CLPP4_ARATH
ID CLPP4_ARATH Reviewed; 292 AA.
AC Q94B60; Q8LAN0; Q9FHJ7; Q9SXJ5; Q9ZS78;
DT 13-NOV-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 134.
DE RecName: Full=ATP-dependent Clp protease proteolytic subunit 4, chloroplastic {ECO:0000303|PubMed:11299370};
DE EC=3.4.21.92;
DE AltName: Full=Endopeptidase ClpP4 {ECO:0000303|PubMed:11299370};
DE Short=nClpP4;
DE AltName: Full=nClpP3;
DE Flags: Precursor;
GN Name=CLPP4 {ECO:0000303|PubMed:11299370}; Synonyms=NCLPP3, NCLPP4;
GN OrderedLocusNames=At5g45390 {ECO:0000312|Araport:AT5G45390};
GN ORFNames=MFC19.5 {ECO:0000312|EMBL:BAB09167.1};
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].
RC STRAIN=cv. Columbia;
RA Clarke A.K.;
RT "A third nuclear-encoded clpP gene from Arabidopsis thaliana.";
RL Submitted (FEB-1998) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10470850; DOI=10.1093/dnares/6.3.183;
RA Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Kotani H.,
RA Miyajima N., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. IX. Sequence
RT features of the regions of 1,011,550 bp covered by seventeen P1 and TAC
RT clones.";
RL DNA Res. 6:183-195(1999).
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 75-86; 180-201; 208-219 AND 269-280, 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 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 FUNCTION, AND INDUCTION.
RX PubMed=16705403; DOI=10.1007/s00425-006-0292-2;
RA Zheng B., MacDonald T.M., Sutinen S., Hurry V., Clarke A.K.;
RT "A nuclear-encoded ClpP subunit of the chloroplast ATP-dependent Clp
RT protease is essential for early development in Arabidopsis thaliana.";
RL Planta 224:1103-1115(2006).
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 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 FUNCTION, UBIQUITINATION, AND INTERACTION WITH CHIP.
RX PubMed=17241447; DOI=10.1111/j.1365-313x.2006.02963.x;
RA Shen G., Yan J., Pasapula V., Luo J., He C., Clarke A.K., Zhang H.;
RT "The chloroplast protease subunit ClpP4 is a substrate of the E3 ligase
RT AtCHIP and plays an important role in chloroplast function.";
RL Plant J. 49:228-237(2007).
RN [16]
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 [17]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT SER-66, CLEAVAGE OF TRANSIT PEPTIDE
RP [LARGE SCALE ANALYSIS] AFTER MET-65, 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 [18]
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 [19]
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).
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 (PubMed:16705403, PubMed:17241447). Essential for Embryogenesis
CC (PubMed:23548781). {ECO:0000250, ECO:0000269|PubMed:16705403,
CC ECO:0000269|PubMed:17241447, 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,
CC PubMed:16980539). Interacts with CHIP (PubMed:17241447). 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:16766689,
CC ECO:0000269|PubMed:16980539, ECO:0000269|PubMed:17241447,
CC ECO:0000269|PubMed:21712416}.
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. Levels decrease in leaves during
CC aging (at protein level). Slightly and transiently repressed by high
CC light stress (at protein level). {ECO:0000269|PubMed:10427773,
CC ECO:0000269|PubMed:11982939, ECO:0000269|PubMed:16705403}.
CC -!- PTM: Ubiquitinated by CHIP. {ECO:0000269|PubMed:17241447}.
CC -!- DISRUPTION PHENOTYPE: Embryo lethal when homozygous.
CC {ECO:0000269|PubMed:23548781}.
CC -!- SIMILARITY: Belongs to the peptidase S14 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA82068.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC Sequence=BAB09167.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAA04393.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AB022329; BAA82068.1; ALT_INIT; mRNA.
DR EMBL; AJ000930; CAA04393.1; ALT_INIT; mRNA.
DR EMBL; AB018113; BAB09167.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED95243.1; -; Genomic_DNA.
