CLPP6_ARATH
ID CLPP6_ARATH Reviewed; 271 AA.
AC Q9SAA2; O48891;
DT 13-NOV-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 138.
DE RecName: Full=ATP-dependent Clp protease proteolytic subunit 6, chloroplastic {ECO:0000303|PubMed:11299370};
DE EC=3.4.21.92;
DE AltName: Full=Endopeptidase ClpP6 {ECO:0000303|PubMed:11299370};
DE Short=nClpP6;
DE AltName: Full=nClpP1;
DE Flags: Precursor;
GN Name=CLPP6 {ECO:0000303|PubMed:11299370}; Synonyms=NCLPP1, NCLPP6;
GN OrderedLocusNames=At1g11750 {ECO:0000312|Araport:AT1G11750};
GN ORFNames=F25C20.10 {ECO:0000312|EMBL:AAD30248.1};
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], SUBUNIT, AND SUBCELLULAR LOCATION.
RX PubMed=9951729; DOI=10.1007/s004250050485;
RA Sokolenko A., Lerbs-Mache S., Altschmied L., Herrmann R.G.;
RT "Clp protease complexes and their diversity in chloroplasts.";
RL Planta 207:286-295(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, INDUCTION, AND SUBCELLULAR
RP LOCATION.
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 [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].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [7]
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 [8]
RP PROTEIN SEQUENCE OF 106-120, 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 [9]
RP INDUCTION.
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 [10]
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 [11]
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 [12]
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 [13]
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 [14]
RP FUNCTION, AND 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 [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 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: 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 Essential protein required for chloroplast development and integrity.
CC {ECO:0000250, ECO:0000269|PubMed:16980539}.
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, PubMed:9951729). The core complex is organized in two
CC heptameric rings, one containing CLPP3,4,5,6 in a 1:2:3:1 ratio and the
CC other 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, ECO:0000269|PubMed:9951729}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma
CC {ECO:0000269|PubMed:11982939, ECO:0000269|PubMed:14593120,
CC ECO:0000269|PubMed:9951729}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=Q9SAA2-1; Sequence=Displayed;
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 during cold acclimation (at
CC protein level). {ECO:0000269|PubMed:10427773,
CC ECO:0000269|PubMed:11982939}.
CC -!- SIMILARITY: Belongs to the peptidase S14 family. {ECO:0000305}.
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DR EMBL; AF016621; AAB99906.1; -; mRNA.
DR EMBL; AC007296; AAD30248.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE28778.1; -; Genomic_DNA.
DR EMBL; AF348580; AAK15551.1; -; mRNA.
DR EMBL; AK229049; BAF00932.1; -; mRNA.
DR EMBL; AY087248; AAM64804.1; -; mRNA.
DR PIR; C86251; C86251.
DR RefSeq; NP_563893.1; NM_101047.3. [Q9SAA2-1]
DR AlphaFoldDB; Q9SAA2; -.
DR SMR; Q9SAA2; -.
DR BioGRID; 22959; 4.
DR IntAct; Q9SAA2; 2.
DR STRING; 3702.AT1G11750.2; -.
DR MEROPS; S14.006; -.
DR PRIDE; Q9SAA2; -.
DR ProteomicsDB; 241065; -. [Q9SAA2-1]
DR EnsemblPlants; AT1G11750.1; AT1G11750.1; AT1G11750. [Q9SAA2-1]
DR GeneID; 837719; -.
DR Gramene; AT1G11750.1; AT1G11750.1; AT1G11750. [Q9SAA2-1]
DR KEGG; ath:AT1G11750; -.
DR Araport; AT1G11750; -.
DR eggNOG; KOG0840; Eukaryota.
DR HOGENOM; CLU_058707_6_4_1; -.
DR InParanoid; Q9SAA2; -.
DR OMA; TFCVGQA; -.
DR PhylomeDB; Q9SAA2; -.
DR PRO; PR:Q9SAA2; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9SAA2; baseline and differential.
DR Genevisible; Q9SAA2; AT.
DR GO; GO:0009570; C:chloroplast stroma; IEA:UniProtKB-SubCell.
DR GO; GO:0009368; C:endopeptidase Clp complex; IBA:GO_Central.
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 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.
PE 1: Evidence at protein level;
KW Alternative splicing; Chloroplast; Direct protein sequencing; Hydrolase;
KW Plastid; Protease; Reference proteome; Serine protease; Transit peptide.
FT TRANSIT 1..77
FT /note="Chloroplast"
FT /evidence="ECO:0000305"
FT CHAIN 78..271
FT /note="ATP-dependent Clp protease proteolytic subunit 6,
FT chloroplastic"
FT /id="PRO_0000308981"
FT REGION 1..30
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 11..30
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 175
FT /note="Nucleophile"
FT /evidence="ECO:0000250"
FT ACT_SITE 200
FT /evidence="ECO:0000250"
FT CONFLICT 144
FT /note="P -> S (in Ref. 1)"
FT /evidence="ECO:0000305"
FT CONFLICT 153
FT /note="A -> T (in Ref. 2; AAB99906)"
FT /evidence="ECO:0000305"
FT CONFLICT 179..180
FT /note="LL -> FF (in Ref. 2; AAB99906)"
FT /evidence="ECO:0000305"
FT CONFLICT 258
FT /note="L -> F (in Ref. 2; AAB99906)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 271 AA; 29382 MW; 5565ADB698D0C776 CRC64;
MAGLAISPPL GLSFSSRTRN PKPTSFLSHN QRNPIRRIVS ALQSPYGDSL KAGLSSNVSG
SPIKIDNKAP RFGVIEAKKG NPPVMPSVMT PGGPLDLSSV LFRNRIIFIG QPINAQVAQR
VISQLVTLAS IDDKSDILMY LNCPGGSTYS VLAIYDCMSW IKPKVGTVAF GVAASQGALL
LAGGEKGMRY AMPNTRVMIH QPQTGCGGHV EDVRRQVNEA IEARQKIDRM YAAFTGQPLE
KVQQYTERDR FLSASEALEF GLIDGLLETE Y
