ID OOPDA_ARATH Reviewed; 791 AA.
AC Q94AM1; Q9LSL3;
DT 22-JAN-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 27-MAR-2024, entry version 145.
DE RecName: Full=Organellar oligopeptidase A, chloroplastic/mitochondrial {ECO:0000303|PubMed:24043784};
DE Short=AtOOP {ECO:0000303|PubMed:24043784};
DE EC=3.4.24.70 {ECO:0000269|PubMed:24043784};
DE AltName: Full=Thimet metalloendopeptidase 1 {ECO:0000303|PubMed:24004003};
DE AltName: Full=Zincin-like metalloproteases family protein 1 {ECO:0000303|PubMed:24004003};
DE Flags: Precursor;
GN Name=OOP {ECO:0000303|PubMed:24043784};
GN Synonyms=PRD1 {ECO:0000303|PubMed:24043784},
GN TOP1 {ECO:0000303|PubMed:24004003};
GN OrderedLocusNames=At5g65620 {ECO:0000312|Araport:AT5G65620};
GN ORFNames=K21L13.14 {ECO:0000312|EMBL:BAA98181.1};
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RA Kaneko T., Katoh T., Asamizu E., Sato S., Nakamura Y., Kotani H.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. XI.";
RL Submitted (APR-1999) to the EMBL/GenBank/DDBJ databases.
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, AND REVIEW OF MITOCHONDRIAL PROTEOLYTIC SYSTEM.
RX PubMed=22085399; DOI=10.1111/j.1399-3054.2011.01542.x;
RA Kwasniak M., Pogorzelec L., Migdal I., Smakowska E., Janska H.;
RT "Proteolytic system of plant mitochondria.";
RL Physiol. Plantarum 145:187-195(2012).
RN [5]
RP FUNCTION, SALICYLIC ACID-BINDING, SUBCELLULAR LOCATION, INDUCTION BY FLG22;
RP PATHOGEN INFECTION AND ELICITOR, DEVELOPMENTAL STAGE, DISRUPTION PHENOTYPE,
RP AND ACTIVITY REGULATION.
RX PubMed=24004003; DOI=10.1111/tpj.12320;
RA Moreau M., Westlake T., Zampogna G., Popescu G., Tian M., Noutsos C.,
RA Popescu S.;
RT "The Arabidopsis oligopeptidases TOP1 and TOP2 are salicylic acid targets
RT that modulate SA-mediated signaling and the immune response.";
RL Plant J. 76:603-614(2013).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 83-791 IN COMPLEX WITH SUBSTRATE,
RP ACTIVE SITE, FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION,
RP MUTAGENESIS OF ALA-226; THR-431; GLU-572; HIS-703 AND TYR-709, AND
RP DISRUPTION PHENOTYPE.
RX PubMed=24043784; DOI=10.1073/pnas.1307637110;
RA Kmiec B., Teixeira P.F., Berntsson R.P., Murcha M.W., Branca R.M.,
RA Radomiljac J.D., Regberg J., Svensson L.M., Bakali A., Langel U.,
RA Lehtioe J., Whelan J., Stenmark P., Glaser E.;
RT "Organellar oligopeptidase (OOP) provides a complementary pathway for
RT targeting peptide degradation in mitochondria and chloroplasts.";
RL Proc. Natl. Acad. Sci. U.S.A. 110:E3761-E3769(2013).
CC -!- FUNCTION: Oligopeptidase degrading short peptides from 8 to 23 amino
CC acid residues. Plays a role in the degradation of transit peptides and
CC of peptides derived from other proteolytic events. Does not exhibit a
CC strict cleavage pattern. Binds salicylic acid.
CC {ECO:0000269|PubMed:24004003, ECO:0000269|PubMed:24043784}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Hydrolysis of oligopeptides, with broad specificity. Gly or
CC Ala commonly occur as P1 or P1' residues, but more distant residues
CC are also important, as is shown by the fact that Z-Gly-Pro-Gly-|-Gly-
CC Pro-Ala is cleaved, but not Z-(Gly)(5).; EC=3.4.24.70;
CC Evidence={ECO:0000269|PubMed:24043784};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000305};
CC Note=Binds 1 zinc ion. {ECO:0000305};
CC -!- ACTIVITY REGULATION: Inhibited by salicylic acid.
CC {ECO:0000269|PubMed:24004003}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion matrix
CC {ECO:0000269|PubMed:24043784}. Plastid, chloroplast stroma
CC {ECO:0000269|PubMed:24004003, ECO:0000269|PubMed:24043784}.
CC -!- DEVELOPMENTAL STAGE: Down-regulated during senescence.
CC {ECO:0000269|PubMed:24004003}.
