ID   PREP2_ARATH             Reviewed;        1080 AA.
AC   Q8VY06; Q9FX91;
DT   19-SEP-2006, integrated into UniProtKB/Swiss-Prot.
DT   01-MAR-2002, sequence version 1.
DT   24-JAN-2024, entry version 132.
DE   RecName: Full=Presequence protease 2, chloroplastic/mitochondrial;
DE            Short=AtPreP2;
DE            Short=PreP 2;
DE            EC=3.4.24.-;
DE   AltName: Full=Zinc metalloprotease 2;
DE            Short=AtZnMP2;
DE   Flags: Precursor;
GN   Name=PREP2; Synonyms=ZNMP2; OrderedLocusNames=At1g49630;
GN   ORFNames=F14J22.13;
OS   Arabidopsis thaliana (Mouse-ear cress).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC   rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX   NCBI_TaxID=3702;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=11130712; DOI=10.1038/35048500;
RA   Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA   Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA   Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA   Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA   Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA   Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA   Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA   Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA   Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA   Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA   Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA   Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA   Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA   Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA   Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT   "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL   Nature 408:816-820(2000).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia;
RX   PubMed=27862469; DOI=10.1111/tpj.13415;
RA   Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA   Town C.D.;
RT   "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT   genome.";
RL   Plant J. 89:789-804(2017).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=14593172; DOI=10.1126/science.1088305;
RA   Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA   Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA   Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA   Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA   Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA   Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA   Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA   Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA   Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA   Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA   Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA   Ecker J.R.;
RT   "Empirical analysis of transcriptional activity in the Arabidopsis
RT   genome.";
RL   Science 302:842-846(2003).
RN   [4]
RP   IDENTIFICATION BY MASS SPECTROMETRY, AND FUNCTION.
RX   PubMed=12138166; DOI=10.1074/jbc.m205500200;
RA   Staahl A., Moberg P., Ytterberg J., Panfilov O.,
RA   Brockenhuus Von Lowenhielm H., Nilsson F., Glaser E.;
RT   "Isolation and identification of a novel mitochondrial metalloprotease
RT   (PreP) that degrades targeting presequences in plants.";
RL   J. Biol. Chem. 277:41931-41939(2002).
RN   [5]
RP   CHARACTERIZATION, IDENTIFICATION BY MASS SPECTROMETRY, TISSUE SPECIFICITY,
RP   AND SUBCELLULAR LOCATION.
RX   PubMed=15827031; DOI=10.1093/pcp/pci107;
RA   Bhushan S., Staahl A., Nilsson S., Lefebvre B., Seki M., Roth C.,
RA   McWilliam D., Wright S.J., Liberles D.A., Shinozaki K., Bruce B.D.,
RA   Boutry M., Glaser E.;
RT   "Catalysis, subcellular localization, expression and evolution of the
RT   targeting peptides degrading protease, AtPreP2.";
RL   Plant Cell Physiol. 46:985-996(2005).
RN   [6]
RP   CLEAVAGE SPECIFICITY.
RX   PubMed=15893767; DOI=10.1016/j.jmb.2005.04.023;
RA   Staahl A., Nilsson S., Lundberg P., Bhushan S., Biverstaahl H., Moberg P.,
RA   Morisset M., Vener A., Maeler L., Langel U., Glaser E.;
RT   "Two novel targeting peptide degrading proteases, PrePs, in mitochondria
RT   and chloroplasts, so similar and still different.";
RL   J. Mol. Biol. 349:847-860(2005).
CC   -!- FUNCTION: ATP-independent protease that degrades both mitochondrial and
CC       chloroplastic transit peptides after their cleavage. Also degrades
CC       other unstructured peptides. Specific for peptides in the range of 10
CC       to 65 residues. Shows a preference for cleavage after small polar
CC       residues and before basic residues, but without any positional
CC       preference. {ECO:0000269|PubMed:12138166}.
CC   -!- COFACTOR:
CC       Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC         Evidence={ECO:0000250|UniProtKB:Q9LJL3};
CC       Note=Binds 1 zinc ion per subunit. {ECO:0000250|UniProtKB:Q9LJL3};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000250|UniProtKB:Q9LJL3};
CC       Note=Binds 2 cations, such as magnesium or calcium, per subunit.
