SubmitCancel

Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.

Q9LJL3

- PREP1_ARATH

UniProt

Q9LJL3 - PREP1_ARATH

(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

Protein

Presequence protease 1, chloroplastic/mitochondrial

Gene
PREP1, ZNMP1, At3g19170, MVI11.6, MVI11.7, MVI11_8
Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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.1 Publication

Cofactori

Binds 1 zinc ion per subunit.
Binds 2 Magnesium ions per subunit.

Enzyme regulationi

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).

pH dependencei

Active from pH 4 to 10.

Temperature dependencei

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi162 – 1621Zinc; catalytic
Active sitei165 – 1651Proton acceptor
Metal bindingi166 – 1661Zinc; catalytic
Metal bindingi262 – 2621Zinc; catalytic

GO - Molecular functioni

  1. metal ion binding Source: UniProtKB-KW
  2. metalloendopeptidase activity Source: TAIR
  3. protein binding Source: IntAct

GO - Biological processi

  1. protein processing Source: TAIR
  2. response to cadmium ion Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Metalloprotease, Protease

Keywords - Ligandi

Magnesium, Metal-binding, Zinc

Enzyme and pathway databases

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

Protein family/group databases

MEROPSiM16.012.

Names & Taxonomyi

Protein namesi
Recommended name:
Presequence protease 1, chloroplastic/mitochondrial (EC:3.4.24.-)
Short name:
AtPreP1
Short name:
PreP 1
Alternative name(s):
Zinc metalloprotease 1
Short name:
AtZnMP1
Gene namesi
Name:PREP1
Synonyms:ZNMP1
Ordered Locus Names:At3g19170
ORF Names:MVI11.6, MVI11.7, MVI11_8
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548: Chromosome 3

Organism-specific databases

TAIRiAT3G19170.

Subcellular locationi

Plastidchloroplast stroma. Mitochondrion matrix 2 Publications

GO - Cellular componenti

  1. apoplast Source: TAIR
  2. chloroplast Source: TAIR
  3. chloroplast envelope Source: TAIR
  4. chloroplast stroma Source: TAIR
  5. mitochondrial matrix Source: UniProtKB-SubCell
  6. mitochondrion Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Mitochondrion, Plastid

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi162 – 1621H → L: Loss of activity. 1 Publication
Mutagenesisi165 – 1651E → Q: Loss of activity. 1 Publication
Mutagenesisi166 – 1661H → L: Loss of activity. 1 Publication
Mutagenesisi179 – 1791E → Q: Decreased activity toward some substrates. 1 Publication
Mutagenesisi194 – 1941N → A: Reduced activity. 1 Publication
Mutagenesisi240 – 2401E → Q: Decreased activity toward some substrates. 1 Publication
Mutagenesisi245 – 2451E → Q: No loss of activity. 1 Publication
Mutagenesisi256 – 2561K → C: Inactive under oxidizing conditions and fully active under reducing conditions; when associated with C-937. 1 Publication
Mutagenesisi262 – 2621E → Q: Loss of activity. 1 Publication
Mutagenesisi264 – 2641K → C: Inactive under oxidizing conditions and fully active under reducing conditions; when associated with C-895. 1 Publication
Mutagenesisi416 – 4161A → C: Little or no effect; when associated with C-700. 1 Publication
Mutagenesisi430 – 4301E → C: Inactive under oxidizing conditions and fully active under reducing conditions; when associated with C-767. 1 Publication
Mutagenesisi700 – 7001N → C: Little or no effect; when associated with C-416. 1 Publication
Mutagenesisi767 – 7671S → C: Inactive under oxidizing conditions and fully active under reducing conditions; when associated with C-430. 1 Publication
Mutagenesisi895 – 8951Q → C: Inactive under oxidizing conditions and fully active under reducing conditions; when associated with C-264. 1 Publication
Mutagenesisi933 – 9331R → A or K: Loss of activity. 1 Publication
Mutagenesisi937 – 9371G → C: Inactive under oxidizing conditions and fully active under reducing conditions; when associated with C-256. 1 Publication
Mutagenesisi939 – 9391Y → F: Loss of activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 8484Chloroplast and mitochondrion Reviewed predictionAdd
BLAST
Chaini85 – 1080996Presequence protease 1, chloroplastic/mitochondrialPRO_0000249938Add
BLAST

Proteomic databases

PaxDbiQ9LJL3.
PRIDEiQ9LJL3.

Expressioni

Tissue specificityi

Expressed only in siliques and flowers.1 Publication

Gene expression databases

ArrayExpressiQ9LJL3.
GenevestigatoriQ9LJL3.

Interactioni

Subunit structurei

Homodimer.

Binary interactionsi

WithEntry#Exp.IntActNotes
ATPBP176146EBI-7143359,EBI-7143406From a different organism.

