAA82065.1; -; mRNA.
DR EMBL; AJ012278; CAB43488.1; -; mRNA.
DR EMBL; AC022521; AAG10637.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE27444.1; -; Genomic_DNA.
DR EMBL; BT024859; ABD65590.1; -; mRNA.
DR EMBL; AY084394; AAM60971.1; -; mRNA.
DR PIR; T52455; T52455.
DR RefSeq; NP_563657.1; NM_100137.4.
DR AlphaFoldDB; Q9S834; -.
DR SMR; Q9S834; -.
DR BioGRID; 24668; 13.
DR IntAct; Q9S834; 1.
DR STRING; 3702.AT1G02560.1; -.
DR MEROPS; S14.A01; -.
DR iPTMnet; Q9S834; -.
DR PaxDb; Q9S834; -.
DR PRIDE; Q9S834; -.
DR ProteomicsDB; 246591; -.
DR EnsemblPlants; AT1G02560.1; AT1G02560.1; AT1G02560.
DR GeneID; 839433; -.
DR Gramene; AT1G02560.1; AT1G02560.1; AT1G02560.
DR KEGG; ath:AT1G02560; -.
DR Araport; AT1G02560; -.
DR TAIR; locus:2196120; AT1G02560.
DR eggNOG; KOG0840; Eukaryota.
DR HOGENOM; CLU_058707_2_1_1; -.
DR InParanoid; Q9S834; -.
DR OMA; TICLGEC; -.
DR OrthoDB; 1274502at2759; -.
DR PhylomeDB; Q9S834; -.
DR PRO; PR:Q9S834; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9S834; baseline and differential.
DR Genevisible; Q9S834; 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:0009532; C:plastid stroma; IDA:TAIR.
DR GO; GO:0009579; C:thylakoid; 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: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; Plastid;
KW Protease; Reference proteome; Serine protease; Transit peptide;
KW Ubl conjugation.
FT TRANSIT 1..100
FT /note="Chloroplast"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CHAIN 101..298
FT /note="ATP-dependent Clp protease proteolytic subunit 5,
FT chloroplastic"
FT /id="PRO_0000308980"
FT ACT_SITE 193
FT /note="Nucleophile"
FT /evidence="ECO:0000250"
FT ACT_SITE 218
FT /evidence="ECO:0000250"
FT MOD_RES 101
FT /note="N-acetylglycine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CONFLICT 115
FT /note="I -> II (in Ref. 7; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 246
FT /note="N -> D (in Ref. 7; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 253
FT /note="Missing (in Ref. 7; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 267
FT /note="Missing (in Ref. 7; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 280
FT /note="L -> I (in Ref. 7; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 285
FT /note="I -> L (in Ref. 7; AA sequence)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 298 AA; 32356 MW; 0B550019A2F6A33C CRC64;
MAHACVSTSA SSLRFTAGFV SASPNGSSFD SPKLSLPFEP LRSRKTNKLV SDRKNWKNST
PKAVYSGNLW TPEIPSPQGV WSIRDDLQVP SSPYFPAYAQ GQGPPPMVQE RFQSIISQLF
QYRIIRCGGA VDDDMANIIV AQLLYLDAVD PTKDIVMYVN SPGGSVTAGM AIFDTMRHIR
PDVSTVCVGL AASMGAFLLS AGTKGKRYSL PNSRIMIHQP LGGAQGGQTD IDIQANEMLH
HKANLNGYLA YHTGQSLEKI NQDTDRDFFM SAKEAKEYGL IDGVIMNPLK ALQPLAAA