CC       {ECO:0000250|UniProtKB:Q9LJL3};
CC   -!- ACTIVITY REGULATION: Completely inhibited by the metal chelator
CC       orthophenanthroline.
CC   -!- SUBUNIT: Homodimer. {ECO:0000250|UniProtKB:Q9LJL3}.
CC   -!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma
CC       {ECO:0000269|PubMed:15827031}. Mitochondrion matrix
CC       {ECO:0000269|PubMed:15827031}.
CC   -!- TISSUE SPECIFICITY: Expressed in leaves, flowers and roots, but not
CC       detected in siliques and shoots. {ECO:0000269|PubMed:15827031}.
CC   -!- SIMILARITY: Belongs to the peptidase M16 family. PreP subfamily.
CC       {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAG13049.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; AC011807; AAG13049.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; CP002684; AEE32451.1; -; Genomic_DNA.
DR   EMBL; CP002684; AEE32452.1; -; Genomic_DNA.
DR   EMBL; CP002684; AEE32453.1; -; Genomic_DNA.
DR   EMBL; AY074305; AAL67002.1; -; mRNA.
DR   EMBL; BT004376; AAO42370.1; -; mRNA.
DR   PIR; A96533; A96533.
DR   RefSeq; NP_175386.2; NM_103851.3.
DR   RefSeq; NP_850961.1; NM_180630.2.
DR   RefSeq; NP_850962.1; NM_180631.2.
DR   AlphaFoldDB; Q8VY06; -.
DR   SMR; Q8VY06; -.
DR   BioGRID; 26612; 15.
DR   STRING; 3702.Q8VY06; -.
DR   MEROPS; M16.018; -.
DR   MetOSite; Q8VY06; -.
DR   PaxDb; 3702-AT1G49630-1; -.
DR   ProteomicsDB; 236597; -.
DR   EnsemblPlants; AT1G49630.1; AT1G49630.1; AT1G49630.
DR   EnsemblPlants; AT1G49630.2; AT1G49630.2; AT1G49630.
DR   EnsemblPlants; AT1G49630.3; AT1G49630.3; AT1G49630.
DR   GeneID; 841387; -.
DR   Gramene; AT1G49630.1; AT1G49630.1; AT1G49630.
DR   Gramene; AT1G49630.2; AT1G49630.2; AT1G49630.
DR   Gramene; AT1G49630.3; AT1G49630.3; AT1G49630.
DR   KEGG; ath:AT1G49630; -.
DR   Araport; AT1G49630; -.
DR   TAIR; AT1G49630; PREP2.
DR   eggNOG; KOG2019; Eukaryota.
DR   HOGENOM; CLU_009165_1_0_1; -.
DR   InParanoid; Q8VY06; -.
DR   OMA; FPFQVHY; -.
DR   OrthoDB; 5477696at2759; -.
DR   PhylomeDB; Q8VY06; -.
DR   PRO; PR:Q8VY06; -.
DR   Proteomes; UP000006548; Chromosome 1.
DR   ExpressionAtlas; Q8VY06; baseline and differential.
DR   GO; GO:0009507; C:chloroplast; IDA:TAIR.
DR   GO; GO:0009570; C:chloroplast stroma; IEA:UniProtKB-SubCell.
DR   GO; GO:0005759; C:mitochondrial matrix; IEA:UniProtKB-SubCell.
DR   GO; GO:0005739; C:mitochondrion; IDA:TAIR.
DR   GO; GO:0005634; C:nucleus; HDA:TAIR.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0008237; F:metallopeptidase activity; IEA:UniProtKB-KW.
DR   GO; GO:0016485; P:protein processing; IDA:TAIR.
DR   Gene3D; 3.30.830.10; Metalloenzyme, LuxS/M16 peptidase-like; 4.
DR   InterPro; IPR011249; Metalloenz_LuxS/M16.
DR   InterPro; IPR011765; Pept_M16_N.
DR   InterPro; IPR007863; Peptidase_M16_C.
DR   InterPro; IPR013578; Peptidase_M16C_assoc.
DR   PANTHER; PTHR43016; PRESEQUENCE PROTEASE; 1.
DR   PANTHER; PTHR43016:SF13; PRESEQUENCE PROTEASE, MITOCHONDRIAL; 1.
