SPP_ARATH
ID SPP_ARATH Reviewed; 1265 AA.
AC Q9FIH8; O48870;
DT 16-MAR-2016, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 125.
DE RecName: Full=Stromal processing peptidase, chloroplastic {ECO:0000305};
DE EC=3.4.24.- {ECO:0000250|UniProtKB:Q40983};
DE AltName: Full=Chloroplast processing enzyme {ECO:0000312|EMBL:AAC39482.1};
DE Flags: Precursor;
GN Name=SPP {ECO:0000305}; Synonyms=CPE {ECO:0000312|EMBL:AAC39482.1};
GN OrderedLocusNames=At5g42390 {ECO:0000312|Araport:AT5G42390};
GN ORFNames=MDH9.8 {ECO:0000312|EMBL:BAB10480.1};
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 [GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9636172; DOI=10.1073/pnas.95.13.7463;
RA Richter S., Lamppa G.K.;
RT "A chloroplast processing enzyme functions as the general stromal
RT processing peptidase.";
RL Proc. Natl. Acad. Sci. U.S.A. 95:7463-7468(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10048488; DOI=10.1093/dnares/5.6.379;
RA Asamizu E., Sato S., Kaneko T., Nakamura Y., Kotani H., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. VIII. Sequence
RT features of the regions of 1,081,958 bp covered by seventeen physically
RT assigned P1 and TAC clones.";
RL DNA Res. 5:379-391(1998).
RN [3]
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 [4]
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 [5]
RP FUNCTION.
RX PubMed=12795700; DOI=10.1046/j.1365-313x.2003.01772.x;
RA Zhong R., Wan J., Jin R., Lamppa G.;
RT "A pea antisense gene for the chloroplast stromal processing peptidase
RT yields seedling lethals in Arabidopsis: survivors show defective GFP import
RT in vivo.";
RL Plant J. 34:802-812(2003).
RN [6]
RP REVIEW.
RX DOI=10.1111/j.1399-3054.2005.00476.x;
RA Richter S., Zhong R., Lamppa G.K.;
RT "Function of the stromal processing peptidase in the chloroplast import
RT pathway.";
RL Physiol. Plantarum 4:362-368(2006).
RN [7]
RP DISRUPTION PHENOTYPE.
RX PubMed=21857988; DOI=10.1371/journal.pone.0023039;
RA Troesch R., Jarvis P.;
RT "The stromal processing peptidase of chloroplasts is essential in
RT Arabidopsis, with knockout mutations causing embryo arrest after the 16-
RT cell stage.";
RL PLoS ONE 6:E23039-E23039(2011).
RN [8]
RP REVIEW.
RX PubMed=22495024; DOI=10.1016/j.bbamcr.2012.03.012;
RA Teixeira P.F., Glaser E.;
RT "Processing peptidases in mitochondria and chloroplasts.";
RL Biochim. Biophys. Acta 1833:360-370(2013).
CC -!- FUNCTION: Cleaves presequences (transit peptides) from chloroplastic
CC protein precursors (PubMed:12795700). Initially recognizes a precursor
CC by binding to the C-terminus of its transit peptide and then removes
CC the transit peptide in a single endoproteolytic step. In a next step,
CC pursues the cleavage of transit peptide to a subfragment form (By
CC similarity). {ECO:0000250|UniProtKB:Q40983,
CC ECO:0000269|PubMed:12795700}.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000250|UniProtKB:Q40983};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000250|UniProtKB:Q40983};
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma
CC {ECO:0000250|UniProtKB:Q40983}.
CC -!- DISRUPTION PHENOTYPE: Embryo lethality. {ECO:0000269|PubMed:21857988}.
CC -!- MISCELLANEOUS: RNAi plants were almost all seedling lethals. Surviving
CC plants exhibited slower shoot and root growth, and grossly aberrant
CC leaf morphology. They also displayed defects in chloroplast protein
CC import. {ECO:0000269|PubMed:12795700}.
CC -!- SIMILARITY: Belongs to the peptidase M16 family. {ECO:0000305}.
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DR EMBL; AF008444; AAC39482.1; -; Genomic_DNA.
DR EMBL; AB016888; BAB10480.1; -; Genomic_DNA.
DR EMBL; CP002688; AED94804.1; -; Genomic_DNA.
DR EMBL; BT000785; AAN31924.1; -; mRNA.
DR PIR; T03302; T03302.
DR RefSeq; NP_199054.1; NM_123604.3.
DR AlphaFoldDB; Q9FIH8; -.
DR SMR; Q9FIH8; -.
DR IntAct; Q9FIH8; 2.
DR STRING; 3702.AT5G42390.1; -.
DR MEROPS; M16.004; -.
DR PaxDb; Q9FIH8; -.
DR PRIDE; Q9FIH8; -.
DR ProteomicsDB; 228456; -.
DR EnsemblPlants; AT5G42390.1; AT5G42390.1; AT5G42390.
DR GeneID; 834245; -.
DR Gramene; AT5G42390.1; AT5G42390.1; AT5G42390.
DR KEGG; ath:AT5G42390; -.
DR Araport; AT5G42390; -.
DR TAIR; locus:2162336; AT5G42390.
DR eggNOG; KOG0959; Eukaryota.
DR HOGENOM; CLU_007907_0_0_1; -.
DR InParanoid; Q9FIH8; -.
