ID   CLPP2_ARATH             Reviewed;         241 AA.
AC   Q9FN42;
DT   13-NOV-2007, integrated into UniProtKB/Swiss-Prot.
DT   01-MAR-2001, sequence version 1.
DT   02-SEP-2026, entry version 150.
DE   RecName: Full=ATP-dependent Clp protease proteolytic subunit 2, mitochondrial {ECO:0000303|PubMed:11299370};
DE            EC=3.4.21.92;
DE   AltName: Full=ATP-dependent Clp protease proteolytic subunit 1, mitochondrial;
DE   AltName: Full=Endopeptidase ClpP2 {ECO:0000303|PubMed:11299370};
DE   AltName: Full=nClpP7;
DE   Flags: Precursor;
GN   Name=CLPP2 {ECO:0000303|PubMed:11299370}; Synonyms=NCLPP7;
GN   OrderedLocusNames=At5g23140 {ECO:0000312|Araport:AT5G23140};
GN   ORFNames=MYJ24.13 {ECO:0000312|EMBL:BAB09831.1};
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 [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=9405937; DOI=10.1093/dnares/4.4.291;
RA   Kotani H., Nakamura Y., Sato S., Kaneko T., Asamizu E., Miyajima N.,
RA   Tabata S.;
RT   "Structural analysis of Arabidopsis thaliana chromosome 5. II. Sequence
RT   features of the regions of 1,044,062 bp covered by thirteen physically
RT   assigned P1 clones.";
RL   DNA Res. 4:291-300(1997).
RN   [2]
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   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia;
RG   The Arabidopsis Information Resource (TAIR);
RT   "Community-consensus reference genome of Arabidopsis thaliana Col-0.";
RL   Submitted (FEB-2026) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=11910074; DOI=10.1126/science.1071006;
RA   Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA   Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA   Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA   Shinagawa A., Shinozaki K.;
RT   "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL   Science 296:141-145(2002).
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   PROTEIN SEQUENCE OF 143-163; 175-185 AND 211-228, 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   [7]
RP   FUNCTION, SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
RX   PubMed=11352464; DOI=10.1023/a:1010677220323;
RA   Halperin T., Zheng B., Itzhaki H., Clarke A.K., Adam Z.;
RT   "Plant mitochondria contain proteolytic and regulatory subunits of the ATP-
RT   dependent Clp protease.";
RL   Plant Mol. Biol. 45:461-468(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, SUBCELLULAR LOCATION, 3D-STRUCTURE
RP   MODELING, AND SUBUNIT.
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   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   [12]
RP   IDENTIFICATION BY MASS SPECTROMETRY, AND CLEAVAGE OF TRANSIT PEPTIDE AFTER
RP   TYR-30.
RX   PubMed=25732537; DOI=10.1093/jxb/erv064;
RA   Carrie C., Venne A.S., Zahedi R.P., Soll J.;
RT   "Identification of cleavage sites and substrate proteins for two
RT   mitochondrial intermediate peptidases in Arabidopsis thaliana.";
RL   J. Exp. Bot. 66:2691-2708(2015).
CC   -!- FUNCTION: Component of the mitochondrial ATP-dependent Clp protease
CC       (PubMed:11352464). Cleaves peptides in various proteins in a process
CC       that requires ATP hydrolysis (By similarity). Has a chymotrypsin-like
CC       activity. Plays a major role in the degradation of misfolded proteins
CC       (By similarity). {ECO:0000250|UniProtKB:Q27539,
CC       ECO:0000269|PubMed:11352464}.
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: Homotetradecamer. {ECO:0000269|PubMed:14593120}.
CC   -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:11352464,
CC       ECO:0000269|PubMed:14593120, ECO:0000305|PubMed:25732537}.
CC   -!- TISSUE SPECIFICITY: Constitutively expressed in leaves, shoots, roots
CC       and flowers. {ECO:0000269|PubMed:11352464}.
CC   -!- SIMILARITY: Belongs to the peptidase S14 family. {ECO:0000305}.
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DR   EMBL; AB006708; BAB09831.1; -; Genomic_DNA.
DR   EMBL; CP002688; AED93126.1; -; Genomic_DNA.
DR   EMBL; OZ408687; CAO7053231.1; -; Genomic_DNA.
DR   EMBL; AK118523; BAC43126.1; -; mRNA.
DR   EMBL; BT005261; AAO63325.1; -; mRNA.
DR   RefSeq; NP_568427.1; NM_122220.5.
DR   AlphaFoldDB; Q9FN42; -.