DR   Pfam; PF08367; M16C_assoc; 1.
DR   Pfam; PF00675; Peptidase_M16; 1.
DR   Pfam; PF05193; Peptidase_M16_C; 1.
DR   SMART; SM01264; M16C_associated; 1.
DR   SUPFAM; SSF63411; LuxS/MPP-like metallohydrolase; 4.
DR   Genevisible; Q8VY06; AT.
PE   1: Evidence at protein level;
KW   Chloroplast; Hydrolase; Magnesium; Metal-binding; Metalloprotease;
KW   Mitochondrion; Plastid; Protease; Reference proteome; Transit peptide;
KW   Zinc.
FT   TRANSIT         1..84
FT                   /note="Chloroplast and mitochondrion"
FT                   /evidence="ECO:0000255"
FT   CHAIN           85..1080
FT                   /note="Presequence protease 2, chloroplastic/mitochondrial"
FT                   /id="PRO_0000249939"
FT   ACT_SITE        164
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000250|UniProtKB:Q9LJL3"
FT   ACT_SITE        239
FT                   /evidence="ECO:0000250|UniProtKB:Q9LJL3"
FT   BINDING         161
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250|UniProtKB:Q9LJL3"
FT   BINDING         165
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250|UniProtKB:Q9LJL3"
FT   BINDING         261
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250|UniProtKB:Q9LJL3"
FT   BINDING         704
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000250|UniProtKB:Q9LJL3"
SQ   SEQUENCE   1080 AA;  121131 MW;  23425D0E7376E39E CRC64;
     MLRSLTCSST ITSTSLFFRS FRQLPRSYLS PSSSTTVVGA SGRNIRRLST LEAAGRRLFL
     RRGLKLLSAA SRGLNGQFSR LSIRAVATQS APSSYPGQDE AEKLGFEKVS EEFISECKSK
     AVLFKHKKTG CEVMSVSNDD ENKVFGIVFR TPPKDSTGIP HILEHSVLCG SRKYPMKEPF
     VELLKGSLHT FLNAFTYPDR TCYPVASTNK KDFYNLVDVY LDAVFFPKCV DDVHTFQQEG
     WHYELNDPSE DISYKGVVFN EMKGVYSQPD NILGRVTQQA LCPENTYGVD SGGDPKDIPK
     LTFEKFKEFH RQYYHPSNAR IWFYGDDDPV HRLRVLSEYL DMFDASPARD SSKVEPQKLF
     SRPRRIVEKY PAGEDGDLKK KHMVCLNWLL SDKPLDLQTQ LALGFLDHLM LGTPASPLRK
     ILLESGLGEA LVNSGMEDEL LQPQFSIGLK GVSDDNVQKV EELVMNTLRK LADEGFDTDA
     VEASMNTIEF SLRENNTGSS PRGLSLMLQS IAKWIYDMDP FEPLKYEEPL KSLKARIAEK
     GSKSVFSPLI EEYILNNPHC VTIEMQPDPE KASLEEAEEK SILEKVKASM TEEDLTELAR
     ATEELRLKQE TPDPPDALKC VPSLNLSDIP KEPIYVPTEV GDINGVKVLR NDLFTNNILY
     TEVVFDMGSV KHELLQLIPL FCQSLLEMGT QDLTFVQLNQ LIGRKTGGIS VYPLTSSVYG
     RDDPCSKIIV RGKSMVGRAE DLFNLMNCVL QEVRFTDQQR FKQFVSQSRA RMENRLRGSG
     QGIAAARMDA MLNVAGWMSE QMGGLSYLEF LHTLEQKVDQ DWEGISSSLE EIRRSFLSRN
     GCIVNMTADG KSLTNTEKYV GKFLDLLPEN PSGELVTWDA RLPLRNEAIV IPTQVNYVGK
     AGNIYSSGYK LDGSSYVISK HISNTWLWDR VRVSGGAYGG SCDFDSHSGV FSFLSYRDPN
     LLKTLDIYDG TGDFLRGLDV DEDTLTKAII GTIGDVDSYQ LPDAKGYTSL LRHLLNVTDE
     ERQIRREEIL STSLKDFKEF AEAIDSVSDK GVAVAVASQE DIDAANRERS NFFEVKKAAL
//