CLPD_ARATH
ID CLPD_ARATH Reviewed; 945 AA.
AC P42762;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1995, sequence version 1.
DT 03-AUG-2022, entry version 154.
DE RecName: Full=Chaperone protein ClpD, chloroplastic {ECO:0000303|PubMed:11299370};
DE EC=3.6.1.- {ECO:0000269|PubMed:21737456};
DE AltName: Full=ATP-dependent Clp protease ATP-binding subunit ClpD homolog;
DE AltName: Full=Casein lytic proteinase D;
DE AltName: Full=ERD1 protein;
DE AltName: Full=Protein EARLY RESPONSIVE TO DEHYDRATION 1 {ECO:0000303|PubMed:10198079};
DE AltName: Full=Protein SENESCENCE ASSOCIATED GENE 15;
DE Flags: Precursor;
GN Name=CLPD {ECO:0000303|PubMed:11299370};
GN Synonyms=ERD1 {ECO:0000303|PubMed:10198079}, SAG15;
GN OrderedLocusNames=At5g51070 {ECO:0000312|Araport:AT5G51070};
GN ORFNames=K3K7.27 {ECO:0000312|EMBL:BAB10330.1};
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].
RC STRAIN=cv. Columbia;
RX PubMed=7504470; DOI=10.1006/bbrc.1993.2381;
RA Kiyosue T., Yamaguchi-Shinozaki K., Shinozaki K.;
RT "Characterization of cDNA for a dehydration-inducible gene that encodes a
RT CLP A, B-like protein in Arabidopsis thaliana L.";
RL Biochem. Biophys. Res. Commun. 196:1214-1220(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10718197; DOI=10.1093/dnares/7.1.31;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Kotani H.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence
RT features of the regions of 3,076,755 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:31-63(2000).
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 SUBCELLULAR LOCATION, AND INDUCTION.
RX PubMed=9375397; DOI=10.1046/j.1365-313x.1997.12040851.x;
RA Nakashima K., Kiyosue T., Yamaguchi-Shinozaki K., Shinozaki K.;
RT "A nuclear gene, erd1, encoding a chloroplast-targeted Clp protease
RT regulatory subunit homolog is not only induced by water stress but also
RT developmentally up-regulated during senescence in Arabidopsis thaliana.";
RL Plant J. 12:851-861(1997).
RN [7]
RP SUBCELLULAR LOCATION, AND INDUCTION BY SENESCENCE.
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 [8]
RP INDUCTION BY OZONE.
RX PubMed=10444084; DOI=10.1104/pp.120.4.1015;
RA Miller J.D., Arteca R.N., Pell E.J.;
RT "Senescence-associated gene expression during ozone-induced leaf senescence
RT in Arabidopsis.";
RL Plant Physiol. 120:1015-1024(1999).
RN [9]
RP SUBCELLULAR LOCATION, AND INDUCTION.
RX PubMed=10198079; DOI=10.1104/pp.119.4.1209;
RA Weaver L.M., Froehlich J.E., Amasino R.M.;
RT "Chloroplast-targeted ERD1 protein declines but its mRNA increases during
RT senescence in Arabidopsis.";
RL Plant Physiol. 119:1209-1216(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 SUBCELLULAR LOCATION, TISSUE SPECIFICITY, AND INDUCTION.
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 [12]
RP NOMENCLATURE, AND DISRUPTION PHENOTYPE.
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 INDUCTION.
RX PubMed=17144892; DOI=10.1111/j.1365-313x.2006.02940.x;
RA Lee U., Rioflorido I., Hong S.W., Larkindale J., Waters E.R., Vierling E.;
RT "The Arabidopsis ClpB/Hsp100 family of proteins: chaperones for stress and
RT chloroplast development.";
RL Plant J. 49:115-127(2007).
RN [14]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR,
RP SUBUNIT, AND SUBCELLULAR LOCATION.
RX PubMed=21737456; DOI=10.1074/jbc.m110.211946;
RA Rosano G.L., Bruch E.M., Ceccarelli E.A.;
RT "Insights into the Clp/HSP100 chaperone system from chloroplasts of
RT Arabidopsis thaliana.";
RL J. Biol. Chem. 286:29671-29680(2011).
RN [15]
RP FUNCTION.
RX PubMed=22545953; DOI=10.1186/1471-2229-12-57;
RA Bruch E.M., Rosano G.L., Ceccarelli E.A.;
RT "Chloroplastic Hsp100 chaperones ClpC2 and ClpD interact in vitro with a
RT transit peptide only when it is located at the N-terminus of a protein.";
RL BMC Plant Biol. 12:57-57(2012).
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).
RN [17]
RP INTERACTION WITH CLPT1, AND FUNCTION.
