COPDA_ARATH
ID COPDA_ARATH Reviewed; 701 AA.
AC Q949P2; Q9LXA6;
DT 22-JAN-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 144.
DE RecName: Full=Probable cytosolic oligopeptidase A {ECO:0000303|PubMed:24043784};
DE EC=3.4.24.70;
DE AltName: Full=Thimet metalloendopeptidase 2 {ECO:0000303|PubMed:24004003};
DE AltName: Full=Zincin-like metalloproteases family protein 2;
GN Name=CYOP {ECO:0000303|PubMed:24043784};
GN Synonyms=TOP2 {ECO:0000303|PubMed:24004003};
GN OrderedLocusNames=At5g10540 {ECO:0000312|Araport:AT5G10540};
GN ORFNames=F12B17.110 {ECO:0000312|EMBL:CAB89389.1};
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;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(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 ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
RN [5]
RP FUNCTION, SALICYLIC ACID-BINDING, INDUCTION BY FLG22; PATHOGEN INFECTION
RP AND ELICITOR, DEVELOPMENTAL STAGE, DISRUPTION PHENOTYPE, AND ACTIVITY
RP 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 FUNCTION, AND SUBCELLULAR LOCATION.
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).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS) IN COMPLEX WITH ZINC.
RX PubMed=24817709; DOI=10.1107/s2053230x14006128;
RA Wang R., Rajagopalan K., Sadre-Bazzaz K., Moreau M., Klessig D.F., Tong L.;
RT "Structure of the Arabidopsis thaliana TOP2 oligopeptidase.";
RL Acta Crystallogr. F 70:555-559(2014).
CC -!- FUNCTION: Oligopeptidase that may be involved in the degradation of
CC proteasome-generated peptides (By similarity). Binds salicylic acid.
CC {ECO:0000250, ECO:0000269|PubMed:24004003,
CC 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 -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000250};
CC Note=Binds 1 zinc ion. {ECO:0000250};
CC -!- ACTIVITY REGULATION: Inhibited by salicylic acid.
CC {ECO:0000269|PubMed:24004003}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm, cytosol {ECO:0000269|PubMed:24043784}.
CC -!- DEVELOPMENTAL STAGE: Up-regulated during senescence.
CC {ECO:0000269|PubMed:24004003}.
CC -!- INDUCTION: Up-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 effect on germination.
CC {ECO:0000269|PubMed:24004003}.
CC -!- SIMILARITY: Belongs to the peptidase M3 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB89389.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL353995; CAB89389.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED91561.1; -; Genomic_DNA.
DR EMBL; AY050978; AAK93655.1; -; mRNA.
DR EMBL; BT002369; AAN86202.1; -; mRNA.
DR PIR; T49985; T49985.
DR RefSeq; NP_568232.1; NM_121092.4.
DR PDB; 4PUT; X-ray; 3.00 A; A=1-701.
DR PDBsum; 4PUT; -.
DR AlphaFoldDB; Q949P2; -.
DR SMR; Q949P2; -.
DR BioGRID; 16197; 31.
DR STRING; 3702.AT5G10540.1; -.
DR MEROPS; M03.A02; -.
DR iPTMnet; Q949P2; -.
DR PaxDb; Q949P2; -.
DR PRIDE; Q949P2; -.
DR ProteomicsDB; 240949; -.
DR EnsemblPlants; AT5G10540.1; AT5G10540.1; AT5G10540.
DR GeneID; 830919; -.
DR Gramene; AT5G10540.1; AT5G10540.1; AT5G10540.
DR KEGG; ath:AT5G10540; -.
DR Araport; AT5G10540; -.
DR TAIR; locus:2142484; AT5G10540.
DR eggNOG; KOG2089; Eukaryota.
DR HOGENOM; CLU_001805_4_1_1; -.
DR InParanoid; Q949P2; -.
DR OMA; SYIAVMQ; -.
DR OrthoDB; 642479at2759; -.
DR PhylomeDB; Q949P2; -.
DR BRENDA; 3.4.24.70; 399.
DR PRO; PR:Q949P2; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q949P2; baseline and differential.
DR Genevisible; Q949P2; AT.
DR GO; GO:0048046; C:apoplast; HDA:TAIR.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005886; C:plasma membrane; HDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004222; F:metalloendopeptidase activity; IBA:GO_Central.
DR GO; GO:0006518; P:peptide metabolic process; IBA:GO_Central.
DR GO; GO:0006508; P:proteolysis; IBA:GO_Central.
DR CDD; cd06456; M3A_DCP; 1.
DR Gene3D; 1.10.1370.10; -; 1.
DR Gene3D; 1.20.1050.40; -; 1.
DR Gene3D; 3.40.390.10; -; 1.
DR InterPro; IPR034005; M3A_DCP.
DR InterPro; IPR024079; MetalloPept_cat_dom_sf.
DR InterPro; IPR024077; Neurolysin/TOP_dom2.
DR InterPro; IPR024080; Neurolysin/TOP_N.
DR InterPro; IPR045666; OpdA_N.
DR InterPro; IPR045090; Pept_M3A_M3B.
DR InterPro; IPR001567; Pept_M3A_M3B_dom.
DR PANTHER; PTHR11804; PTHR11804; 1.
DR Pfam; PF01432; Peptidase_M3; 1.
DR Pfam; PF19310; TOP_N; 1.
