DJ1D_ARATH
ID DJ1D_ARATH Reviewed; 388 AA.
AC Q9M8R4; Q9C5D5;
DT 06-MAR-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 25-MAY-2022, entry version 117.
DE RecName: Full=Protein DJ-1 homolog D;
DE Short=AtDJ1D;
DE AltName: Full=Lactoylglutathione lyase DJ1D;
DE EC=4.4.1.5;
GN Name=DJ1D; OrderedLocusNames=At3g02720; ORFNames=F13E7.34;
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=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(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 FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND MUTAGENESIS OF
RP GLU-19; GLU-94; CYS-120; HIS-121; GLU-212; GLU-287; CYS-313 AND HIS-314.
RX PubMed=23651081; DOI=10.1111/febs.12321;
RA Kwon K., Choi D., Hyun J.K., Jung H.S., Baek K., Park C.;
RT "Novel glyoxalases from Arabidopsis thaliana.";
RL FEBS J. 280:3328-3339(2013).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS), AND OXIDATION AT CYS-120 AND
RP CYS-313.
RX PubMed=22232184; DOI=10.1107/s1744309111050597;
RA Seo K.H., Zhuang N., Cha J.Y., Son D., Lee K.H.;
RT "Crystallization and preliminary X-ray data analysis of a DJ-1 homologue
RT from Arabidopsis thaliana (AtDJ-1D).";
RL Acta Crystallogr. F 68:101-104(2012).
CC -!- FUNCTION: Possesses glyoxalase I activity. Catalyzes the conversion of
CC hemimercaptal, formed from methylglyoxal and glutathione, to S-
CC lactoylglutathione. May be involved in oxidative stress response.
CC {ECO:0000269|PubMed:23651081}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(R)-S-lactoylglutathione = glutathione + methylglyoxal;
CC Xref=Rhea:RHEA:19069, ChEBI:CHEBI:17158, ChEBI:CHEBI:57474,
CC ChEBI:CHEBI:57925; EC=4.4.1.5;
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.1 mM for methylglyoxal {ECO:0000269|PubMed:23651081};
CC KM=0.27 mM for glutathione {ECO:0000269|PubMed:23651081};
CC Note=kcat is 1700 min(-1) with methylglyoxal as substrate. kcat is
CC 2200 min(-1) with glutathione as substrate.;
CC pH dependence:
CC Optimum pH is 6.8. {ECO:0000269|PubMed:23651081};
CC Temperature dependence:
CC Optimum temperature is 45 degrees Celsius.
CC {ECO:0000269|PubMed:23651081};
CC -!- SUBUNIT: Homotrimer. {ECO:0000305|PubMed:23651081}.
CC -!- PTM: Cys-120 and Cys-313 are oxidized to sulfinic acid.
CC {ECO:0000269|PubMed:22232184}.
CC -!- SIMILARITY: Belongs to the peptidase C56 family. {ECO:0000305}.
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DR EMBL; AC018363; AAF26988.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE73851.1; -; Genomic_DNA.
DR EMBL; AF360323; AAK26033.2; -; mRNA.
DR EMBL; BT000947; AAN41347.1; -; mRNA.
DR RefSeq; NP_186921.1; NM_111140.5.
DR PDB; 3UK7; X-ray; 2.05 A; A/B/C=1-388.
DR PDB; 4OFW; X-ray; 2.30 A; A/B/C/D/E/F=3-388.
DR PDB; 4OGG; X-ray; 1.60 A; A/B/C=3-388.
DR PDBsum; 3UK7; -.
DR PDBsum; 4OFW; -.
DR PDBsum; 4OGG; -.
DR AlphaFoldDB; Q9M8R4; -.
DR SMR; Q9M8R4; -.
DR STRING; 3702.AT3G02720.1; -.
DR MEROPS; C56.A01; -.
DR PaxDb; Q9M8R4; -.
DR PRIDE; Q9M8R4; -.
DR ProteomicsDB; 224062; -.
DR EnsemblPlants; AT3G02720.1; AT3G02720.1; AT3G02720.
DR GeneID; 820875; -.
DR Gramene; AT3G02720.1; AT3G02720.1; AT3G02720.
DR KEGG; ath:AT3G02720; -.
DR Araport; AT3G02720; -.
DR TAIR; locus:2075532; AT3G02720.
DR eggNOG; KOG2764; Eukaryota.