RX PubMed=25149061; DOI=10.1186/s12870-014-0228-0;
RA Colombo C.V., Ceccarelli E.A., Rosano G.L.;
RT "Characterization of the accessory protein ClpT1 from Arabidopsis thaliana:
RT oligomerization status and interaction with Hsp100 chaperones.";
RL BMC Plant Biol. 14:228-228(2014).
CC -!- FUNCTION: Molecular chaperone that interact with a ClpP-like protease
CC involved in degradation of denatured proteins in the chloroplast
CC (PubMed:21737456). The ATPase activity of CLPD is stimulated by CLPT1
CC (PubMed:25149061). Has no ADPase activity (PubMed:21737456). Interacts
CC with transit peptides with a positional preference (PubMed:21737456,
CC PubMed:22545953). Localization of the signal sequence at the N-terminal
CC end of a protein seems mandatory for interaction to take place
CC (PubMed:22545953). {ECO:0000269|PubMed:21737456,
CC ECO:0000269|PubMed:22545953, ECO:0000269|PubMed:25149061}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216;
CC Evidence={ECO:0000269|PubMed:21737456};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:21737456};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=19.8 mM for ATP {ECO:0000269|PubMed:21737456};
CC Vmax=0.19 nmol/min/ug enzyme {ECO:0000269|PubMed:21737456};
CC pH dependence:
CC Optimum pH is 7.5. {ECO:0000269|PubMed:21737456};
CC Temperature dependence:
CC Optimum temperature is 45 degrees Celsius.
CC {ECO:0000269|PubMed:21737456};
CC -!- SUBUNIT: Homodimer and homohexamer (PubMed:21737456). Hexamerization
CC upon addition of ATP (PubMed:21737456). Interacts with CLPT1
CC (PubMed:25149061). Stably associated with the import machinery
CC (PubMed:21737456). {ECO:0000269|PubMed:21737456,
CC ECO:0000269|PubMed:25149061}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma
CC {ECO:0000269|PubMed:10198079, ECO:0000269|PubMed:10427773,
CC ECO:0000269|PubMed:11982939, ECO:0000269|PubMed:21737456,
CC ECO:0000269|PubMed:9375397}.
CC -!- TISSUE SPECIFICITY: Expressed in stems and leaves.
CC {ECO:0000269|PubMed:11982939}.
CC -!- INDUCTION: By dehydration and salt stresses. Induced after one hour of
CC dehydration-stress and reaches maximal levels after 10 hours. Induced
CC by cold, ozone, senescence and dark-induced etiolation. Down-regulated
CC by ozone (at protein level). Not induced by heat stress.
CC {ECO:0000269|PubMed:10198079, ECO:0000269|PubMed:10427773,
CC ECO:0000269|PubMed:10444084, ECO:0000269|PubMed:11982939,
CC ECO:0000269|PubMed:17144892, ECO:0000269|PubMed:9375397}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype. {ECO:0000303|Ref.12}.
CC -!- MISCELLANEOUS: CLPD is consistently found in two distinct forms, the
CC full-length protein and a lower molecular weight form porcessed at the
CC C-terminus. The processed form might be the active form and not the
CC full-length protein. {ECO:0000269|PubMed:21737456}.
CC -!- SIMILARITY: Belongs to the ClpA/ClpB family. ClpD subfamily.
CC {ECO:0000305}.
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DR EMBL; D17582; BAA04506.1; -; mRNA.
DR EMBL; AB023044; BAB10330.1; -; Genomic_DNA.
DR EMBL; AB017063; BAB10330.1; JOINED; Genomic_DNA.
DR EMBL; CP002688; AED96029.1; -; Genomic_DNA.
DR EMBL; AY035112; AAK59617.1; -; mRNA.
DR EMBL; AY133868; AAM91802.1; -; mRNA.
DR PIR; JN0901; JN0901.
DR RefSeq; NP_568750.1; NM_124486.3.
DR AlphaFoldDB; P42762; -.
DR SMR; P42762; -.
DR BioGRID; 20425; 1.
DR IntAct; P42762; 1.
DR STRING; 3702.AT5G51070.1; -.
DR PaxDb; P42762; -.
DR PRIDE; P42762; -.
DR ProteomicsDB; 246773; -.
DR EnsemblPlants; AT5G51070.1; AT5G51070.1; AT5G51070.
DR GeneID; 835180; -.
DR Gramene; AT5G51070.1; AT5G51070.1; AT5G51070.
DR KEGG; ath:AT5G51070; -.
DR Araport; AT5G51070; -.
DR TAIR; locus:2157363; AT5G51070.
DR eggNOG; KOG1051; Eukaryota.
DR HOGENOM; CLU_005070_4_1_1; -.
DR InParanoid; P42762; -.
DR OMA; SFNRKKE; -.
DR OrthoDB; 611758at2759; -.
DR PhylomeDB; P42762; -.
