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Protein

ATP-dependent Clp protease proteolytic subunit 4, chloroplastic

Gene

CLPP4

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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 (PubMed:16705403, PubMed:17241447). Essential for Embryogenesis (PubMed:23548781).By similarity3 Publications

Catalytic activityi

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).

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei158 – 1581NucleophileBy similarity
Active sitei183 – 1831By similarity

GO - Molecular functioni

GO - Biological processi

  • chloroplast organization Source: TAIR
  • regulation of timing of transition from vegetative to reproductive phase Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Serine protease

Enzyme and pathway databases

BioCyciARA:AT5G45390-MONOMER.

Protein family/group databases

MEROPSiS14.010.

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-dependent Clp protease proteolytic subunit 4, chloroplastic1 Publication (EC:3.4.21.92)
Alternative name(s):
Endopeptidase ClpP41 Publication
Short name:
nClpP4
nClpP3
Gene namesi
Name:CLPP41 Publication
Synonyms:NCLPP3, NCLPP4
Ordered Locus Names:At5g45390Imported
ORF Names:MFC19.5Imported
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G45390.

Subcellular locationi

GO - Cellular componenti

  • chloroplast Source: TAIR
  • chloroplast envelope Source: TAIR
  • chloroplastic endopeptidase Clp complex Source: TAIR
  • chloroplast stroma Source: TAIR
  • chloroplast thylakoid membrane Source: TAIR
  • plastid stroma Source: TAIR
  • thylakoid Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Plastid

Pathology & Biotechi

Disruption phenotypei

Embryo lethal when homozygous.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 6565ChloroplastCombined sourcesAdd
BLAST
Chaini66 – 292227ATP-dependent Clp protease proteolytic subunit 4, chloroplasticPRO_0000308979Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei66 – 661N-acetylserineCombined sources

Post-translational modificationi

Ubiquitinated by CHIP.1 Publication

Keywords - PTMi

Acetylation, Ubl conjugation

Proteomic databases

PaxDbiQ94B60.
PRIDEiQ94B60.

Expressioni

Tissue specificityi

Mostly expressed in leaves. Also detected in stems, and to a lower extent, in roots (at protein level).1 Publication

Inductioni

Repressed in darkness. Levels decrease in leaves during aging (at protein level). Slightly and transiently repressed by high light stress (at protein level).3 Publications

Gene expression databases

GenevisibleiQ94B60. AT.

Interactioni

Subunit structurei

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). Interacts with CHIP (PubMed:17241447). 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).6 Publications

Protein-protein interaction databases

BioGridi19824. 5 interactions.
IntActiQ94B60. 2 interactions.
STRINGi3702.AT5G45390.1.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1R91model-A1-292[»]
ProteinModelPortaliQ94B60.
SMRiQ94B60. Positions 79-250.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the peptidase S14 family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG0840. Eukaryota.
COG0740. LUCA.
HOGENOMiHOG000285833.
KOiK01358.
OMAiERDYWMD.
PhylomeDBiQ94B60.

Family and domain databases

Gene3Di3.90.226.10. 1 hit.
HAMAPiMF_00444. ClpP.
InterProiIPR001907. ClpP.
IPR029045. ClpP/crotonase-like_dom.
IPR023562. ClpP/TepA.
IPR033135. ClpP_His_AS.
[Graphical view]
PANTHERiPTHR10381. PTHR10381. 1 hit.
PfamiPF00574. CLP_protease. 1 hit.
[Graphical view]
PRINTSiPR00127. CLPPROTEASEP.
SUPFAMiSSF52096. SSF52096. 1 hit.
PROSITEiPS00382. CLP_PROTEASE_HIS. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q94B60-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGTLSLSSSL KPSLVSSRLN SSSSASSSSF PKPNNLYLKP TKLISPPLRT
60 70 80 90 100
TSPSPLRFAN ASIEMSQTQE SAIRGAESDV MGLLLRERIV FLGSSIDDFV
110 120 130 140 150
ADAIMSQLLL LDAKDPKKDI KLFINSPGGS LSATMAIYDV VQLVRADVST
160 170 180 190 200
IALGIAASTA SIILGAGTKG KRFAMPNTRI MIHQPLGGAS GQAIDVEIQA
210 220 230 240 250
KEVMHNKNNV TSIIAGCTSR SFEQVLKDID RDRYMSPIEA VEYGLIDGVI
260 270 280 290
DGDSIIPLEP VPDRVKPRVN YEEISKDPMK FLTPEIPDDE IY
Length:292
Mass (Da):31,498
Last modified:December 1, 2001 - v1
Checksum:i227B514CF1C1CE4C
GO