DR EMBL; AY042832; AAK68772.1; -; mRNA.
DR EMBL; BT006321; AAP13429.1; -; mRNA.
DR EMBL; AY087717; AAM65254.1; -; mRNA.
DR PIR; T52452; T52452.
DR RefSeq; NP_568644.1; NM_123907.4.
DR AlphaFoldDB; Q94B60; -.
DR SMR; Q94B60; -.
DR BioGRID; 19824; 8.
DR IntAct; Q94B60; 2.
DR STRING; 3702.AT5G45390.1; -.
DR MEROPS; S14.010; -.
DR iPTMnet; Q94B60; -.
DR PaxDb; Q94B60; -.
DR PRIDE; Q94B60; -.
DR ProteomicsDB; 241064; -.
DR EnsemblPlants; AT5G45390.1; AT5G45390.1; AT5G45390.
DR GeneID; 834575; -.
DR Gramene; AT5G45390.1; AT5G45390.1; AT5G45390.
DR KEGG; ath:AT5G45390; -.
DR Araport; AT5G45390; -.
DR TAIR; locus:2163538; AT5G45390.
DR eggNOG; KOG0840; Eukaryota.
DR HOGENOM; CLU_058707_1_0_1; -.
DR OMA; PDKVKPR; -.
DR OrthoDB; 1274502at2759; -.
DR PhylomeDB; Q94B60; -.
DR PRO; PR:Q94B60; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q94B60; baseline and differential.
DR Genevisible; Q94B60; 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:0009535; C:chloroplast thylakoid membrane; 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:0009536; C:plastid; 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:0009658; P:chloroplast organization; IMP:TAIR.
DR GO; GO:0006515; P:protein quality control for misfolded or incompletely synthesized proteins; IBA:GO_Central.
DR GO; GO:0048510; P:regulation of timing of transition from vegetative to reproductive phase; IMP:TAIR.
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 Acetylation; Chloroplast; Direct protein sequencing; Hydrolase; Plastid;
KW Protease; Reference proteome; Serine protease; Transit peptide;
KW Ubl conjugation.
FT TRANSIT 1..65
FT /note="Chloroplast"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CHAIN 66..292
FT /note="ATP-dependent Clp protease proteolytic subunit 4,
FT chloroplastic"
FT /id="PRO_0000308979"
FT ACT_SITE 158
FT /note="Nucleophile"
FT /evidence="ECO:0000250"
FT ACT_SITE 183
FT /evidence="ECO:0000250"
FT MOD_RES 66
FT /note="N-acetylserine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CONFLICT 1..3
FT /note="MGT -> TRP (in Ref. 2; CAA04393)"
FT /evidence="ECO:0000305"
FT CONFLICT 57
FT /note="R -> T (in Ref. 2; CAA04393)"
FT /evidence="ECO:0000305"
FT CONFLICT 171
FT /note="K -> N (in Ref. 2; CAA04393)"
FT /evidence="ECO:0000305"
FT CONFLICT 193
FT /note="A -> V (in Ref. 6; AAM65254)"
FT /evidence="ECO:0000305"
FT CONFLICT 279
FT /note="M -> I (in Ref. 6; AAM65254)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 292 AA; 31498 MW; 227B514CF1C1CE4C CRC64;
MGTLSLSSSL KPSLVSSRLN SSSSASSSSF PKPNNLYLKP TKLISPPLRT TSPSPLRFAN
ASIEMSQTQE SAIRGAESDV MGLLLRERIV FLGSSIDDFV ADAIMSQLLL LDAKDPKKDI
KLFINSPGGS LSATMAIYDV VQLVRADVST IALGIAASTA SIILGAGTKG KRFAMPNTRI
MIHQPLGGAS GQAIDVEIQA KEVMHNKNNV TSIIAGCTSR SFEQVLKDID RDRYMSPIEA
VEYGLIDGVI DGDSIIPLEP VPDRVKPRVN YEEISKDPMK FLTPEIPDDE IY
