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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)DescriptionActionsGraphical viewLength
Active sitei158NucleophileBy similarity1
Active sitei183By similarity1

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

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)DescriptionActionsGraphical viewLength
Transit peptidei1 – 65ChloroplastCombined sourcesAdd BLAST65
ChainiPRO_000030897966 – 292ATP-dependent Clp protease proteolytic subunit 4, chloroplasticAdd BLAST227

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei66N-acetylserineCombined sources1

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 interactors.
IntActiQ94B60. 2 interactors.
STRINGi3702.AT5G45390.1.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1R91model-A1-292[»]
ProteinModelPortaliQ94B60.
SMRiQ94B60.
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.
OrthoDBiEOG09360JU9.
PhylomeDBiQ94B60.

Family and domain databases

Gene3Di3.90.226.10. 1 hit.
HAMAPiMF_00444. ClpP. 1 hit.
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 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
The sequence BAB09167 differs from that shown. Reason: Erroneous gene model prediction.Curated
The sequence CAA04393 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti1 – 3MGT → TRP in CAA04393 (Ref. 2) Curated3
Sequence conflicti57R → T in CAA04393 (Ref. 2) Curated1
Sequence conflicti171K → N in CAA04393 (Ref. 2) Curated1
Sequence conflicti193A → V in AAM65254 (Ref. 6) Curated1
Sequence conflicti279M → I in AAM65254 (Ref. 6) Curated1

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_123907.4.
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_123907.4.
UniGeneiAt.387.
At.67124.

3D structure databases

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

Protein-protein interaction databases

BioGridi19824. 5 interactors.
IntActiQ94B60. 2 interactors.
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.
OrthoDBiEOG09360JU9.
PhylomeDBiQ94B60.

Miscellaneous databases

PROiQ94B60.

Gene expression databases

GenevisibleiQ94B60. AT.

Family and domain databases

Gene3Di3.90.226.10. 1 hit.
HAMAPiMF_00444. ClpP. 1 hit.
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...

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: November 30, 2016
This is version 105 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.