DR HOGENOM; CLU_000445_44_3_1; -.
DR InParanoid; Q9M8R4; -.
DR OMA; GRSCTAY; -.
DR OrthoDB; 699862at2759; -.
DR PhylomeDB; Q9M8R4; -.
DR PRO; PR:Q9M8R4; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9M8R4; baseline and differential.
DR Genevisible; Q9M8R4; AT.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0019172; F:glyoxalase III activity; IDA:TAIR.
DR GO; GO:0004462; F:lactoylglutathione lyase activity; IEA:UniProtKB-EC.
DR Gene3D; 3.40.50.880; -; 2.
DR InterPro; IPR006286; C56_PfpI.
DR InterPro; IPR029062; Class_I_gatase-like.
DR InterPro; IPR002818; DJ-1/PfpI.
DR PANTHER; PTHR42733; PTHR42733; 1.
DR Pfam; PF01965; DJ-1_PfpI; 2.
DR SUPFAM; SSF52317; SSF52317; 2.
DR TIGRFAMs; TIGR01382; PfpI; 2.
DR PROSITE; PS51276; PEPTIDASE_C56_PFPI; 2.
PE 1: Evidence at protein level;
KW 3D-structure; Lyase; Oxidation; Reference proteome; Repeat;
KW Stress response.
FT CHAIN 1..388
FT /note="Protein DJ-1 homolog D"
FT /id="PRO_0000421816"
FT DOMAIN 5..190
FT /note="PfpI endopeptidase 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00608"
FT DOMAIN 198..383
FT /note="PfpI endopeptidase 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00608"
FT ACT_SITE 120
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00608"
FT ACT_SITE 121
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00608"
FT ACT_SITE 313
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00608"
FT ACT_SITE 314
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00608"
FT MOD_RES 120
FT /note="Cysteine sulfenic acid (-SOH)"
FT /evidence="ECO:0000269|PubMed:22232184"
FT MOD_RES 313
FT /note="Cysteine sulfinic acid (-SO2H)"
FT /evidence="ECO:0000269|PubMed:22232184"
FT MUTAGEN 19
FT /note="E->A: Reduces catalytic activity 1.5-fold. Almost
FT abolishes catalytic activity; when associated with A-212."
FT /evidence="ECO:0000269|PubMed:23651081"
FT MUTAGEN 94
FT /note="E->A: Reduces catalytic activity 10-fold. Almost
FT abolishes catalytic activity; when associated with A-287."
FT /evidence="ECO:0000269|PubMed:23651081"
FT MUTAGEN 120
FT /note="C->A: Reduces catalytic activity 2-fold. Abolishes
FT catalytic activity; when associated with A-313."
FT /evidence="ECO:0000269|PubMed:23651081"
FT MUTAGEN 121
FT /note="H->A: Reduces catalytic activity 3-fold. Almost
FT abolishes catalytic activity; when associated with A-314."
FT /evidence="ECO:0000269|PubMed:23651081"
FT MUTAGEN 212
FT /note="E->A: Reduces catalytic activity 2-fold. Almost
FT abolishes catalytic activity; when associated with A-19."
FT /evidence="ECO:0000269|PubMed:23651081"
FT MUTAGEN 287
FT /note="E->A: Reduces catalytic activity 6-fold. Almost
FT abolishes catalytic activity; when associated with A-94."
FT /evidence="ECO:0000269|PubMed:23651081"
FT MUTAGEN 313
FT /note="C->A: Reduces catalytic activity 2-fold. Abolishes
FT catalytic activity; when associated with A-120."
FT /evidence="ECO:0000269|PubMed:23651081"
FT MUTAGEN 314
FT /note="H->A: Reduces catalytic activity 3-fold. Almost
FT abolishes catalytic activity; when associated with A-121."