DR PROSITE; PS00142; ZINC_PROTEASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Coiled coil; Cytoplasm; Hydrolase;
KW Metal-binding; Metalloprotease; Protease; Reference proteome; Zinc.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CHAIN 2..701
FT /note="Probable cytosolic oligopeptidase A"
FT /id="PRO_0000425139"
FT COILED 148..194
FT /evidence="ECO:0000255"
FT ACT_SITE 484
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10095"
FT BINDING 483
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10095,
FT ECO:0000269|PubMed:24817709, ECO:0007744|PDB:4PUT"
FT BINDING 487
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10095,
FT ECO:0000269|PubMed:24817709, ECO:0007744|PDB:4PUT"
FT BINDING 513
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:24817709,
FT ECO:0007744|PDB:4PUT"
FT BINDING 615..621
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT MOD_RES 2
FT /note="N-acetylalanine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT HELIX 7..9
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 11..13
FT /evidence="ECO:0007829|PDB:4PUT"
FT TURN 21..23
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 26..50
FT /evidence="ECO:0007829|PDB:4PUT"
FT TURN 55..58
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 59..82
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 86..107
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 110..121
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 123..127
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 130..145
FT /evidence="ECO:0007829|PDB:4PUT"
FT TURN 146..149
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 152..181
FT /evidence="ECO:0007829|PDB:4PUT"
FT STRAND 184..187
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 190..193
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 198..210
FT /evidence="ECO:0007829|PDB:4PUT"
FT TURN 218..220
FT /evidence="ECO:0007829|PDB:4PUT"
FT STRAND 223..228
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 229..238
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 242..252
FT /evidence="ECO:0007829|PDB:4PUT"
FT TURN 253..256
FT /evidence="ECO:0007829|PDB:4PUT"
FT STRAND 257..259
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 264..280
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 286..291
FT /evidence="ECO:0007829|PDB:4PUT"
FT STRAND 294..296
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 298..329
FT /evidence="ECO:0007829|PDB:4PUT"
FT TURN 333..336
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 340..354
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 359..361
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 363..365
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 368..383
FT /evidence="ECO:0007829|PDB:4PUT"
FT STRAND 386..389
FT /evidence="ECO:0007829|PDB:4PUT"
FT STRAND 402..407
FT /evidence="ECO:0007829|PDB:4PUT"
FT STRAND 413..422
FT /evidence="ECO:0007829|PDB:4PUT"
FT TURN 425..427
FT /evidence="ECO:0007829|PDB:4PUT"
FT STRAND 433..438
FT /evidence="ECO:0007829|PDB:4PUT"
FT STRAND 450..452
FT /evidence="ECO:0007829|PDB:4PUT"
FT STRAND 455..462
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 475..492
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 499..501
FT /evidence="ECO:0007829|PDB:4PUT"
FT TURN 503..506
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 509..512
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 514..520
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 521..523
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 526..532
FT /evidence="ECO:0007829|PDB:4PUT"
FT TURN 536..538
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 544..555
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 558..577
FT /evidence="ECO:0007829|PDB:4PUT"
FT STRAND 583..585
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 587..598
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 610..612
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 614..617
FT /evidence="ECO:0007829|PDB:4PUT"
FT TURN 622..626
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 627..645
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 650..661
FT /evidence="ECO:0007829|PDB:4PUT"
FT TURN 662..666
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 673..681
FT /evidence="ECO:0007829|PDB:4PUT"
FT HELIX 688..693
FT /evidence="ECO:0007829|PDB:4PUT"
SQ SEQUENCE 701 AA; 79044 MW; 6181EA05A261B5F1 CRC64;
MASEDTLSSN PLLQNFDFPP FDSVDAHHVR PGIRALLQQL EAELEQLEKA VEPSWPKLVE
PLEKIIDRLS VVWGMINHLK AVKDTPELRA AIEEVQPEKV KFQLRLGQSK PIYNAFKAIR
ESPDWNSLSE ARQRLVEAQI KEAVLSGIAL EDDKREEFNK IEQELEKLSH KFSENVLDAT
KKFEKLITDK KEIEGLPPSA LGLFAQAAVS KGHETATADT GPWLITLDAP SYLPVMQHAK
NRALREEVYR AYLSRASSGD LDNTAIIDQI LKLRLEKAKL LGYRNYAEVS MATKMATVEK
ADELLEKLRS ASWDPAVQDI EDLKSFAKNQ GAAEADSLTH WDITFWSERL RESKYDINEE
ELRPYFSLPK VMDALFGLAK TLFGIDVVPA DGVAPVWNSD VRFYCVKDSS GNPTAYFYFD
PYSRPSEKRD GAWMDEVFSR SRVMAQKGSS VRLPVAQMVC NQTPPVGDKP SLMTFREVET
VFHEFGHALQ HMLTKEDEGL VAGIRNIEWD AVELPSQFME NWCYHRDTLM SIAKHYQTGE
TLPENVYKKL LAARTFRAGS LSLRQLKFAT VDLELHTKYM PGGAETIYEV DQRVSIKTQV
IPPLPEDRFL CSFSHIFAGG YAAGYYSYKW AEVLSADAFS AFEDAGLDDI KAVKETGQRF
RNTILALGGG KAPLKVFVEF RGREPSPEPL LRHNGLLAAS A
