CLPT2_ARATH
ID CLPT2_ARATH Reviewed; 241 AA.
AC Q8GW78; Q8LBJ1; Q9SZ71;
DT 05-OCT-2010, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 25-MAY-2022, entry version 103.
DE RecName: Full=ATP-dependent Clp protease ATP-binding subunit CLPT2, chloroplastic {ECO:0000303|Ref.6};
DE Flags: Precursor;
GN Name=CLPT2 {ECO:0000303|Ref.6};
GN Synonyms=CLPS2 {ECO:0000303|PubMed:14593120}; OrderedLocusNames=At4g12060;
GN ORFNames=F16J13.130;
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=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
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 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 [4]
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 [5]
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 [6]
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 [7]
RP INTERACTION WITH AHK2.
RX PubMed=18642946; DOI=10.1021/pr0703831;
RA Dortay H., Gruhn N., Pfeifer A., Schwerdtner M., Schmuelling T., Heyl A.;
RT "Toward an interaction map of the two-component signaling pathway of
RT Arabidopsis thaliana.";
RL J. Proteome Res. 7:3649-3660(2008).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE SCALE
RP ANALYSIS].
RX PubMed=18431481; DOI=10.1371/journal.pone.0001994;
RA Zybailov B., Rutschow H., Friso G., Rudella A., Emanuelsson O., Sun Q.,
RA van Wijk K.J.;
RT "Sorting signals, N-terminal modifications and abundance of the chloroplast
RT proteome.";
RL PLoS ONE 3:E1994-E1994(2008).
RN [9]
RP FUNCTION, DISRUPTION PHENOTYPE, AND SUBUNIT.
RX PubMed=21266658; DOI=10.1105/tpc.110.082321;
RA Sjoegren L.L., Clarke A.K.;
RT "Assembly of the chloroplast ATP-dependent Clp protease in Arabidopsis is
RT regulated by the ClpT accessory proteins.";
RL Plant Cell 23:322-332(2011).
RN [10]
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 [11]
RP INTERACTION WITH CLPS1.
RX PubMed=23898032; DOI=10.1105/tpc.113.112557;
RA Nishimura K., Asakura Y., Friso G., Kim J., Oh S.H., Rutschow H.,
RA Ponnala L., van Wijk K.J.;
RT "ClpS1 is a conserved substrate selector for the chloroplast Clp protease
RT system in Arabidopsis.";
RL Plant Cell 25:2276-2301(2013).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (1.99 ANGSTROMS) OF 76-241, DISRUPTION PHENOTYPE,
RP IDENTIFICATION BY MASS SPECTROMETRY, CLEAVAGE OF TRANSIT PEPTIDE AFTER
RP SER-75, FUNCTION, INTERACTION WITH CPN21, MUTAGENESIS OF THR-119;
RP 161-MET--PHE-164 AND THR-172, AND DOMAIN.
RX PubMed=25921872; DOI=10.1105/tpc.15.00106;
RA Kim J., Kimber M.S., Nishimura K., Friso G., Schultz L., Ponnala L.,
RA van Wijk K.J.;
RT "Structures, functions, and interactions of ClpT1 and ClpT2 in the Clp
RT protease system of Arabidopsis chloroplasts.";
RL Plant Cell 27:1477-1496(2015).
CC -!- FUNCTION: Accessory protein regulating the assembly of the plastidial
CC Clp protease system (PubMed:21266658, PubMed:25921872). CLPT1 first
CC binds to the heptameric P-ring containing the CLP3-6 subunits followed
CC by CLPT2, and only then does the P-ring combine with the R-ring
CC composed of the clpP1 and CLPR1-4 subunits (PubMed:21266658). Once the
CC core complex is fully assembled, it then associates to the CLPC
CC chaperone partner to form the functional protease (PubMed:21266658).
CC CLPT2 and CLPT1 are partially redundant (PubMed:25921872).
CC {ECO:0000269|PubMed:21266658, ECO:0000269|PubMed:25921872}.
CC -!- SUBUNIT: Monomer and homodimer (PubMed:21266658). The dimers monomerize
CC before association to the P-ring (PubMed:21266658). Component of the
CC chloroplastic Clp protease core complex which consist of at least 16
CC proteins: CLPP4 (3 copies), CLPP5 (3 copies), CLPR4 (2 copies), ClpP1
CC (1 copy), CLPP6 (1 copy), CLPR2 (1 copy), CLPT1 (1 copy), CLPT2 (1
CC copy) and 3 copies of CLPP3 and/or CLPR1 and/or CLPR3 (PubMed:21266658,
CC PubMed:14593120). Interacts with AHK2 (PubMed:18642946). Interacts with
CC CPN21 (PubMed:25921872). No interactions with CLPS1 (PubMed:23898032).
CC {ECO:0000269|PubMed:14593120, ECO:0000269|PubMed:18642946,
CC ECO:0000269|PubMed:21266658, ECO:0000269|PubMed:23898032,
CC ECO:0000269|PubMed:25921872}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:14593120, ECO:0000269|PubMed:18431481}.
CC -!- DOMAIN: The MYFF motif is functionally important for stabilization of
CC the overall ClpPR complex. {ECO:0000269|PubMed:25921872}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype (PubMed:21266658,
CC PubMed:25921872). Clpt1 and clpt2 double mutants show delayed
CC development, reduced plant growth, and virescent, serrated leaves
CC (PubMed:25921872). Clpt1 and clpt2 double mutants are seedling lethal
CC under autotrophic conditions (PubMed:21266658).