CC -!- INDUCTION: Not regulated by pathogen infection, elicitor treatment and
CC flg22, a 22-amino acid sequence of the conserved N-terminal part of
CC flagellin. {ECO:0000269|PubMed:24004003}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype and no effect on
CC germination; probably due to the presence of the presequence proteases
CC PREP1 and PREP2. {ECO:0000269|PubMed:24004003,
CC ECO:0000269|PubMed:24043784}.
CC -!- SIMILARITY: Belongs to the peptidase M3 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA98181.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AB026639; BAA98181.1; ALT_INIT; Genomic_DNA.
DR EMBL; CP002688; AED98078.1; -; Genomic_DNA.
DR EMBL; AY045936; AAK76610.1; -; mRNA.
DR EMBL; AY142682; AAN13220.1; -; mRNA.
DR RefSeq; NP_569013.1; NM_125960.3.
DR PDB; 4KA7; X-ray; 1.80 A; A=83-791.
DR PDB; 4KA8; X-ray; 1.90 A; A=83-791.
DR PDBsum; 4KA7; -.
DR PDBsum; 4KA8; -.
DR AlphaFoldDB; Q94AM1; -.
DR SMR; Q94AM1; -.
DR BioGRID; 21930; 31.
DR STRING; 3702.Q94AM1; -.
DR MEROPS; M03.A01; -.
DR iPTMnet; Q94AM1; -.
DR PaxDb; 3702-AT5G65620-1; -.
DR ProteomicsDB; 249360; -.
DR EnsemblPlants; AT5G65620.1; AT5G65620.1; AT5G65620.
DR GeneID; 836688; -.
DR Gramene; AT5G65620.1; AT5G65620.1; AT5G65620.
DR KEGG; ath:AT5G65620; -.
DR Araport; AT5G65620; -.
DR TAIR; AT5G65620; OOP.
DR eggNOG; KOG2089; Eukaryota.
DR HOGENOM; CLU_001805_4_1_1; -.
DR InParanoid; Q94AM1; -.
DR OMA; CHPDIRI; -.
DR PhylomeDB; Q94AM1; -.
DR BRENDA; 3.4.24.70; 399.
DR PRO; PR:Q94AM1; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q94AM1; baseline and differential.
DR Genevisible; Q94AM1; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0005759; C:mitochondrial matrix; IEA:UniProtKB-SubCell.
DR GO; GO:0009536; C:plastid; HDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004222; F:metalloendopeptidase activity; IEA:UniProtKB-EC.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR CDD; cd06456; M3A_DCP; 1.
DR Gene3D; 1.10.1370.40; -; 3.
DR InterPro; IPR034005; M3A_DCP.
DR InterPro; IPR045666; OpdA_N.
DR InterPro; IPR045090; Pept_M3A_M3B.
DR InterPro; IPR001567; Pept_M3A_M3B_dom.
DR PANTHER; PTHR11804:SF83; LD37516P; 1.
DR PANTHER; PTHR11804; PROTEASE M3 THIMET OLIGOPEPTIDASE-RELATED; 1.
DR Pfam; PF01432; Peptidase_M3; 1.
DR Pfam; PF19310; TOP_N; 1.
DR SUPFAM; SSF55486; Metalloproteases ('zincins'), catalytic domain; 1.
DR PROSITE; PS00142; ZINC_PROTEASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Chloroplast; Coiled coil; Hydrolase; Metal-binding;
KW Metalloprotease; Mitochondrion; Plastid; Protease; Reference proteome;
KW Transit peptide; Zinc.
FT TRANSIT 1..82
FT /note="Chloroplast and mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN 83..791
FT /note="Organellar oligopeptidase A,
FT chloroplastic/mitochondrial"
FT /id="PRO_0000425138"
FT COILED 118..138
FT /evidence="ECO:0000255"
FT COILED 239..259
FT /evidence="ECO:0000255"
FT ACT_SITE 572
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10095,
FT ECO:0000269|PubMed:24043784"
FT BINDING 571
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10095"
FT BINDING 575
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10095"
FT BINDING 601
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10095"
FT BINDING 703..709
FT /ligand="substrate"
FT MUTAGEN 226
FT /note="A->W: No effect on catalytic activity."
FT /evidence="ECO:0000269|PubMed:24043784"
FT MUTAGEN 431
FT /note="T->W: No effect on catalytic activity."
FT /evidence="ECO:0000269|PubMed:24043784"
FT MUTAGEN 572
FT /note="E->Q: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:24043784"
FT MUTAGEN 703
FT /note="H->F: Loss of activity."
