NILP2_ARATH
ID NILP2_ARATH Reviewed; 307 AA.
AC Q94JV5; Q9LE50;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 127.
DE RecName: Full=Deaminated glutathione amidase, chloroplastic/cytosolic {ECO:0000305};
DE Short=dGSH amidase {ECO:0000303|PubMed:30692244};
DE EC=3.5.1.128 {ECO:0000269|PubMed:30692244};
DE AltName: Full=Nitrilase-like protein 2 {ECO:0000303|PubMed:12435743};
DE AltName: Full=Protein nitrilase 1 homolog {ECO:0000303|PubMed:30692244};
DE Short=AtNit1 {ECO:0000303|PubMed:30692244};
DE Short=Protein Nit1 homolog {ECO:0000303|PubMed:30692244};
DE Flags: Precursor;
GN Name=NLP2 {ECO:0000303|PubMed:12435743};
GN Synonyms=NIT1 {ECO:0000303|PubMed:30692244};
GN OrderedLocusNames=At4g08790 {ECO:0000312|Araport:AT4G08790};
GN ORFNames=T32A17.100 {ECO:0000312|EMBL:CAB82115.1};
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=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
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 GENE FAMILY, AND NOMENCLATURE.
RX PubMed=12435743; DOI=10.1074/jbc.m205699200;
RA Piotrowski M., Janowitz T., Kneifel H.;
RT "Plant C-N hydrolases and the identification of a plant N-
RT carbamoylputrescine amidohydrolase involved in polyamine biosynthesis.";
RL J. Biol. Chem. 278:1708-1712(2003).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBCELLULAR
RP LOCATION (ISOFORMS 1 AND 2), ALTERNATIVE INITIATION, DISRUPTION PHENOTYPE,
RP AND MUTAGENESIS OF MET-29.
RX PubMed=30692244; DOI=10.1042/bcj20180931;
RA Niehaus T.D., Patterson J.A., Alexander D.C., Folz J.S., Pyc M.,
RA MacTavish B.S., Bruner S.D., Mullen R.T., Fiehn O., Hanson A.D.;
RT "The metabolite repair enzyme Nit1 is a dual-targeted amidase that disposes
RT of damaged glutathione in Arabidopsis.";
RL Biochem. J. 476:683-697(2019).
CC -!- FUNCTION: Catalyzes the hydrolysis of the amide bond in N-(4-
CC oxoglutarate)-L-cysteinylglycine (deaminated glutathione), a metabolite
CC repair reaction to dispose of the harmful deaminated glutathione
CC (PubMed:30692244). Possesses amidase activity toward deaminated
CC ophthalmate in vitro (PubMed:30692244). {ECO:0000269|PubMed:30692244}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N-(4-oxoglutaryl)-L-cysteinylglycine = 2-oxoglutarate +
CC L-cysteinylglycine; Xref=Rhea:RHEA:54532, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:16810, ChEBI:CHEBI:61694, ChEBI:CHEBI:138256;
CC EC=3.5.1.128; Evidence={ECO:0000269|PubMed:30692244};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:54533;
CC Evidence={ECO:0000269|PubMed:30692244};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N-(4-carboxy-4-oxobutanoyl)-L-ethylglycylglycine = 2-
CC oxoglutarate + N-(2-aminobutanoyl)glycine; Xref=Rhea:RHEA:17125,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:16810, ChEBI:CHEBI:144697,
CC ChEBI:CHEBI:144699; Evidence={ECO:0000269|PubMed:30692244};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:17126;
CC Evidence={ECO:0000269|PubMed:30692244};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=35 uM for N-(4-oxoglutarate)-L-cysteinylglycine
CC {ECO:0000269|PubMed:30692244};
CC KM=6.7 uM for ophthalmate {ECO:0000269|PubMed:30692244};
CC Vmax=7.9 umol/min/mg enzyme with N-(4-oxoglutarate)-L-
CC cysteinylglycine as substrate {ECO:0000269|PubMed:30692244};
CC Vmax=5.6 umol/min/mg enzyme with ophthalmate as substrate
CC {ECO:0000269|PubMed:30692244};
CC Note=kcat is 4.2 sec(-1) with N-(4-oxoglutarate)-L-cysteinylglycine
CC as substrate (PubMed:30692244). kcat is 3.0 sec(-1) with ophthalmate
CC as substrate (PubMed:30692244). {ECO:0000269|PubMed:30692244};
CC -!- SUBCELLULAR LOCATION: [Isoform 1]: Plastid, chloroplast
CC {ECO:0000269|PubMed:30692244}.
CC -!- SUBCELLULAR LOCATION: [Isoform 2]: Cytoplasm
CC {ECO:0000269|PubMed:30692244}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative initiation; Named isoforms=2;
CC Name=1 {ECO:0000305}; Synonyms=Full-length, FL
CC {ECO:0000303|PubMed:30692244};
CC IsoId=Q94JV5-1; Sequence=Displayed;
CC Name=2 {ECO:0000305}; Synonyms=Truncated, Tr
CC {ECO:0000303|PubMed:30692244};
CC IsoId=Q94JV5-2; Sequence=VSP_060389;
CC -!- DISRUPTION PHENOTYPE: No visible phenotype under normal growth
CC conditions, but the accumuluation of N-(4-oxoglutarate)-L-
CC cysteinylglycine (deaminated glutathione) in mutant plants is up to 70-
CC fold higher than in the wild type. {ECO:0000269|PubMed:30692244}.