DR OMA; QPIGKEE; -.
DR OrthoDB; 148438at2759; -.
DR PhylomeDB; Q9FIH8; -.
DR BRENDA; 3.4.21.102; 399.
DR PRO; PR:Q9FIH8; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9FIH8; baseline and differential.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0005739; C:mitochondrion; HDA:TAIR.
DR GO; GO:0009536; C:plastid; 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:0003729; F:mRNA binding; IDA:TAIR.
DR GO; GO:0009793; P:embryo development ending in seed dormancy; IMP:TAIR.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR InterPro; IPR011249; Metalloenz_LuxS/M16.
DR InterPro; IPR011765; Pept_M16_N.
DR InterPro; IPR007863; Peptidase_M16_C.
DR Pfam; PF00675; Peptidase_M16; 1.
DR Pfam; PF05193; Peptidase_M16_C; 2.
DR SUPFAM; SSF63411; SSF63411; 3.
PE 2: Evidence at transcript level;
KW Chloroplast; Hydrolase; Metal-binding; Metalloprotease; Plastid; Protease;
KW Reference proteome; Transit peptide; Zinc.
FT TRANSIT 1..143
FT /note="Chloroplast"
FT /evidence="ECO:0000303|PubMed:9636172, ECO:0000303|Ref.6"
FT CHAIN 144..1265
FT /note="Stromal processing peptidase, chloroplastic"
FT /id="PRO_0000435733"
FT ACT_SITE 243
FT /note="Proton acceptor"
FT /evidence="ECO:0000305"
FT ACT_SITE 314
FT /evidence="ECO:0000305"
FT BINDING 240
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000305"
FT BINDING 244
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000305"
FT BINDING 321
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000305"
FT CONFLICT 673
FT /note="P -> L (in Ref. 1; AAC39482)"
FT /evidence="ECO:0000305"
FT CONFLICT 1110
FT /note="N -> K (in Ref. 1; AAC39482)"
FT /evidence="ECO:0000305"
FT CONFLICT 1134
FT /note="S -> N (in Ref. 1; AAC39482)"
FT /evidence="ECO:0000305"
FT CONFLICT 1183
FT /note="P -> Q (in Ref. 1; AAC39482)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1265 AA; 140607 MW; 7B4814823D273A37 CRC64;
MASSSSSIFT GVKFSPILAP FNSGDSRRSR YLKDSRNKVR FNPSSPRLTP HRVRVEAPSL
IPYNGLWAAQ PNSHKGRLKR NIVSGKEATG ISLSQGRNFC LTCKRNQAGI RRALPSAFVD
RTAFSLSRSS LTSSLRKHSQ IVNATLGPDE PHAAGTAWPD GIVAERQDLD LLPPEIDSAE
LEAFLGCELP SHPKLHRGQL KNGLRYLILP NKVPPNRFEA HMEVHVGSID EEEDEQGIAH
MIEHVAFLGS KKREKLLGTG ARSNAYTDFH HTVFHIHSPT HTKDSEDDLF PSVLDALNEI
AFHPKFLSSR VEKERRAILS ELQMMNTIEY RVDCQLLQHL HSENKLGRRF PIGLEEQIKK
WDVDKIRKFH ERWYFPANAT LYIVGDIDNI PRIVHNIEAV FGKNGLDNES TPSSPSPGAF
GAMANFLVPK LPAGLGGTFS NEKTNTADQS KMIKRERHAI RPPVEHNWSL PGTSVDLKPP
QIFKHELLQN FAINMFCKIP VSKVQTFGDL RNVLMKRIFL SALHFRINTR YKSSNPPFTS
VELDHSDSGR EGCTVTTLTV TAEPQNWQNA VKVAVQEVRR LKEFGVTRGE LTRYMDALLK
DSEHLAAMID NVSSVDNLDF IMESDALSHT VMDQTQGHET LVAVAGTVTL EEVNTVGAKV
LEFISDFGRP TAPLPAAIVA CVPTKVHVDG VGESDFNISP DEIIESVKSG LLAPIEAEPE
LEVPKELISQ SQLKELTLQR NPCFVPIPGS GLTKLHDKET GITQLRLSNG IAVNYKKSTT
ESRAGVMRLI VGGGRAAETS DSKGAVVVGV RTLSEGGRVG DFSREQVELF CVNHLINCSL
ESTEEFIAME FRFTLRDNGM QAAFQLLHMV LERSVWLEDA FDRARQLYLS YFRSIPKSLE
RATAHKLMIA MLNGDERFVE PTPKSLQSLN LESVKDAVMS HFVGDNMEVS IVGDFSEEEI
ERCILDYLGT VKASHDSAKP PGSEPILFRQ PTAGLQFQQV FLKDTDERAC AYIAGPAPNR
WGFTVDGDDL FQSVSKLPVA HDGLLKSEEQ LLEGGDRELQ KKLRAHPLFF GVTMGLLAEI
INSRLFTTVR DSLGLTYDVS FELNLFDRLN LGWYVISVTS TPGKVYKAVD ACKSVLRGLH
SNQIAPRELD RAKRTLLMRH EAELKSNAYW LNLLAHLQAS SVPRKELSCI KELVSLYEAA
SIEDIYLAYN QLRVDEDSLY SCIGIAGAQA GEEITVLSEE EEPEDVFSGV VPVGRGSSMT
TRPTT