DR PRO; PR:P42762; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; P42762; baseline and differential.
DR Genevisible; P42762; 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:0009536; C:plastid; HDA:TAIR.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IDA:TAIR.
DR GO; GO:0065003; P:protein-containing complex assembly; IDA:TAIR.
DR Gene3D; 1.10.1780.10; -; 1.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR003593; AAA+_ATPase.
DR InterPro; IPR003959; ATPase_AAA_core.
DR InterPro; IPR019489; Clp_ATPase_C.
DR InterPro; IPR036628; Clp_N_dom_sf.
DR InterPro; IPR004176; Clp_R_dom.
DR InterPro; IPR001270; ClpA/B.
DR InterPro; IPR018368; ClpA/B_CS1.
DR InterPro; IPR028299; ClpA/B_CS2.
DR InterPro; IPR041546; ClpA/ClpB_AAA_lid.
DR InterPro; IPR027417; P-loop_NTPase.
DR Pfam; PF00004; AAA; 1.
DR Pfam; PF07724; AAA_2; 1.
DR Pfam; PF17871; AAA_lid_9; 1.
DR Pfam; PF02861; Clp_N; 2.
DR Pfam; PF10431; ClpB_D2-small; 1.
DR PRINTS; PR00300; CLPPROTEASEA.
DR SMART; SM00382; AAA; 2.
DR SMART; SM01086; ClpB_D2-small; 1.
DR SUPFAM; SSF52540; SSF52540; 2.
DR SUPFAM; SSF81923; SSF81923; 1.
DR PROSITE; PS51903; CLP_R; 1.
DR PROSITE; PS00870; CLPAB_1; 1.
DR PROSITE; PS00871; CLPAB_2; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Chaperone; Chloroplast; Hydrolase; Nucleotide-binding;
KW Plastid; Reference proteome; Repeat; Stress response; Transit peptide.
FT TRANSIT 1..89
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 90..945
FT /note="Chaperone protein ClpD, chloroplastic"
FT /id="PRO_0000005505"
FT DOMAIN 90..233
FT /note="Clp R"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01251"
FT REGION 90..146
FT /note="Repeat 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01251"
FT REGION 168..233
FT /note="Repeat 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01251"
FT REGION 233..264
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 271..523
FT /note="I"
FT REGION 555..586
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 590..781
FT /note="II"
FT BINDING 316..323
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 664..671
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
SQ SEQUENCE 945 AA; 103235 MW; 81EF2332C78F656B CRC64;
MEVLSTSSPL TLHSHRLLSA SSSSSHVTSI AASSLSSFAS SYLGISLSNR TIHRFSTTPT
NLRRFPQRKR KKFTPISAVF ERFTERAIRA IIFSQKEAKS LGKDMVYTQH LLLGLIAEDR
DPQGFLGSGI TIDKAREAVW SIWDEANSDS KQEEASSTSY SKSTDMPFSI STKRVFEAAV
EYSRTMDCQY IAPEHIAVGL FTVDDGSAGR VLKRLGANMN LLTAAALTRL KGEIAKDGRE
PSSSSKGSFE SPPSGRIAGS GPGGKKAKNV LEQFCVDLTA RASEGLIDPV IGREKEVQRV
IQILCRRTKN NPILLGEAGV GKTAIAEGLA ISIAEASAPG FLLTKRIMSL DIGLLMAGAK
ERGELEARVT ALISEVKKSG KVILFIDEVH TLIGSGTVGR GNKGSGLDIA NLLKPSLGRG
ELQCIASTTL DEFRSQFEKD KALARRFQPV LINEPSEEDA VKILLGLREK YEAHHNCKYT
MEAIDAAVYL SSRYIADRFL PDKAIDLIDE AGSRARIEAF RKKKEDAICI LSKPPNDYWQ
EIKTVQAMHE VVLSSRQKQD DGDAISDESG ELVEESSLPP AAGDDEPILV GPDDIAAVAS
VWSGIPVQQI TADERMLLMS LEDQLRGRVV GQDEAVAAIS RAVKRSRVGL KDPDRPIAAM
LFCGPTGVGK TELTKALAAN YFGSEESMLR LDMSEYMERH TVSKLIGSPP GYVGFEEGGM
LTEAIRRRPF TVVLFDEIEK AHPDIFNILL QLFEDGHLTD SQGRRVSFKN ALIIMTSNVG
SLAIAKGRHG SIGFILDDDE EAASYTGMKA LVVEELKNYF RPELLNRIDE IVIFRQLEKA
QMMEILNLML QDLKSRLVAL GVGLEVSEPV KELICKQGYD PAYGARPLRR TVTEIVEDPL
SEAFLAGSFK PGDTAFVVLD DTGNPSVRTK PDSSTIRVTD KTSIA