Protein-protein interaction databases

IntActiQ9LJL3. 4 interactions.
MINTiMINT-7231907.

Structurei

Secondary structure

1
1080
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi101 – 1044
Beta strandi107 – 1159
Turni116 – 1194
Beta strandi120 – 1278
Turni128 – 1303
Beta strandi133 – 1386
Beta strandi142 – 15110
Beta strandi155 – 1584
Helixi160 – 1678
Helixi180 – 1878
Beta strandi190 – 1934
Beta strandi199 – 21012
Helixi211 – 22616
Helixi229 – 2313
Helixi235 – 2406
Beta strandi243 – 2453
Beta strandi254 – 2563
Helixi258 – 2669
Helixi270 – 28213
Helixi287 – 2893
Turni296 – 2983
Helixi299 – 3013
Helixi304 – 31411
Helixi317 – 3193
Beta strandi320 – 3289
Helixi330 – 34112
Helixi349 – 3524
Beta strandi365 – 3728
Beta strandi375 – 3773
Helixi379 – 3813
Beta strandi383 – 3908
Helixi398 – 41215
Helixi418 – 4258
Beta strandi430 – 4323
Beta strandi436 – 4383
Beta strandi440 – 4434
Beta strandi445 – 4539
Helixi455 – 4573
Helixi458 – 47518
Helixi479 – 49517
Helixi503 – 51513
Turni516 – 5183
Helixi523 – 5253
Helixi528 – 54114
Helixi543 – 55412
Turni555 – 5573
Beta strandi561 – 5699
Helixi572 – 58918
Helixi593 – 61018
Helixi616 – 6194
Helixi627 – 6293
Beta strandi640 – 65314
Beta strandi657 – 66711
Turni673 – 6753
Helixi676 – 6783
Helixi679 – 68810
Beta strandi692 – 6943
Helixi696 – 70611
Beta strandi707 – 71913
Beta strandi722 – 73615
Helixi737 – 7393
Helixi740 – 75314
Helixi759 – 77921
Helixi781 – 79111
Helixi795 – 80410
Helixi806 – 82116
Helixi823 – 83715
Beta strandi844 – 8496
Helixi851 – 86616
Beta strandi888 – 8914
Beta strandi895 – 90410
Helixi905 – 9084
Helixi915 – 92511
Helixi927 – 9315
Turni932 – 9365
Beta strandi939 – 9468
Turni947 – 9504
Beta strandi951 – 96010
Helixi963 – 9708
Helixi972 – 9776
Helixi983 – 99715
Helixi1003 – 101513
Helixi1020 – 103112
Helixi1035 – 105117
Beta strandi1053 – 10586
Helixi1060 – 106910
Turni1070 – 10723
Beta strandi1074 – 10774

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2FGEX-ray2.10A/B86-1080[»]
ProteinModelPortaliQ9LJL3.
SMRiQ9LJL3. Positions 100-1078.

Miscellaneous databases

EvolutionaryTraceiQ9LJL3.

Family & Domainsi

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili571 – 61242 Reviewed predictionAdd
BLAST

Sequence similaritiesi

Keywords - Domaini

Coiled coil, Transit peptide

Phylogenomic databases

eggNOGiCOG1026.
HOGENOMiHOG000008829.
InParanoidiQ9LJL3.
KOiK06972.
OMAiANNERSN.
PhylomeDBiQ9LJL3.

Family and domain databases

Gene3Di3.30.830.10. 2 hits.
InterProiIPR011249. Metalloenz_LuxS/M16.
IPR011237. Pept_M16_dom.
IPR011765. Pept_M16_N.
IPR007863. Peptidase_M16_C.
IPR013578. Peptidase_M16C_assoc.
[Graphical view]
PfamiPF08367. M16C_assoc. 1 hit.
PF00675. Peptidase_M16. 1 hit.
PF05193. Peptidase_M16_C. 1 hit.
[Graphical view]
SUPFAMiSSF63411. SSF63411. 4 hits.

Sequencei

Sequence statusi: Complete.

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

This entry describes 1 isoform i produced by alternative splicing. Align

Note: A number of isoforms are produced. According to EST sequences.

Isoform 1 (identifier: Q9LJL3-1) [UniParc]FASTAAdd to Basket

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.

