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UniProtKB/Swiss-Prot entry Q9LJL3


[Entry info] [Name and origin] [References] [Comments] [Cross-references] [Keywords] [Features] [Sequence] [Tools]

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Entry information
Entry name PREP1_ARATH
Primary accession number Q9LJL3
Secondary accession number Q8RUN6
Integrated into Swiss-Prot on September 19, 2006
Sequence was last modified on September 19, 2006 (Sequence version 2)
Annotations were last modified on    September 2, 2008 (Entry version 43)
Name and origin of the protein
Protein name Presequence protease 1, chloroplastic/mitochondrial [Precursor]
Synonyms PreP 1
AtPreP1
EC 3.4.24.-
Zinc metalloprotease 1
AtZnMP1
Gene name
Name: PREP1
Synonyms: ZNMP1
OrderedLocusNames: At3g19170
ORFNames: MVI11.6, MVI11.7, MVI11_8
From
Arabidopsis thaliana (Mouse-ear cress) [TaxID: 3702] 
Taxonomy Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
Protein existence 1: Evidence at protein level;
References
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
DOI=10.1093/dnares/7.3.217; PubMed=10907853 [NCBI, ExPASy, EBI, Israel, Japan]
Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S.;
"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.";
DNA Res. 7:217-221(2000).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
DOI=10.1126/science.1088305; PubMed=14593172 [NCBI, ExPASy, EBI, Israel, Japan]
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).
[3]
IDENTIFICATION BY MASS SPECTROMETRY, AND FUNCTION.
DOI=10.1074/jbc.M205500200; PubMed=12138166 [NCBI, ExPASy, EBI, Israel, Japan]
Staahl A., Moberg P., Ytterberg J., Panfilov O., Brockenhuus Von Lowenhielm H., Nilsson F., Glaser E.;
"Isolation and identification of a novel mitochondrial metalloprotease (PreP) that degrades targeting presequences in plants.";
J. Biol. Chem. 277:41931-41939(2002).
[4]
CHARACTERIZATION, MUTAGENESIS OF HIS-162; GLU-165; HIS-166; GLU-240 AND GLU-245, AND SUBCELLULAR LOCATION.
DOI=10.1046/j.1365-313X.2003.01904.x; PubMed=14617063 [NCBI, ExPASy, EBI, Israel, Japan]
Moberg P., Staahl A., Bhushan S., Wright S.J., Eriksson A., Bruce B.D., Glaser E.;
"Characterization of a novel zinc metalloprotease involved in degrading targeting peptides in mitochondria and chloroplasts.";
Plant J. 36:616-628(2003).
[5]
CHARACTERIZATION, IDENTIFICATION BY MASS SPECTROMETRY, TISSUE SPECIFICITY, AND SUBCELLULAR LOCALIZATION.
DOI=10.1093/pcp/pci107; PubMed=15827031 [NCBI, ExPASy, EBI, Israel, Japan]
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.;
"Catalysis, subcellular localization, expression and evolution of the targeting peptides degrading protease, AtPreP2.";
Plant Cell Physiol. 46:985-996(2005).
[6]
CLEAVAGE SPECIFICITY.
DOI=10.1016/j.jmb.2005.04.023; PubMed=15893767 [NCBI, ExPASy, EBI, Israel, Japan]
Staahl A., Nilsson S., Lundberg P., Bhushan S., Biverstaahl H., Moberg P., Morisset M., Vener A., Maeler L., Langel U., Glaser E.;
"Two novel targeting peptide degrading proteases, PrePs, in mitochondria and chloroplasts, so similar and still different.";
J. Mol. Biol. 349:847-860(2005).
[7]
X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 86-1080, AND 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.
DOI=10.1038/sj.emboj.7601080; PubMed=16601675 [NCBI, ExPASy, EBI, Israel, Japan]
Johnson K.A., Bhushan S., Staahl A., Hallberg B.M., Frohn A., Glaser E., Eneqvist T.;
"The closed structure of presequence protease PreP forms a unique 10,000 Angstroms3 chamber for proteolysis.";
EMBO J. 25:1977-1986(2006).
