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ATP-dependent Clp protease proteolytic subunit 6, chloroplastic (EC 3.4.21.92) (Endopeptidase ClpP6) (nClpP6) (nClpP1)

 CLPP6_ARATH             Reviewed;         271 AA.
Q9SAA2; O48891;
13-NOV-2007, integrated into UniProtKB/Swiss-Prot.
01-MAY-2000, sequence version 1.
25-APR-2018, entry version 118.
RecName: Full=ATP-dependent Clp protease proteolytic subunit 6, chloroplastic {ECO:0000303|PubMed:11299370};
EC=3.4.21.92;
AltName: Full=Endopeptidase ClpP6 {ECO:0000303|PubMed:11299370};
Short=nClpP6;
AltName: Full=nClpP1;
Flags: Precursor;
Name=CLPP6 {ECO:0000303|PubMed:11299370}; Synonyms=NCLPP1, NCLPP6;
OrderedLocusNames=At1g11750 {ECO:0000312|Araport:AT1G11750};
ORFNames=F25C20.10 {ECO:0000312|EMBL:AAD30248.1};
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [MRNA], SUBUNIT, AND SUBCELLULAR LOCATION.
PubMed=9951729; DOI=10.1007/s004250050485;
Sokolenko A., Lerbs-Mache S., Altschmied L., Herrmann R.G.;
"Clp protease complexes and their diversity in chloroplasts.";
Planta 207:286-295(1998).
[2]
NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, INDUCTION, AND
SUBCELLULAR LOCATION.
STRAIN=cv. Columbia; TISSUE=Seedling;
PubMed=11982939; DOI=10.1034/j.1399-3054.2002.1140113.x;
Zheng B., Halperin T., Hruskova-Heidingsfeldova O., Adam Z.,
Clarke A.K.;
"Characterization of chloroplast Clp proteins in Arabidopsis:
localization, tissue specificity and stress responses.";
Physiol. Plantarum 114:92-101(2002).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=11130712; DOI=10.1038/35048500;
Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S.,
White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y.,
Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W.,
Chung M.K., Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K.,
Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y.,
Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L.,
Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E.,
Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B.,
Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P.,
Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A.,
Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I.,
Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D.,
Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M.,
Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M.,
Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.;
"Sequence and analysis of chromosome 1 of the plant Arabidopsis
thaliana.";
Nature 408:816-820(2000).
[4]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J.,
Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[6]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J.,
Hayashizaki Y., Shinozaki K.;
"Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
[7]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
Feldmann K.A.;
"Full-length cDNA from Arabidopsis thaliana.";
Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
[8]
PROTEIN SEQUENCE OF 106-120, SUBUNIT, AND IDENTIFICATION BY MASS
SPECTROMETRY.
PubMed=11278690; DOI=10.1074/jbc.M010503200;
Peltier J.-B., Ytterberg J., Liberles D.A., Roepstorff P.,
van Wijk K.J.;
"Identification of a 350-kDa ClpP protease complex with 10 different
Clp isoforms in chloroplasts of Arabidopsis thaliana.";
J. Biol. Chem. 276:16318-16327(2001).
[9]
INDUCTION.
PubMed=10427773; DOI=10.1093/oxfordjournals.pcp.a029571;
Nakabayashi K., Ito M., Kiyosue T., Shinozaki K., Watanabe A.;
"Identification of clp genes expressed in senescing Arabidopsis
leaves.";
Plant Cell Physiol. 40:504-514(1999).
[10]
GENE FAMILY, AND NOMENCLATURE.
PubMed=11299370; DOI=10.1104/pp.125.4.1912;
Adam Z., Adamska I., Nakabayashi K., Ostersetzer O., Haussuhl K.,
Manuell A., Zheng B., Vallon O., Rodermel S.R., Shinozaki K.,
Clarke A.K.;
"Chloroplast and mitochondrial proteases in Arabidopsis. A proposed
nomenclature.";
Plant Physiol. 125:1912-1918(2001).
[11]
IDENTIFICATION BY MASS SPECTROMETRY, SUBUNIT, SUBCELLULAR LOCATION,
AND 3D-STRUCTURE MODELING.