CC -!- SIMILARITY: Belongs to the nitrilase superfamily. NIT1/NIT2 family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB78004.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB82115.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL161512; CAB78004.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161813; CAB82115.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE82678.1; -; Genomic_DNA.
DR EMBL; AF372904; AAK49620.1; -; mRNA.
DR EMBL; AY133544; AAM91374.1; -; mRNA.
DR PIR; D85088; D85088.
DR RefSeq; NP_567340.1; NM_116949.4. [Q94JV5-1]
DR AlphaFoldDB; Q94JV5; -.
DR SMR; Q94JV5; -.
DR BioGRID; 11748; 1.
DR IntAct; Q94JV5; 1.
DR STRING; 3702.AT4G08790.1; -.
DR iPTMnet; Q94JV5; -.
DR PaxDb; Q94JV5; -.
DR PRIDE; Q94JV5; -.
DR ProMEX; Q94JV5; -.
DR ProteomicsDB; 251171; -. [Q94JV5-1]
DR EnsemblPlants; AT4G08790.1; AT4G08790.1; AT4G08790. [Q94JV5-1]
DR GeneID; 826449; -.
DR Gramene; AT4G08790.1; AT4G08790.1; AT4G08790. [Q94JV5-1]
DR KEGG; ath:AT4G08790; -.
DR Araport; AT4G08790; -.
DR TAIR; locus:2138208; AT4G08790.
DR eggNOG; KOG0807; Eukaryota.
DR HOGENOM; CLU_030130_1_2_1; -.
DR InParanoid; Q94JV5; -.
DR OMA; MTCYDVR; -.
DR OrthoDB; 1154369at2759; -.
DR PhylomeDB; Q94JV5; -.
DR BioCyc; ARA:AT4G08790-MON; -.
DR BRENDA; 3.5.1.128; 399.
DR PRO; PR:Q94JV5; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q94JV5; baseline and differential.
DR Genevisible; Q94JV5; AT.
DR GO; GO:0009507; C:chloroplast; IDA:TAIR.
DR GO; GO:0005737; C:cytoplasm; IDA:TAIR.
DR GO; GO:0009536; C:plastid; HDA:TAIR.
DR GO; GO:0050406; F:[acetyl-CoA carboxylase]-phosphatase activity; IEA:RHEA.
DR GO; GO:0110050; F:deaminated glutathione amidase activity; IDA:TAIR.
DR GO; GO:0110051; P:metabolite repair; IDA:TAIR.
DR GO; GO:0006807; P:nitrogen compound metabolic process; IEA:InterPro.
DR CDD; cd07572; nit; 1.
DR Gene3D; 3.60.110.10; -; 1.
DR InterPro; IPR003010; C-N_Hydrolase.
DR InterPro; IPR036526; C-N_Hydrolase_sf.
DR InterPro; IPR045254; Nit1/2_C-N_Hydrolase.
DR Pfam; PF00795; CN_hydrolase; 1.
DR SUPFAM; SSF56317; SSF56317; 1.
DR PROSITE; PS50263; CN_HYDROLASE; 1.
PE 1: Evidence at protein level;
KW Alternative initiation; Chloroplast; Cytoplasm; Hydrolase; Plastid;
KW Reference proteome; Transit peptide.
FT TRANSIT 1..36
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 37..307
FT /note="Deaminated glutathione amidase,
FT chloroplastic/cytosolic"
FT /id="PRO_0000426705"
FT DOMAIN 37..286
FT /note="CN hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00054"
FT ACT_SITE 76
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00054"
FT ACT_SITE 147
FT /note="Proton donor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00054"
FT ACT_SITE 188
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00054"
FT VAR_SEQ 1..28
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000269|PubMed:30692244"
FT /id="VSP_060389"
FT MUTAGEN 29
FT /note="M->L: No cytoplasmic localization."
FT /evidence="ECO:0000269|PubMed:30692244"
SQ SEQUENCE 307 AA; 33971 MW; EFB45469A2779D81 CRC64;
MNAYSVSLDF TKPSLFTRIT LSSQIPLTMA TTVNKTVRVA AAQMTSVNDL MTNFATCSRL
VQEAALAGAK LICFPENFSF VGDKEGESVK IAEPLDGPVM ERYCSLARDS NIWLSLGGFQ
ERFDDTHLCN THVVIDDAGM IRDTYQKMHL FDVDVPGGSS YKESSFTVPG TKIVSVDSPV
GRLGLTVCYD LRFPKIYQQL RFEQKAQVLL VPSAFTKVTG EAHWEILLRA RAIETQCYVI
AAAQAGKHNE KRESYGDTLI IDPWGTVVGR LPDRVSTGIV VADIDFSLID SVRTKMPIDK
QRVSIDL