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.
  • COFACTOR: Binds 1 zinc ion per subunit.
  • COFACTOR: Binds 2 Magnesium ions per subunit.
  • ENZYME REGULATION: Inactive in the absence of MgCl(2) and CaCl(2) and full activation at 10 mM concentrations of either ion. Completely inhibited by the metal chelator orthophenanthroline, but not affected by phenylmethylsulphonylfluoride (PMSF) or N-ethylmaleimide (NEM).
  • 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;
  • SUBUNIT: Homodimer.
  • SUBCELLULAR LOCATION: Plastid, chloroplast stroma. Mitochondrion matrix.
  • TISSUE SPECIFICITY: Expressed only in siliques and flowers.
  • 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.
  • SIMILARITY: Belongs to the peptidase M16 family. PreP subfamily [view classification].
Copyright
Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms. Distributed under the Creative Commons Attribution-NoDerivs License.
Cross-references
Sequence databases
EMBL
AP000419; BAB02957.1; ALT_INIT; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AY090240; AAL90904.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AY091051; AAM13872.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
BT006362; AAP21170.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
BT002372; AAN86205.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
RefSeq NP_188548.2; -.
UniGene At.27915
3D structure databases
PDB
2FGE; X-ray; 2.10 A; A/B=86-1080.[ExPASy / RCSB / EBI]
PDBsum 2FGE; -.
ModBase Q9LJL3.
Protein family/group databases
MEROPS M16.012; -.
Organism-specific databases
GeneFarm 2137; 225.
TAIR At3g19170; -.
Gene expression databases
GermOnline AT3G19170; Arabidopsis thaliana.
Ontologies
GO
GO:0005759; Cellular component: mitochondrial matrix (inferred from electronic annotation from UniProtKB-SubCell).
QuickGo view.
Family and domain databases
InterPro IPR011237; Pept_M16_core.
IPR011765; Pept_M16_N.
IPR001431; Pept_M16_Zn_BS.
IPR007863; Peptidase_M16_C.
IPR013578; Peptidase_M16C_assoc.
Graphical view of domain structure.
Gene3D G3DSA:3.30.830.10; Pept_M16_core; 1.
Pfam PF08367; M16C_assoc; 1.
PF00675; Peptidase_M16; 1.
PF05193; Peptidase_M16_C; 2.
Pfam graphical view of domain structure.
PROSITE PS00143; INSULINASE; FALSE_NEG.
BLOCKS Q9LJL3.
Proteomic databases
ProMEX Q9LJL3; -.
Genome annotation databases
GeneID 821451; -.
GenomeReviews BA000014_GR; AT3G19170.
KEGG ath:AT3G19170; -.
NMPDR fig|3702.1.peg.14130; -.
Other
ProtoNet Q9LJL3.
UniRef View cluster of proteins with at least 50% / 90% / 100% identity.
Keywords
3D-structure; Chloroplast; Coiled coil; Complete proteome; Hydrolase; Magnesium; Metal-binding; Metalloprotease; Mitochondrion; Plastid; Protease; Transit peptide; Zinc.
Features
SEVIEWER logo Feature table viewer FT aligner logo Feature aligner
KeyFrom    To Length Description FTId
TRANSIT   1     84  84     Chloroplast and mitochondrion (Potential). 
CHAIN   85   1080  996     Presequence protease 1, chloroplastic/mitochondrial. PRO_0000249938
COILED   571    612  42     Potential. 
ACT_SITE   165    165        Proton acceptor. 
METAL   162    162        Zinc; catalytic. 
METAL   166    166        Zinc; catalytic. 
METAL   262    262        Zinc; catalytic. 
MUTAGEN   162    162        H->L: Loss of activity. 
MUTAGEN   165    165        E->Q: Loss of activity. 
MUTAGEN   166    166        H->L: Loss of activity. 
MUTAGEN   179    179        E->Q: Decreased activity toward some substrates. 
MUTAGEN   194    194        N->A: Reduced activity. 
MUTAGEN   240    240        E->Q: Decreased activity toward some substrates. 
MUTAGEN   245    245        E->Q: No loss of activity. 