PubMed=14593120; DOI=10.1074/jbc.M309212200;
Peltier J.-B., Ripoll D.R., Friso G., Rudella A., Cai Y.,
Ytterberg J., Giacomelli L., Pillardy J., van Wijk K.J.;
"Clp protease complexes from photosynthetic and non-photosynthetic
plastids and mitochondria of plants, their predicted three-dimensional
structures, and functional implications.";
J. Biol. Chem. 279:4768-4781(2004).
[12]
NOMENCLATURE.
DOI=10.1111/j.1399-3054.2005.00452.x;
Clarke A.K., MacDonald T.M., Sjoegren L.L.;
"The ATP-dependent Clp protease in chloroplasts of higher plants.";
Physiol. Plantarum 123:406-412(2005).
[13]
IDENTIFICATION BY MASS SPECTROMETRY, AND SUBUNIT.
PubMed=16766689; DOI=10.1105/tpc.106.042861;
Rudella A., Friso G., Alonso J.M., Ecker J.R., van Wijk K.J.;
"Downregulation of ClpR2 leads to reduced accumulation of the ClpPRS
protease complex and defects in chloroplast biogenesis in
Arabidopsis.";
Plant Cell 18:1704-1721(2006).
[14]
FUNCTION, AND SUBUNIT.
PubMed=16980539; DOI=10.1105/tpc.106.044594;
Sjoegren L.L.E., Stanne T.M., Zheng B., Sutinen S., Clarke A.K.;
"Structural and functional insights into the chloroplast ATP-dependent
Clp protease in Arabidopsis.";
Plant Cell 18:2635-2649(2006).
[15]
IDENTIFICATION BY MASS SPECTROMETRY, AND SUBUNIT.
PubMed=21712416; DOI=10.1105/tpc.111.086454;
Olinares P.D., Kim J., Davis J.I., van Wijk K.J.;
"Subunit stoichiometry, evolution, and functional implications of an
asymmetric plant plastid ClpP/R protease complex in Arabidopsis.";
Plant Cell 23:2348-2361(2011).
[16]
REVIEW.
PubMed=22085372; DOI=10.1111/j.1399-3054.2011.01541.x;
Clarke A.K.;
"The chloroplast ATP-dependent Clp protease in vascular plants - new
dimensions and future challenges.";
Physiol. Plantarum 145:235-244(2012).
-!- FUNCTION: Cleaves peptides in various proteins in a process that
requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a
major role in the degradation of misfolded proteins (By
similarity). Essential protein required for chloroplast
development and integrity. {ECO:0000250,
ECO:0000269|PubMed:16980539}.
-!- CATALYTIC ACTIVITY: Hydrolysis of proteins to small peptides in
the presence of ATP and magnesium. Alpha-casein is the usual test
substrate. In the absence of ATP, only oligopeptides shorter than
five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec;
and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-
Leu- and -Tyr-|-Trp bonds also occurs).
-!- SUBUNIT: Component of the chloroplastic Clp protease core complex
which consist of at least 16 proteins: CLPP4 (3 copies), CLPP5 (3
copies), CLPR4 (2 copies), ClpP1 (1 copy), CLPP6 (1 copy), CLPR2
(1 copy), CLPT1 (1 copy), CLPT2 (1 copy) and 3 copies of CLPP3
and/or CLPR1 and/or CLPR3 (PubMed:11278690, PubMed:14593120,
PubMed:16766689, PubMed:16980539, PubMed:9951729). The core
complex is organized in two heptameric rings, one containing
CLPP3,4,5,6 in a 1:2:3:1 ratio and the other CLPP1 and CLPR1,2,3,4
in a 3:1:1:1:1 ratio (PubMed:21712416).
{ECO:0000269|PubMed:11278690, ECO:0000269|PubMed:14593120,
ECO:0000269|PubMed:16766689, ECO:0000269|PubMed:16980539,
ECO:0000269|PubMed:21712416, ECO:0000269|PubMed:9951729}.