DR   SMR; Q9FN42; -.
DR   FunCoup; Q9FN42; 3640.
DR   IntAct; Q9FN42; 1.
DR   STRING; 3702.Q9FN42; -.
DR   MEROPS; S14.A02; -.
DR   PaxDb; 3702-Q9FN42; -.
DR   ProteomicsDB; 246659; -.
DR   GeneID; 832378; -.
DR   KEGG; ath:AT5G23140; -.
DR   Araport; AT5G23140; -.
DR   TAIR; AT5G23140; NCLPP7.
DR   eggNOG; KOG0840; Eukaryota.
DR   HOGENOM; CLU_058707_3_1_1; -.
DR   InParanoid; Q9FN42; -.
DR   OMA; RDYWMKA; -.
DR   OrthoDB; 2017408at2759; -.
DR   PhylomeDB; Q9FN42; -.
DR   PRO; PR:Q9FN42; -.
DR   Proteomes; UP000006548; Chromosome 5.
DR   ExpressionAtlas; Q9FN42; baseline and differential.
DR   GO; GO:0009507; C:chloroplast; ISM:TAIR.
DR   GO; GO:0009570; C:chloroplast stroma; IDA:TIGR.
DR   GO; GO:0009535; C:chloroplast thylakoid membrane; IDA:TAIR.
DR   GO; GO:0009840; C:chloroplastic endopeptidase Clp complex; IDA:TAIR.
DR   GO; GO:0005829; C:cytosol; HDA:TAIR.
DR   GO; GO:0005759; C:mitochondrial matrix; IDA:TIGR.
DR   GO; GO:0005739; C:mitochondrion; IDA:TAIR.
DR   GO; GO:0009536; C:plastid; 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:0050897; F:cobalt ion binding; HDA:TAIR.
DR   GO; GO:0004252; F:serine-type endopeptidase activity; IBA:GO_Central.
DR   GO; GO:0008270; F:zinc ion binding; HDA:TAIR.
DR   GO; GO:0006515; P:protein quality control for misfolded or incompletely synthesized proteins; IBA:GO_Central.
DR   GO; GO:0006508; P:proteolysis; IEA:InterPro.
DR   CDD; cd07017; S14_ClpP_2; 1.
DR   FunFam; 3.90.226.10:FF:000001; ATP-dependent Clp protease proteolytic subunit; 1.
DR   Gene3D; 3.90.226.10; 2-enoyl-CoA Hydratase, Chain A, domain 1; 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   NCBIfam; NF001368; PRK00277.1; 1.
DR   NCBIfam; NF009205; PRK12553.1; 1.
DR   PANTHER; PTHR10381; ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT; 1.
DR   PANTHER; PTHR10381:SF11; ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT, MITOCHONDRIAL; 1.
DR   Pfam; PF00574; CLP_protease; 1.
DR   PRINTS; PR00127; CLPPROTEASEP.
DR   SUPFAM; SSF52096; ClpP/crotonase; 1.
DR   PROSITE; PS00382; CLP_PROTEASE_HIS; 1.
DR   PROSITE; PS00381; CLP_PROTEASE_SER; 1.
PE   1: Evidence at protein level;
KW   Direct protein sequencing; Hydrolase; Mitochondrion; Protease;
KW   Reference proteome; Serine protease; Transit peptide.
FT   TRANSIT         1..30
FT                   /note="Mitochondrion"
FT                   /evidence="ECO:0000269|PubMed:25732537"
FT   CHAIN           31..241
FT                   /note="ATP-dependent Clp protease proteolytic subunit 2,
FT                   mitochondrial"
FT                   /id="PRO_0000308977"
FT   ACT_SITE        127
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000250|UniProtKB:Q27539"
FT   ACT_SITE        152
FT                   /evidence="ECO:0000250|UniProtKB:Q27539"
SQ   SEQUENCE   241 AA;  26283 MW;  DFC93372387E542A CRC64;
     MMRGLVSGAK MLSSTPSSMA TSIATGRRSY SLIPMVIEHS SRGERAYDIF SRLLKERIIC
     INGPINDDTS HVVVAQLLYL ESENPSKPIH MYLNSPGGHV TAGLAIYDTM QYIRSPISTI
     CLGQAASMAS LLLAAGAKGQ RRSLPNATVM IHQPSGGYSG QAKDITIHTK QIVRVWDALN
     ELYVKHTGQP LDVVANNMDR DHFMTPEEAK AFGIIDEVID ERPLELVKDA VGNESKDKSS
     S
//