FT /evidence="ECO:0000269|PubMed:24043784"
FT MUTAGEN 709
FT /note="Y->F: Loss of activity."
FT /evidence="ECO:0000269|PubMed:24043784"
FT HELIX 95..97
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 99..101
FT /evidence="ECO:0007829|PDB:4KA7"
FT TURN 109..111
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 114..116
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 117..138
FT /evidence="ECO:0007829|PDB:4KA7"
FT TURN 143..146
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 147..170
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 174..195
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 198..208
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 213..215
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 218..233
FT /evidence="ECO:0007829|PDB:4KA7"
FT TURN 234..237
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 240..270
FT /evidence="ECO:0007829|PDB:4KA7"
FT STRAND 273..275
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 278..281
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 286..298
FT /evidence="ECO:0007829|PDB:4KA7"
FT STRAND 306..309
FT /evidence="ECO:0007829|PDB:4KA7"
FT STRAND 311..313
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 317..326
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 330..341
FT /evidence="ECO:0007829|PDB:4KA7"
FT TURN 342..344
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 347..349
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 352..368
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 374..379
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 386..417
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 421..424
FT /evidence="ECO:0007829|PDB:4KA7"
FT TURN 428..430
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 431..443
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 447..450
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 451..453
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 456..471
FT /evidence="ECO:0007829|PDB:4KA7"
FT STRAND 474..477
FT /evidence="ECO:0007829|PDB:4KA7"
FT STRAND 490..495
FT /evidence="ECO:0007829|PDB:4KA7"
FT STRAND 501..510
FT /evidence="ECO:0007829|PDB:4KA7"
FT TURN 513..515
FT /evidence="ECO:0007829|PDB:4KA7"
FT STRAND 521..526
FT /evidence="ECO:0007829|PDB:4KA7"
FT STRAND 543..550
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 563..580
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 587..589
FT /evidence="ECO:0007829|PDB:4KA7"
FT TURN 591..594
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 597..599
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 602..608
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 609..612
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 614..620
FT /evidence="ECO:0007829|PDB:4KA7"
FT TURN 624..626
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 632..640
FT /evidence="ECO:0007829|PDB:4KA7"
FT TURN 641..645
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 646..663
FT /evidence="ECO:0007829|PDB:4KA7"
FT TURN 664..666
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 675..686
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 697..700
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 702..705
FT /evidence="ECO:0007829|PDB:4KA7"
FT TURN 708..714
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 715..733
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 738..749
FT /evidence="ECO:0007829|PDB:4KA7"
FT TURN 750..754
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 761..769
FT /evidence="ECO:0007829|PDB:4KA7"
FT HELIX 776..781
FT /evidence="ECO:0007829|PDB:4KA7"
SQ SEQUENCE 791 AA; 88757 MW; A9FA856C21864876 CRC64;
MLMATPTSRA SLNLLRRSPK PKYFSSSSCH FRPSTFRKSY PCPIWSSSFS FCLPPPRSTT
STSLSSSSFR PFSSPPSMSS AAAAAVESVV SDETLSSNPL LQDFDFPPFD SVDASHVRPG
IRALLQHLEA ELEELEKSVE PTWPKLVEPL EKIVDRLTVV WGMINHLKAV KDTPELRAAI
EDVQPEKVKF QLRLGQSKPI YNAFKAIRES PDWSSLSEAR QRLVEAQIKE AVLIGIALDD
EKREEFNKIE QELEKLSHKF SENVLDATKK FEKLITDKKE IEGLPPSALG LFAQAAVSKG
HENATAENGP WIITLDAPSY LPVMQHAKNR ALREEVYRAY LSRASSGDLD NTAIIDQILK
LRLEKAKLLG YNNYAEVSMA MKMATVEKAA ELLEKLRSAS WDAAVQDMED LKSFAKNQGA
AESDSMTHWD TTFWSERLRE SKYDINEEEL RPYFSLPKVM DGLFSLAKTL FGIDIEPADG
LAPVWNNDVR FYRVKDSSGN PIAYFYFDPY SRPSEKRGGA WMDEVVSRSR VMAQKGSSVR
LPVAHMVCNQ TPPVGDKPSL MTFREVETVF HEFGHALQHM LTKQDEGLVA GIRNIEWDAV
ELPSQFMENW CYHRDTLMSI AKHYETGETL PEEVYKKLLA ARTFRAGSFS LRQLKFASVD
LELHTKYVPG GPESIYDVDQ RVSVKTQVIP PLPEDRFLCS FSHIFAGGYA AGYYSYKWAE
VLSADAFSAF EDAGLDDIKA VKETGQRFRN TILALGGGKA PLKVFVEFRG REPSPEPLLR
HNGLLAASAS A
//
