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Q9LJL3 (PREP1_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 90. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Presequence protease 1, chloroplastic/mitochondrial

Short name=AtPreP1
Short name=PreP 1
EC=3.4.24.-
Alternative name(s):
Zinc metalloprotease 1
Short name=AtZnMP1
Gene names
Name:PREP1
Synonyms:ZNMP1
Ordered Locus Names:At3g19170
ORF Names:MVI11.6, MVI11.7, MVI11_8
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length1080 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

ATP-independent protease that degrades both mitochondrial and chloroplastic transit peptides after their cleavage. Also degrades other unstructured peptides. Specific for peptides in the range of 10 to 65 residues. Shows a preference for cleavage after small polar residues and before basic residues, with a bias for positively charged amino acid residues. Ref.4

Cofactor

Binds 1 zinc ion per subunit.

Binds 2 Magnesium ions per subunit.

Enzyme regulation

Inactive in the absence of MgCl2 and CaCl2 and full activation at 10 mM concentrations of either ion. Completely inhibited by the metal chelator orthophenanthroline, but not affected by phenylmethylsulfonyl fluoride (PMSF) or N-ethylmaleimide (NEM).

Subunit structure

Homodimer.

Subcellular location

Plastidchloroplast stroma. Mitochondrion matrix Ref.5 Ref.6.

Tissue specificity

Expressed only in siliques and flowers. Ref.6

Miscellaneous

The 2 enzymes halves enclose a large proteolytic chamber spacious enough to hold peptide substrates, but sufficiently small to exclude larger, folded proteins. Since the active site includes residues from both the N- and C-terminal part of the protein, proteolysis can occur only when the chamber is closed. Covalently locking the 2 halves of the protease with disulfide bonds induces a loss of activity.

Sequence similarities

Belongs to the peptidase M16 family. PreP subfamily.

Biophysicochemical properties

pH dependence:

Active from pH 4 to 10.

Temperature dependence:

Optimum temperature is 28 degrees Celsius. Active from 4 to 40 degrees Celsius.

Sequence caution

The sequence BAB02957.1 differs from that shown. Reason: Erroneous initiation.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

ATPBP176146EBI-7143359,EBI-7143406From a different organism.

Alternative products

This entry describes 1 isoform produced by alternative splicing. [Select]

Note: A number of isoforms are produced. According to EST sequences.
Isoform 1 (identifier: Q9LJL3-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 8484Chloroplast and mitochondrion Potential
Chain85 – 1080996Presequence protease 1, chloroplastic/mitochondrial
PRO_0000249938

Regions

Coiled coil571 – 61242 Potential

Sites

Active site1651Proton acceptor
Metal binding1621Zinc; catalytic
Metal binding1661Zinc; catalytic
Metal binding2621Zinc; catalytic

Experimental info

Mutagenesis1621H → L: Loss of activity. Ref.5
Mutagenesis1651E → Q: Loss of activity. Ref.5
Mutagenesis1661H → L: Loss of activity. Ref.5
Mutagenesis1791E → Q: Decreased activity toward some substrates. Ref.8
Mutagenesis1941N → A: Reduced activity. Ref.8
Mutagenesis2401E → Q: Decreased activity toward some substrates. Ref.5
Mutagenesis2451E → Q: No loss of activity. Ref.5
Mutagenesis2561K → C: Inactive under oxidizing conditions and fully active under reducing conditions; when associated with C-937. Ref.8
Mutagenesis2621E → Q: Loss of activity. Ref.8
Mutagenesis2641K → C: Inactive under oxidizing conditions and fully active under reducing conditions; when associated with C-895. Ref.8
Mutagenesis4161A → C: Little or no effect; when associated with C-700. Ref.8
Mutagenesis4301E → C: Inactive under oxidizing conditions and fully active under reducing conditions; when associated with C-767. Ref.8
Mutagenesis7001N → C: Little or no effect; when associated with C-416. Ref.8
Mutagenesis7671S → C: Inactive under oxidizing conditions and fully active under reducing conditions; when associated with C-430. Ref.8
Mutagenesis8951Q → C: Inactive under oxidizing conditions and fully active under reducing conditions; when associated with C-264. Ref.8
Mutagenesis9331R → A or K: Loss of activity. Ref.8
Mutagenesis9371G → C: Inactive under oxidizing conditions and fully active under reducing conditions; when associated with C-256. Ref.8
Mutagenesis9391Y → F: Loss of activity. Ref.8

