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ATP-dependent Clp protease proteolytic subunit-related protein 4, chloroplastic (ClpR4) (Protein HAPPY ON NORFLURAZON 5)

 CLPR4_ARATH             Reviewed;         305 AA.
Q8LB10; O23548; Q8RXG1;
13-NOV-2007, integrated into UniProtKB/Swiss-Prot.
01-OCT-2002, sequence version 1.
25-APR-2018, entry version 96.
RecName: Full=ATP-dependent Clp protease proteolytic subunit-related protein 4, chloroplastic {ECO:0000303|PubMed:11299370};
Short=ClpR4 {ECO:0000303|PubMed:11299370};
AltName: Full=Protein HAPPY ON NORFLURAZON 5 {ECO:0000303|PubMed:21208309};
Flags: Precursor;
Name=CLPR4 {ECO:0000303|PubMed:11299370};
Synonyms=HON5 {ECO:0000303|PubMed:21208309};
OrderedLocusNames=At4g17040 {ECO:0000312|Araport:AT4G17040};
ORFNames=dl4550c {ECO:0000312|EMBL:CAB10484.1},
FCAALL.413 {ECO:0000312|EMBL:CAB80975.1};
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 [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=9461215; DOI=10.1038/35140;
Bevan M., Bancroft I., Bent E., Love K., Goodman H.M., Dean C.,
Bergkamp R., Dirkse W., van Staveren M., Stiekema W., Drost L.,
Ridley P., Hudson S.-A., Patel K., Murphy G., Piffanelli P.,
Wedler H., Wedler E., Wambutt R., Weitzenegger T., Pohl T., Terryn N.,
Gielen J., Villarroel R., De Clercq R., van Montagu M., Lecharny A.,
Aubourg S., Gy I., Kreis M., Lao N., Kavanagh T., Hempel S.,
Kotter P., Entian K.-D., Rieger M., Schaefer M., Funk B.,
Mueller-Auer S., Silvey M., James R., Monfort A., Pons A.,
Puigdomenech P., Douka A., Voukelatou E., Milioni D., Hatzopoulos P.,
Piravandi E., Obermaier B., Hilbert H., Duesterhoeft A., Moores T.,
Jones J.D.G., Eneva T., Palme K., Benes V., Rechmann S., Ansorge W.,
Cooke R., Berger C., Delseny M., Voet M., Volckaert G., Mewes H.-W.,
Klosterman S., Schueller C., Chalwatzis N.;
"Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of
Arabidopsis thaliana.";
Nature 391:485-488(1998).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=10617198; DOI=10.1038/47134;
Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G.,
Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N.,
Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M.,
Weichselgartner M., de Simone V., Obermaier B., Mache R., Mueller M.,
Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T.,
Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I.,
Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P.,
Langham S.-A., McCullagh B., Bilham L., Robben J.,
van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F.,
Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E.,
Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W.,
Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P.,
Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H.,
De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R.,
van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S.,
Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R.,
Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S.,
Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H.,
Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S.,
Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A.,
Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R.,
Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S.,
Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E.,
Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A.,
Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T.,
Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C.,
Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S.,
Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K.,
Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L.,
Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J.,
Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J.,
Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D.,
Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D.,
Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C.,
Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C.,
Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R.,
Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S.,
Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A.,
Chen E., Marra M.A., Martienssen R., McCombie W.R.;
"Sequence and analysis of chromosome 4 of the plant Arabidopsis
thaliana.";
Nature 402:769-777(1999).
[3]
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).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
PubMed=11910074; DOI=10.1126/science.1071006;
Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M.,
Hayashizaki Y., Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T.,
Shibata K., Shinagawa A., Shinozaki K.;
"Functional annotation of a full-length Arabidopsis cDNA collection.";
Science 296:141-145(2002).
[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].
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.
[7]
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).
[8]
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).
[9]
NOMENCLATURE, AND DISRUPTION PHENOTYPE.
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).
[10]
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).
[11]
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).
[12]
DISRUPTION PHENOTYPE.
PubMed=19525416; DOI=10.1105/tpc.108.063784;
Kim J., Rudella A., Ramirez Rodriguez V., Zybailov B., Olinares P.D.,
van Wijk K.J.;
"Subunits of the plastid ClpPR protease complex have differential
contributions to embryogenesis, plastid biogenesis, and plant
development in Arabidopsis.";
Plant Cell 21:1669-1692(2009).
[13]
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).
[14]
FUNCTION.
PubMed=21208309; DOI=10.1111/j.1365-313X.2010.04454.x;
Saini G., Meskauskiene R., Pijacka W., Roszak P., Sjoegren L.L.,
Clarke A.K., Straus M., Apel K.;
"'happy on norflurazon' (hon) mutations implicate perturbance of
plastid homeostasis with activating stress acclimatization and
changing nuclear gene expression in norflurazon-treated seedlings.";
Plant J. 65:690-702(2011).
[15]
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: Involved in plastid protein homeostasis.
{ECO:0000269|PubMed:21208309}.
-!- 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:14593120, PubMed:16766689,
PubMed:16980539). 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:14593120, ECO:0000269|PubMed:16766689,
ECO:0000269|PubMed:16980539, ECO:0000269|PubMed:21712416}.