FT /evidence="ECO:0000269|PubMed:23651081"
FT STRAND 6..10
FT /evidence="ECO:0007829|PDB:4OGG"
FT HELIX 17..29
FT /evidence="ECO:0007829|PDB:4OGG"
FT STRAND 33..37
FT /evidence="ECO:0007829|PDB:4OGG"
FT STRAND 49..53
FT /evidence="ECO:0007829|PDB:4OGG"
FT STRAND 56..59
FT /evidence="ECO:0007829|PDB:4OGG"
FT STRAND 61..64
FT /evidence="ECO:0007829|PDB:4OGG"
FT HELIX 74..76
FT /evidence="ECO:0007829|PDB:4OGG"
FT HELIX 79..81
FT /evidence="ECO:0007829|PDB:4OGG"
FT STRAND 83..87
FT /evidence="ECO:0007829|PDB:4OGG"
FT HELIX 92..96
FT /evidence="ECO:0007829|PDB:4OGG"
FT HELIX 100..111
FT /evidence="ECO:0007829|PDB:4OGG"
FT STRAND 116..118
FT /evidence="ECO:0007829|PDB:4OGG"
FT TURN 120..122
FT /evidence="ECO:0007829|PDB:3UK7"
FT HELIX 123..128
FT /evidence="ECO:0007829|PDB:4OGG"
FT HELIX 141..143
FT /evidence="ECO:0007829|PDB:4OGG"
FT HELIX 144..149
FT /evidence="ECO:0007829|PDB:4OGG"
FT STRAND 163..166
FT /evidence="ECO:0007829|PDB:4OGG"
FT STRAND 169..174
FT /evidence="ECO:0007829|PDB:4OGG"
FT HELIX 175..177
FT /evidence="ECO:0007829|PDB:4OGG"
FT HELIX 178..188
FT /evidence="ECO:0007829|PDB:4OGG"
FT STRAND 192..195
FT /evidence="ECO:0007829|PDB:4OGG"
FT STRAND 199..203
FT /evidence="ECO:0007829|PDB:4OGG"
FT HELIX 210..223
FT /evidence="ECO:0007829|PDB:4OGG"
FT STRAND 226..230
FT /evidence="ECO:0007829|PDB:4OGG"
FT STRAND 242..246
FT /evidence="ECO:0007829|PDB:4OGG"
FT STRAND 249..252
FT /evidence="ECO:0007829|PDB:4OGG"
FT STRAND 254..257
FT /evidence="ECO:0007829|PDB:4OGG"
FT TURN 267..269
FT /evidence="ECO:0007829|PDB:4OGG"
FT HELIX 272..274
FT /evidence="ECO:0007829|PDB:4OGG"
FT STRAND 276..280
FT /evidence="ECO:0007829|PDB:4OGG"
FT HELIX 285..289
FT /evidence="ECO:0007829|PDB:4OGG"
FT HELIX 293..304
FT /evidence="ECO:0007829|PDB:4OGG"
FT STRAND 309..311
FT /evidence="ECO:0007829|PDB:4OGG"
FT HELIX 313..315
FT /evidence="ECO:0007829|PDB:3UK7"
FT HELIX 316..322
FT /evidence="ECO:0007829|PDB:4OGG"
FT TURN 323..327
FT /evidence="ECO:0007829|PDB:4OGG"
FT HELIX 334..336
FT /evidence="ECO:0007829|PDB:4OGG"
FT HELIX 337..342
FT /evidence="ECO:0007829|PDB:4OGG"
FT STRAND 357..359
FT /evidence="ECO:0007829|PDB:4OGG"
FT STRAND 362..364
FT /evidence="ECO:0007829|PDB:4OGG"
FT HELIX 368..370
FT /evidence="ECO:0007829|PDB:4OGG"
FT HELIX 371..382
FT /evidence="ECO:0007829|PDB:4OGG"
FT STRAND 385..387
FT /evidence="ECO:0007829|PDB:4OGG"
SQ SEQUENCE 388 AA; 41646 MW; 0DC71FF2B605D0E6 CRC64;
MANSRTVLIL CGDYMEDYEV MVPFQALQAF GITVHTVCPG KKAGDSCPTA VHDFCGHQTY
FESRGHNFTL NATFDEVDLS KYDGLVIPGG RAPEYLALTA SVVELVKEFS RSGKPIASIC
HGQLILAAAD TVNGRKCTAY ATVGPSLVAA GAKWVEPITP DVCVVDGSLI TAATYEGHPE
FIQLFVKALG GKITGANKRI LFLCGDYMED YEVKVPFQSL QALGCQVDAV CPEKKAGDRC
PTAIHDFEGD QTYSEKPGHT FALTTNFDDL VSSSYDALVI PGGRAPEYLA LNEHVLNIVK
EFMNSEKPVA SICHGQQILA AAGVLKGRKC TAYPAVKLNV VLGGGTWLEP DPIDRCFTDG
NLVTGAAWPG HPEFVSQLMA LLGIQVSF