MUTAGEN   256    256        K->C: Inactive under oxidizing conditions and fully active under reducing conditions; when associated with C-937. 
MUTAGEN   262    262        E->Q: Loss of activity. 
MUTAGEN   264    264        K->C: Inactive under oxidizing conditions and fully active under reducing conditions; when associated with C-895. 
MUTAGEN   416    416        A->C: Little or no effect; when associated with C-700. 
MUTAGEN   430    430        E->C: Inactive under oxidizing conditions and fully active under reducing conditions; when associated with C-767. 
MUTAGEN   700    700        N->C: Little or no effect; when associated with C-416. 
MUTAGEN   767    767        S->C: Inactive under oxidizing conditions and fully active under reducing conditions; when associated with C-430. 
MUTAGEN   895    895        Q->C: Inactive under oxidizing conditions and fully active under reducing conditions; when associated with C-264. 
MUTAGEN   933    933        R->A,K: Loss of activity. 
MUTAGEN   937    937        G->C: Inactive under oxidizing conditions and fully active under reducing conditions; when associated with C-256. 
MUTAGEN   939    939        Y->F: Loss of activity. 
HELIX   101    104  4      
STRAND   107    115  9      
TURN   116    119  4      
STRAND   120    127  8      
TURN   128    130  3      
STRAND   133    138  6      
STRAND   142    151  10      
STRAND   155    158  4      
HELIX   160    167  8      
HELIX   180    187  8      
STRAND   190    193  4      
STRAND   199    210  12      
HELIX   211    226  16      
HELIX   229    231  3      
HELIX   235    240  6      
STRAND   243    245  3      
STRAND   254    256  3      
HELIX   258    266  9      
HELIX   270    282  13      
HELIX   287    289  3      
TURN   296    298  3      
HELIX   299    301  3      
HELIX   304    314  11      
HELIX   317    319  3      
STRAND   320    328  9      
HELIX   330    341  12      
HELIX   349    352  4      
STRAND   365    372  8      
STRAND   375    377  3      
HELIX   379    381  3      
STRAND   383    390  8      
HELIX   398    412  15      
HELIX   418    425  8      
STRAND   430    432  3      
STRAND   436    438  3      
STRAND   440    443  4      
STRAND   445    453  9      
HELIX   455    457  3      
HELIX   458    475  18      
HELIX   479    495  17      
HELIX   503    515  13      
TURN   516    518  3      
HELIX   523    525  3      
HELIX   528    541  14      
HELIX   543    554  12      
TURN   555    557  3      
STRAND   561    569  9      
HELIX   572    589  18      
HELIX   593    610  18      
HELIX   616    619  4      
HELIX   627    629  3      
STRAND   640    653  14      
STRAND   657    667  11      
TURN   673    675  3      
HELIX   676    678  3      
HELIX   679    688  10      
STRAND   692    694  3      
HELIX   696    706  11      
STRAND   707    719  13      
STRAND   722    736  15      
HELIX   737    739  3      
HELIX   740    753  14      
HELIX   759    779  21      
HELIX   781    791  11      
HELIX   795    804  10      
HELIX   806    821  16      
HELIX   823    837  15      
STRAND   844    849  6      
HELIX   851    866  16      
STRAND   888    891  4      
STRAND   895    904  10      
HELIX   905    908  4      
HELIX   915    925  11      
HELIX   927    931  5      
TURN   932    936  5      
STRAND   939    946  8      
TURN   947    950  4      
STRAND   951    960  10      
HELIX   963    970  8      
HELIX   972    977  6      
HELIX   983    997  15      
HELIX   1003   1015  13      
HELIX   1020   1031  12      
HELIX   1035   1051  17      
STRAND   1053   1058  6      
HELIX   1060   1069  10      
TURN   1070   1072  3      
STRAND   1074   1077  4      
Sequence information
Length: 1080 AA [This is the length of the unprocessed precursor] Molecular weight: 121015 Da [This is the MW of the unprocessed precursor] CRC64: 9FD259970195B9FC [This is a checksum on the sequence]
        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 

Q9LJL3 in FASTA format

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