Secondary structure

.............................................................................................................................................................. 1080
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified September 19, 2006. Version 2.
Checksum: 9FD259970195B9FC

FASTA1,080121,015
        10         20         30         40         50         60 
MLRTVSCLAS RSSSSLFFRF FRQFPRSYMS LTSSTAALRV PSRNLRRISS PSVAGRRLLL 

        70         80         90        100        110        120 
RRGLRIPSAA VRSVNGQFSR LSVRAVATQP APLYPDVGQD EAEKLGFEKV SEEFISECKS 

       130        140        150        160        170        180 
KAILFKHKKT GCEVMSVSNE DENKVFGVVF RTPPKDSTGI PHILEHSVLC GSRKYPVKEP 

       190        200        210        220        230        240 
FVELLKGSLH TFLNAFTYPD RTCYPVASTN TKDFYNLVDV YLDAVFFPKC VDDAHTFQQE 

       250        260        270        280        290        300 
GWHYELNDPS EDISYKGVVF NEMKGVYSQP DNILGRIAQQ ALSPENTYGV DSGGDPKDIP 

       310        320        330        340        350        360 
NLTFEEFKEF HRQYYHPSNA RIWFYGDDDP VHRLRVLSEY LDMFEASPSP NSSKIKFQKL 

       370        380        390        400        410        420 
FSEPVRLVEK YPAGRDGDLK KKHMLCVNWL LSEKPLDLQT QLALGFLDHL MLGTPASPLR 

       430        440        450        460        470        480 
KILLESGLGE ALVSSGLSDE LLQPQFGIGL KGVSEENVQK VEELIMDTLK KLAEEGFDND 

       490        500        510        520        530        540 
AVEASMNTIE FSLRENNTGS FPRGLSLMLQ SISKWIYDMD PFEPLKYTEP LKALKTRIAE 

       550        560        570        580        590        600 
EGSKAVFSPL IEKLILNNSH RVTIEMQPDP EKATQEEVEE KNILEKVKAA MTEEDLAELA 

       610        620        630        640        650        660 
RATEELKLKQ ETPDPPEALR CVPSLNLGDI PKEPTYVPTE VGDINGVKVL RHDLFTNDII 

       670        680        690        700        710        720 
YTEVVFDIGS LKHELLPLVP LFCQSLLEMG TKDLTFVQLN QLIGRKTGGI SVYPLTSSVR 

       730        740        750        760        770        780 
GKDEPCSKII VRGKSMAGRA DDLFNLMNCL LQEVQFTDQQ RFKQFVSQSR ARMENRLRGS 

       790        800        810        820        830        840 
GHGIAAARMD AMLNIAGWMS EQMGGLSYLE FLHTLEKKVD EDWEGISSSL EEIRRSLLAR 

       850        860        870        880        890        900 
NGCIVNMTAD GKSLTNVEKS VAKFLDLLPE NPSGGLVTWD GRLPLRNEAI VIPTQVNYVG 

       910        920        930        940        950        960 
KAGNIYSTGY ELDGSAYVIS KHISNTWLWD RVRVSGGAYG GFCDFDSHSG VFSYLSYRDP 

       970        980        990       1000       1010       1020 
NLLKTLDIYD GTGDFLRGLD VDQETLTKAI IGTIGDVDSY QLPDAKGYSS LLRHLLGVTD 

      1030       1040       1050       1060       1070       1080 
EERQRKREEI LTTSLKDFKD FAQAIDVVRD KGVAVAVASA EDIDAANNER SNFFEVKKAL 