CC {ECO:0000269|PubMed:21266658, ECO:0000269|PubMed:25921872}.
CC -!- SIMILARITY: Belongs to the ClpA/ClpB family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB40947.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB78249.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL049638; CAB40947.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161533; CAB78249.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE83092.1; -; Genomic_DNA.
DR EMBL; AK119030; BAC43606.1; -; mRNA.
DR EMBL; AY087178; AAM64734.1; -; mRNA.
DR PIR; T06613; T06613.
DR RefSeq; NP_567386.1; NM_117276.3.
DR PDB; 4Y0C; X-ray; 1.99 A; A/B=76-241.
DR PDBsum; 4Y0C; -.
DR AlphaFoldDB; Q8GW78; -.
DR SMR; Q8GW78; -.
DR BioGRID; 12112; 11.
DR IntAct; Q8GW78; 1.
DR STRING; 3702.AT4G12060.1; -.
DR PaxDb; Q8GW78; -.
DR PRIDE; Q8GW78; -.
DR ProteomicsDB; 222096; -.
DR EnsemblPlants; AT4G12060.1; AT4G12060.1; AT4G12060.
DR GeneID; 826814; -.
DR Gramene; AT4G12060.1; AT4G12060.1; AT4G12060.
DR KEGG; ath:AT4G12060; -.
DR Araport; AT4G12060; -.
DR TAIR; locus:2118066; AT4G12060.
DR eggNOG; ENOG502RY68; Eukaryota.
DR HOGENOM; CLU_086193_0_0_1; -.
DR InParanoid; Q8GW78; -.
DR OMA; EVMPAHI; -.
DR OrthoDB; 1280014at2759; -.
DR PhylomeDB; Q8GW78; -.
DR PRO; PR:Q8GW78; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q8GW78; baseline and differential.
DR Genevisible; Q8GW78; 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:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0009532; C:plastid stroma; IDA:TAIR.
DR GO; GO:0043424; F:protein histidine kinase binding; IPI:UniProtKB.
DR Gene3D; 1.10.1780.10; -; 1.
DR InterPro; IPR036628; Clp_N_dom_sf.
DR InterPro; IPR004176; Clp_R_dom.
DR InterPro; IPR044217; CLPT1/2.
DR PANTHER; PTHR47016; PTHR47016; 1.
DR Pfam; PF02861; Clp_N; 2.
DR SUPFAM; SSF81923; SSF81923; 1.
DR PROSITE; PS51903; CLP_R; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Chloroplast; Plastid; Reference proteome; Repeat;
KW Transit peptide.
FT TRANSIT 1..75
FT /note="Chloroplast"
FT /evidence="ECO:0000305|PubMed:25921872"
FT CHAIN 76..241
FT /note="ATP-dependent Clp protease ATP-binding subunit
FT CLPT2, chloroplastic"
FT /id="PRO_0000398663"
FT DOMAIN 91..237
FT /note="Clp R"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01251"
FT REGION 94..159
FT /note="Repeat 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01251"
FT REGION 171..237
FT /note="Repeat 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01251"
FT MUTAGEN 119
FT /note="T->V: No effect."
FT /evidence="ECO:0000269|PubMed:25921872"
FT MUTAGEN 161..164
FT /note="MYFF->AAAA: Loss of stabilization of ClpP and ClpR
FT ring interaction, but no effect on the interaction with the
FT ClpP ring."
FT /evidence="ECO:0000269|PubMed:25921872"
FT MUTAGEN 172
FT /note="T->V: No effect."
FT /evidence="ECO:0000269|PubMed:25921872"
FT CONFLICT 66
FT /note="P -> R (in Ref. 4; AAM64734)"
FT /evidence="ECO:0000305"
FT CONFLICT 73
FT /note="A -> V (in Ref. 4; AAM64734)"
FT /evidence="ECO:0000305"
FT CONFLICT 173
FT /note="E -> Q (in Ref. 4; AAM64734)"
FT /evidence="ECO:0000305"
FT HELIX 78..80
FT /evidence="ECO:0007829|PDB:4Y0C"
FT HELIX 96..111
FT /evidence="ECO:0007829|PDB:4Y0C"
FT STRAND 115..117
FT /evidence="ECO:0007829|PDB:4Y0C"
FT HELIX 119..129
FT /evidence="ECO:0007829|PDB:4Y0C"
FT HELIX 133..140
FT /evidence="ECO:0007829|PDB:4Y0C"
FT HELIX 145..156
FT /evidence="ECO:0007829|PDB:4Y0C"
FT HELIX 173..187
FT /evidence="ECO:0007829|PDB:4Y0C"
FT HELIX 197..206
FT /evidence="ECO:0007829|PDB:4Y0C"
FT HELIX 211..218
FT /evidence="ECO:0007829|PDB:4Y0C"
FT HELIX 223..233
FT /evidence="ECO:0007829|PDB:4Y0C"
SQ SEQUENCE 241 AA; 26561 MW; 92961CCDDDF3DFAB CRC64;
MAAHSSCNFA LTNPIISQID SFSKKKLSVP LYFFSTRKAL TNPWLGVVDS SLSLTSPVSA
LQTNRPRRIH KSAISSLPTA NPDLVVSDAK KPKWSWRAIK SFAMGELEAR KLKYPNTGTE
ALLMGILIEG TSFTSKFLRA NKIMLYKVRE ETVKLLGKAD MYFFSPEHPP LTEDAQRALD
SALDQNLKAG GIGEVMPAHI LLGIWSEVES PGHKILATLG FTDEKSKELE SFASESGFLD
E