« Hide

MLRTVSCLAS RSSSSLFFRF FRQFPRSYMS LTSSTAALRV PSRNLRRISS     50
PSVAGRRLLL RRGLRIPSAA VRSVNGQFSR LSVRAVATQP APLYPDVGQD 100
EAEKLGFEKV SEEFISECKS KAILFKHKKT GCEVMSVSNE DENKVFGVVF 150
RTPPKDSTGI PHILEHSVLC GSRKYPVKEP FVELLKGSLH TFLNAFTYPD 200
RTCYPVASTN TKDFYNLVDV YLDAVFFPKC VDDAHTFQQE GWHYELNDPS 250
EDISYKGVVF NEMKGVYSQP DNILGRIAQQ ALSPENTYGV DSGGDPKDIP 300
NLTFEEFKEF HRQYYHPSNA RIWFYGDDDP VHRLRVLSEY LDMFEASPSP 350
NSSKIKFQKL FSEPVRLVEK YPAGRDGDLK KKHMLCVNWL LSEKPLDLQT 400
QLALGFLDHL MLGTPASPLR KILLESGLGE ALVSSGLSDE LLQPQFGIGL 450
KGVSEENVQK VEELIMDTLK KLAEEGFDND AVEASMNTIE FSLRENNTGS 500
FPRGLSLMLQ SISKWIYDMD PFEPLKYTEP LKALKTRIAE EGSKAVFSPL 550
IEKLILNNSH RVTIEMQPDP EKATQEEVEE KNILEKVKAA MTEEDLAELA 600
RATEELKLKQ ETPDPPEALR CVPSLNLGDI PKEPTYVPTE VGDINGVKVL 650
RHDLFTNDII YTEVVFDIGS LKHELLPLVP LFCQSLLEMG TKDLTFVQLN 700
QLIGRKTGGI SVYPLTSSVR GKDEPCSKII VRGKSMAGRA DDLFNLMNCL 750
LQEVQFTDQQ RFKQFVSQSR ARMENRLRGS GHGIAAARMD AMLNIAGWMS 800
EQMGGLSYLE FLHTLEKKVD EDWEGISSSL EEIRRSLLAR NGCIVNMTAD 850
GKSLTNVEKS VAKFLDLLPE NPSGGLVTWD GRLPLRNEAI VIPTQVNYVG 900
KAGNIYSTGY ELDGSAYVIS KHISNTWLWD RVRVSGGAYG GFCDFDSHSG 950
VFSYLSYRDP NLLKTLDIYD GTGDFLRGLD VDQETLTKAI IGTIGDVDSY 1000
QLPDAKGYSS LLRHLLGVTD EERQRKREEI LTTSLKDFKD FAQAIDVVRD 1050
KGVAVAVASA EDIDAANNER SNFFEVKKAL 1080
Length:1,080
Mass (Da):121,015
Last modified:September 19, 2006 - v2
Checksum:i9FD259970195B9FC
GO

Sequence cautioni

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

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
RefSeqiNP_188548.2. NM_112804.4. [Q9LJL3-1]
UniGeneiAt.27915.

Genome annotation databases

EnsemblPlantsiAT3G19170.1; AT3G19170.1; AT3G19170. [Q9LJL3-1]
GeneIDi821451.
KEGGiath:AT3G19170.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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 .
RefSeqi NP_188548.2. NM_112804.4. [Q9LJL3-1 ]
UniGenei At.27915.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2FGE X-ray 2.10 A/B 86-1080 [» ]
ProteinModelPortali Q9LJL3.
SMRi Q9LJL3. Positions 100-1078.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

IntActi Q9LJL3. 4 interactions.
MINTi MINT-7231907.

Protein family/group databases

MEROPSi M16.012.

Proteomic databases

PaxDbi Q9LJL3.
PRIDEi Q9LJL3.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblPlantsi AT3G19170.1 ; AT3G19170.1 ; AT3G19170 . [Q9LJL3-1 ]
GeneIDi 821451.
KEGGi ath:AT3G19170.

Organism-specific databases

GeneFarmi 2137. 225.
TAIRi AT3G19170.

Phylogenomic databases

eggNOGi COG1026.
HOGENOMi HOG000008829.
InParanoidi Q9LJL3.
KOi K06972.
OMAi ANNERSN.
PhylomeDBi Q9LJL3.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTracei Q9LJL3.
PROi Q9LJL3.

Gene expression databases

ArrayExpressi Q9LJL3.
Genevestigatori Q9LJL3.

Family and domain databases

Gene3Di 3.30.830.10. 2 hits.
InterProi IPR011249. Metalloenz_LuxS/M16.
IPR011237. Pept_M16_dom.
IPR011765. Pept_M16_N.
IPR007863. Peptidase_M16_C.
IPR013578. Peptidase_M16C_assoc.
[Graphical view ]
Pfami PF08367. M16C_assoc. 1 hit.
PF00675. Peptidase_M16. 1 hit.
PF05193. Peptidase_M16_C. 1 hit.
[Graphical view ]
SUPFAMi SSF63411. SSF63411. 4 hits.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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.

Entry informationi

Entry nameiPREP1_ARATH
AccessioniPrimary (citable) accession number: Q9LJL3
Secondary accession number(s): Q8RUN6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 19, 2006
Last sequence update: September 19, 2006
Last modified: June 11, 2014
This is version 92 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

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.

Keywords - Technical termi

3D-structure, Complete proteome, 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

External Data

Dasty 3

Similar proteinsi