-!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma
{ECO:0000269|PubMed:11982939, ECO:0000269|PubMed:14593120,
ECO:0000269|PubMed:9951729}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=1;
Comment=A number of isoforms are produced. According to EST
sequences.;
Name=1;
IsoId=Q9SAA2-1; Sequence=Displayed;
-!- TISSUE SPECIFICITY: Mostly expressed in leaves. Also detected in
stems, and to a lower extent, in roots (at protein level).
{ECO:0000269|PubMed:11982939}.
-!- INDUCTION: Repressed in darkness. Induced during cold acclimation
(at protein level). {ECO:0000269|PubMed:10427773,
ECO:0000269|PubMed:11982939}.
-!- SIMILARITY: Belongs to the peptidase S14 family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AF016621; AAB99906.1; -; mRNA.
EMBL; AC007296; AAD30248.1; -; Genomic_DNA.
EMBL; CP002684; AEE28778.1; -; Genomic_DNA.
EMBL; AF348580; AAK15551.1; -; mRNA.
EMBL; AK229049; BAF00932.1; -; mRNA.
EMBL; AY087248; AAM64804.1; -; mRNA.
PIR; C86251; C86251.
RefSeq; NP_563893.1; NM_101047.3. [Q9SAA2-1]
UniGene; At.10512; -.
UniGene; At.72667; -.
PDB; 1R93; Model; -; A=1-271.
PDBsum; 1R93; -.
ProteinModelPortal; Q9SAA2; -.
SMR; Q9SAA2; -.
BioGrid; 22959; 3.
IntAct; Q9SAA2; 1.
MEROPS; S14.006; -.
PRIDE; Q9SAA2; -.
EnsemblPlants; AT1G11750.1; AT1G11750.1; AT1G11750. [Q9SAA2-1]
GeneID; 837719; -.
Gramene; AT1G11750.1; AT1G11750.1; AT1G11750. [Q9SAA2-1]
KEGG; ath:AT1G11750; -.
Araport; AT1G11750; -.
HOGENOM; HOG000285833; -.
InParanoid; Q9SAA2; -.
KO; K01358; -.
PhylomeDB; Q9SAA2; -.
PRO; PR:Q9SAA2; -.
Proteomes; UP000006548; Chromosome 1.
ExpressionAtlas; Q9SAA2; baseline and differential.
Genevisible; Q9SAA2; AT.
GO; GO:0009570; C:chloroplast stroma; IEA:UniProtKB-SubCell.
GO; GO:0004252; F:serine-type endopeptidase activity; IEA:InterPro.
CDD; cd07017; S14_ClpP_2; 1.
HAMAP; MF_00444; ClpP; 1.
InterPro; IPR001907; ClpP.
InterPro; IPR029045; ClpP/crotonase-like_dom_sf.
InterPro; IPR023562; ClpP/TepA.
InterPro; IPR033135; ClpP_His_AS.
PANTHER; PTHR10381; PTHR10381; 1.
Pfam; PF00574; CLP_protease; 1.
PRINTS; PR00127; CLPPROTEASEP.
SUPFAM; SSF52096; SSF52096; 1.
PROSITE; PS00382; CLP_PROTEASE_HIS; 1.
1: Evidence at protein level;
3D-structure; Alternative splicing; Chloroplast; Complete proteome;
Direct protein sequencing; Hydrolase; Plastid; Protease;
Reference proteome; Serine protease; Transit peptide.
TRANSIT 1 77 Chloroplast. {ECO:0000305}.
CHAIN 78 271 ATP-dependent Clp protease proteolytic
subunit 6, chloroplastic.
/FTId=PRO_0000308981.
ACT_SITE 175 175 Nucleophile. {ECO:0000250}.
ACT_SITE 200 200 {ECO:0000250}.
CONFLICT 144 144 P -> S (in Ref. 1). {ECO:0000305}.
CONFLICT 153 153 A -> T (in Ref. 2; AAB99906).
{ECO:0000305}.
CONFLICT 179 180 LL -> FF (in Ref. 2; AAB99906).
{ECO:0000305}.
CONFLICT 258 258 L -> F (in Ref. 2; AAB99906).
{ECO:0000305}.
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


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