Sequence cautioni

The sequence BAA82068.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
The sequence BAB09167.1 differs from that shown. Reason: Erroneous gene model prediction. Curated
The sequence CAA04393.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti1 – 33MGT → TRP in CAA04393 (Ref. 2) Curated
Sequence conflicti57 – 571R → T in CAA04393 (Ref. 2) Curated
Sequence conflicti171 – 1711K → N in CAA04393 (Ref. 2) Curated
Sequence conflicti193 – 1931A → V in AAM65254 (Ref. 6) Curated
Sequence conflicti279 – 2791M → I in AAM65254 (Ref. 6) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB022329 mRNA. Translation: BAA82068.1. Different initiation.
AJ000930 mRNA. Translation: CAA04393.1. Different initiation.
AB018113 Genomic DNA. Translation: BAB09167.1. Sequence problems.
CP002688 Genomic DNA. Translation: AED95243.1.
AY042832 mRNA. Translation: AAK68772.1.
BT006321 mRNA. Translation: AAP13429.1.
AY087717 mRNA. Translation: AAM65254.1.
PIRiT52452.
RefSeqiNP_568644.1. NM_123907.3.
UniGeneiAt.387.
At.67124.

Genome annotation databases

EnsemblPlantsiAT5G45390.1; AT5G45390.1; AT5G45390.
GeneIDi834575.
GrameneiAT5G45390.1; AT5G45390.1; AT5G45390.
KEGGiath:AT5G45390.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB022329 mRNA. Translation: BAA82068.1. Different initiation.
AJ000930 mRNA. Translation: CAA04393.1. Different initiation.
AB018113 Genomic DNA. Translation: BAB09167.1. Sequence problems.
CP002688 Genomic DNA. Translation: AED95243.1.
AY042832 mRNA. Translation: AAK68772.1.
BT006321 mRNA. Translation: AAP13429.1.
AY087717 mRNA. Translation: AAM65254.1.
PIRiT52452.
RefSeqiNP_568644.1. NM_123907.3.
UniGeneiAt.387.
At.67124.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1R91model-A1-292[»]
ProteinModelPortaliQ94B60.
SMRiQ94B60. Positions 79-250.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi19824. 5 interactions.
IntActiQ94B60. 2 interactions.
STRINGi3702.AT5G45390.1.

Protein family/group databases

MEROPSiS14.010.

Proteomic databases

PaxDbiQ94B60.
PRIDEiQ94B60.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G45390.1; AT5G45390.1; AT5G45390.
GeneIDi834575.
GrameneiAT5G45390.1; AT5G45390.1; AT5G45390.
KEGGiath:AT5G45390.

Organism-specific databases

TAIRiAT5G45390.

Phylogenomic databases

eggNOGiKOG0840. Eukaryota.
COG0740. LUCA.
HOGENOMiHOG000285833.
KOiK01358.
OMAiERDYWMD.
PhylomeDBiQ94B60.

Enzyme and pathway databases

BioCyciARA:AT5G45390-MONOMER.

Miscellaneous databases

PROiQ94B60.

Gene expression databases

GenevisibleiQ94B60. AT.