-!- SUBCELLULAR LOCATION: Plastid, chloroplast
{ECO:0000269|PubMed:14593120}.
-!- DISRUPTION PHENOTYPE: Embryo lethal (Ref.9). Delayed embryogenesis
and albino embryos, with seedling development blocked in the
cotyledon stage (PubMed:19525416). Under heterotrophic growth
conditions, seedlings develop into small albino to virescent
seedlings (PubMed:19525416). {ECO:0000269|PubMed:19525416,
ECO:0000303|Ref.9}.
-!- SIMILARITY: Belongs to the peptidase S14 family. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=CAB10484.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
Sequence=CAB80975.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; Z97342; CAB10484.1; ALT_SEQ; Genomic_DNA.
EMBL; AL161545; CAB80975.1; ALT_SEQ; Genomic_DNA.
EMBL; CP002687; AEE83842.1; -; Genomic_DNA.
EMBL; AK117499; BAC42162.1; -; mRNA.
EMBL; AY081275; AAL91164.1; -; mRNA.
EMBL; BT000050; AAN15369.1; -; mRNA.
EMBL; AY087492; AAM65035.1; -; mRNA.
PIR; G71438; G71438.
RefSeq; NP_567521.1; NM_117808.3.
UniGene; At.19677; -.
PDB; 1R99; Model; -; A=1-305.
PDBsum; 1R99; -.
ProteinModelPortal; Q8LB10; -.
SMR; Q8LB10; -.
BioGrid; 12705; 5.
IntAct; Q8LB10; 1.
STRING; 3702.AT4G17040.1; -.
MEROPS; S14.001; -.
PaxDb; Q8LB10; -.
PRIDE; Q8LB10; -.
EnsemblPlants; AT4G17040.1; AT4G17040.1; AT4G17040.
GeneID; 827412; -.
Gramene; AT4G17040.1; AT4G17040.1; AT4G17040.
KEGG; ath:AT4G17040; -.
Araport; AT4G17040; -.
TAIR; locus:2130449; AT4G17040.
eggNOG; KOG0840; Eukaryota.
eggNOG; COG0740; LUCA.
HOGENOM; HOG000285833; -.
InParanoid; Q8LB10; -.
KO; K01358; -.
OMA; YRTPPPD; -.
OrthoDB; EOG09360IL8; -.
PhylomeDB; Q8LB10; -.
PRO; PR:Q8LB10; -.
Proteomes; UP000006548; Chromosome 4.
ExpressionAtlas; Q8LB10; baseline and differential.
Genevisible; Q8LB10; AT.
GO; GO:0009507; C:chloroplast; IDA:TAIR.
GO; GO:0009941; C:chloroplast envelope; IDA:TAIR.
GO; GO:0009570; C:chloroplast stroma; IDA:TAIR.
GO; GO:0009536; C:plastid; IDA:TAIR.
GO; GO:0009532; C:plastid stroma; IDA:TAIR.
GO; GO:0004252; F:serine-type endopeptidase activity; IEA:InterPro.
GO; GO:0010468; P:regulation of gene expression; IMP:TAIR.
GO; GO:0000302; P:response to reactive oxygen species; IMP:TAIR.
CDD; cd07017; S14_ClpP_2; 1.
InterPro; IPR001907; ClpP.
InterPro; IPR029045; ClpP/crotonase-like_dom_sf.
InterPro; IPR023562; ClpP/TepA.
PANTHER; PTHR10381; PTHR10381; 1.
Pfam; PF00574; CLP_protease; 1.
PRINTS; PR00127; CLPPROTEASEP.
SUPFAM; SSF52096; SSF52096; 1.
1: Evidence at protein level;
3D-structure; Chloroplast; Complete proteome; Plastid;
Reference proteome; Transit peptide.
TRANSIT 1 68 Chloroplast. {ECO:0000255}.
CHAIN 69 305 ATP-dependent Clp protease proteolytic
subunit-related protein 4, chloroplastic.
/FTId=PRO_0000308985.
CONFLICT 143 143 E -> K (in Ref. 5; AAL91164/AAN15369).
{ECO:0000305}.
SEQUENCE 305 AA; 33440 MW; 7902D9ECF220B92F CRC64;
MEVAAATATS FTTLRARTSA IIPSSTRNLR SKPRFSSSSS LRASLSNGFL SPYTGGSISS
DLCGAKLRAE SLNPLNFSSS KPKRGVVTMV IPFSKGSAHE QPPPDLASYL FKNRIVYLGM
SLVPSVTELI LAEFLYLQYE DEEKPIYLYI NSTGTTKNGE KLGYDTEAFA IYDVMGYVKP
PIFTLCVGNA WGEAALLLTA GAKGNRSALP SSTIMIKQPI ARFQGQATDV EIARKEIKHI
KTEMVKLYSK HIGKSPEQIE ADMKRPKYFS PTEAVEYGII DKVVYNERGS QDRGVVSDLK
KAQLI


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