« Hide

References

« Hide 'large scale' references
[1]"Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC clones."
Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S.
DNA Res. 7:217-221(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: cv. Columbia.
[2]The Arabidopsis Information Resource (TAIR)
Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: cv. Columbia.
[3]"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. expand/collapse author list , 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.
[4]"Isolation and identification of a novel mitochondrial metalloprotease (PreP) that degrades targeting presequences in plants."
Staahl A., Moberg P., Ytterberg J., Panfilov O., Brockenhuus Von Lowenhielm H., Nilsson F., Glaser E.
J. Biol. Chem. 277:41931-41939(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION.
[5]"Characterization of a novel zinc metalloprotease involved in degrading targeting peptides in mitochondria and chloroplasts."
Moberg P., Staahl A., Bhushan S., Wright S.J., Eriksson A., Bruce B.D., Glaser E.
Plant J. 36:616-628(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION, MUTAGENESIS OF HIS-162; GLU-165; HIS-166; GLU-240 AND GLU-245, SUBCELLULAR LOCATION.
[6]"Catalysis, subcellular localization, expression and evolution of the targeting peptides degrading protease, AtPreP2."
Bhushan S., Staahl A., Nilsson S., Lefebvre B., Seki M., Roth C., McWilliam D., Wright S.J., Liberles D.A., Shinozaki K., Bruce B.D., Boutry M., Glaser E.
Plant Cell Physiol. 46:985-996(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION, IDENTIFICATION BY MASS SPECTROMETRY, TISSUE SPECIFICITY, SUBCELLULAR LOCATION.
[7]"Two novel targeting peptide degrading proteases, PrePs, in mitochondria and chloroplasts, so similar and still different."
Staahl A., Nilsson S., Lundberg P., Bhushan S., Biverstaahl H., Moberg P., Morisset M., Vener A., Maeler L., Langel U., Glaser E.
J. Mol. Biol. 349:847-860(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: CLEAVAGE SPECIFICITY.
[8]"The closed structure of presequence protease PreP forms a unique 10,000 Angstroms3 chamber for proteolysis."
Johnson K.A., Bhushan S., Staahl A., Hallberg B.M., Frohn A., Glaser E., Eneqvist T.
EMBO J. 25:1977-1986(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 86-1080, MUTAGENESIS OF GLU-179; ASN-194; LYS-256; GLU-262; LYS-264; ALA-416; GLU-430; ASN-700; SER-767; GLN-895; ARG-933; GLY-937 AND TYR-939.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AP000419 Genomic DNA. Translation: BAB02957.1. Different initiation.
CP002686 Genomic DNA. Translation: AEE76201.1.
AY090240 mRNA. Translation: AAL90904.1.
AY091051 mRNA. Translation: AAM13872.1.
BT006362 mRNA. Translation: AAP21170.1.
BT002372 mRNA. Translation: AAN86205.1.
RefSeqNP_188548.2. NM_112804.4.
UniGeneAt.27915.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2FGEX-ray2.10A/B86-1080[»]
ProteinModelPortalQ9LJL3.
SMRQ9LJL3. Positions 100-1078.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActQ9LJL3. 4 interactions.
MINTMINT-7231907.

Protein family/group databases

MEROPSM16.012.

Proteomic databases

PaxDbQ9LJL3.
PRIDEQ9LJL3.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT3G19170.1; AT3G19170.1; AT3G19170. [Q9LJL3-1]
GeneID821451.
KEGGath:AT3G19170.

Organism-specific databases

GeneFarm2137. 225.
TAIRAT3G19170.

Phylogenomic databases

eggNOGCOG1026.
HOGENOMHOG000008829.
InParanoidQ9LJL3.
KOK06972.
OMAIGKWIYD.
PhylomeDBQ9LJL3.
ProtClustDBCLSN2690450.

Enzyme and pathway databases

BioCycARA:GQT-1641-MONOMER.
ARA:GQT-1642-MONOMER.

Gene expression databases

ArrayExpressQ9LJL3.
GenevestigatorQ9LJL3.

Family and domain databases

Gene3D3.30.830.10. 2 hits.
InterProIPR011249. Metalloenz_LuxS/M16.
IPR011237. Pept_M16_dom.
IPR011765. Pept_M16_N.
IPR007863. Peptidase_M16_C.
IPR013578. Peptidase_M16C_assoc.
[Graphical view]
PfamPF08367. M16C_assoc. 1 hit.
PF00675. Peptidase_M16. 1 hit.
PF05193. Peptidase_M16_C. 1 hit.
[Graphical view]
SUPFAMSSF63411. SSF63411. 4 hits.
ProtoNetSearch...

Other

EvolutionaryTraceQ9LJL3.
PROQ9LJL3.

Entry information

Entry namePREP1_ARATH
AccessionPrimary (citable) accession number: Q9LJL3
Secondary accession number(s): Q8RUN6
Entry history
Integrated into UniProtKB/Swiss-Prot: September 19, 2006
Last sequence update: September 19, 2006
Last modified: April 16, 2014
This is version 90 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Peptidase families

Classification of peptidase families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names