Family and domain databases

Gene3Di3.90.226.10. 1 hit.
HAMAPiMF_00444. ClpP.
InterProiIPR001907. ClpP.
IPR029045. ClpP/crotonase-like_dom.
IPR023562. ClpP/TepA.
IPR033135. ClpP_His_AS.
[Graphical view]
PANTHERiPTHR10381. PTHR10381. 1 hit.
PfamiPF00574. CLP_protease. 1 hit.
[Graphical view]
PRINTSiPR00127. CLPPROTEASEP.
SUPFAMiSSF52096. SSF52096. 1 hit.
PROSITEiPS00382. CLP_PROTEASE_HIS. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Identification of clp genes expressed in senescing Arabidopsis leaves."
    Nakabayashi K., Ito M., Kiyosue T., Shinozaki K., Watanabe A.
    Plant Cell Physiol. 40:504-514(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], INDUCTION.
    Strain: cv. Columbia.
  2. "A third nuclear-encoded clpP gene from Arabidopsis thaliana."
    Clarke A.K.
    Submitted (FEB-1998) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: cv. Columbia.
  3. "Structural analysis of Arabidopsis thaliana chromosome 5. IX. Sequence features of the regions of 1,011,550 bp covered by seventeen P1 and TAC clones."
    Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Kotani H., Miyajima N., Tabata S.
    DNA Res. 6:183-195(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  4. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  5. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    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.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  6. "Full-length cDNA from Arabidopsis thaliana."
    Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A.
    Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  7. "Identification of a 350-kDa ClpP protease complex with 10 different Clp isoforms in chloroplasts of Arabidopsis thaliana."
    Peltier J.-B., Ytterberg J., Liberles D.A., Roepstorff P., van Wijk K.J.
    J. Biol. Chem. 276:16318-16327(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 75-86; 180-201; 208-219 AND 269-280, SUBUNIT, IDENTIFICATION BY MASS SPECTROMETRY.
  8. Cited for: GENE FAMILY, NOMENCLATURE.
  9. "Characterization of chloroplast Clp proteins in Arabidopsis: localization, tissue specificity and stress responses."
    Zheng B., Halperin T., Hruskova-Heidingsfeldova O., Adam Z., Clarke A.K.
    Physiol. Plantarum 114:92-101(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION, INDUCTION, TISSUE SPECIFICITY.
    Strain: cv. Columbia.
    Tissue: Seedling.
  10. "Clp protease complexes from photosynthetic and non-photosynthetic plastids and mitochondria of plants, their predicted three-dimensional structures, and functional implications."
    Peltier J.-B., Ripoll D.R., Friso G., Rudella A., Cai Y., Ytterberg J., Giacomelli L., Pillardy J., van Wijk K.J.
    J. Biol. Chem. 279:4768-4781(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY, SUBUNIT, SUBCELLULAR LOCATION, 3D-STRUCTURE MODELING.
  11. "The ATP-dependent Clp protease in chloroplasts of higher plants."
    Clarke A.K., MacDonald T.M., Sjoegren L.L.
    Physiol. Plantarum 123:406-412(2005)
    Cited for: NOMENCLATURE.
  12. "A nuclear-encoded ClpP subunit of the chloroplast ATP-dependent Clp protease is essential for early development in Arabidopsis thaliana."
    Zheng B., MacDonald T.M., Sutinen S., Hurry V., Clarke A.K.
    Planta 224:1103-1115(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INDUCTION.
  13. "Downregulation of ClpR2 leads to reduced accumulation of the ClpPRS protease complex and defects in chloroplast biogenesis in Arabidopsis."
    Rudella A., Friso G., Alonso J.M., Ecker J.R., van Wijk K.J.
    Plant Cell 18:1704-1721(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY, SUBUNIT.
  14. "Structural and functional insights into the chloroplast ATP-dependent Clp protease in Arabidopsis."
    Sjoegren L.L.E., Stanne T.M., Zheng B., Sutinen S., Clarke A.K.
    Plant Cell 18:2635-2649(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT.
  15. "The chloroplast protease subunit ClpP4 is a substrate of the E3 ligase AtCHIP and plays an important role in chloroplast function."
    Shen G., Yan J., Pasapula V., Luo J., He C., Clarke A.K., Zhang H.
    Plant J. 49:228-237(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, UBIQUITINATION, INTERACTION WITH CHIP.
  16. "Subunit stoichiometry, evolution, and functional implications of an asymmetric plant plastid ClpP/R protease complex in Arabidopsis."
    Olinares P.D., Kim J., Davis J.I., van Wijk K.J.
    Plant Cell 23:2348-2361(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY, SUBUNIT.
  17. "Comparative large-scale characterisation of plant vs. mammal proteins reveals similar and idiosyncratic N-alpha acetylation features."
    Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T., Giglione C.
    Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-66, CLEAVAGE OF TRANSIT PEPTIDE [LARGE SCALE ANALYSIS] AFTER MET-65, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  18. "The chloroplast ATP-dependent Clp protease in vascular plants - new dimensions and future challenges."
    Clarke A.K.
    Physiol. Plantarum 145:235-244(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  19. "Modified Clp protease complex in the ClpP3 null mutant and consequences for chloroplast development and function in Arabidopsis."
    Kim J., Olinares P.D., Oh S.H., Ghisaura S., Poliakov A., Ponnala L., van Wijk K.J.
    Plant Physiol. 162:157-179(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE.

Entry informationi

Entry nameiCLPP4_ARATH
AccessioniPrimary (citable) accession number: Q94B60
Secondary accession number(s): Q8LAN0
, Q9FHJ7, Q9SXJ5, Q9ZS78
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 13, 2007
Last sequence update: December 1, 2001
Last modified: March 16, 2016
This is version 101 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Peptidase families
    Classification of peptidase families and list of entries
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.