NIT2_YEAST
ID NIT2_YEAST Reviewed; 307 AA.
AC P47016; D6VW60; Q71SQ0;
DT 01-FEB-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1996, sequence version 1.
DT 03-AUG-2022, entry version 138.
DE RecName: Full=Deaminated glutathione amidase {ECO:0000303|PubMed:28373563};
DE Short=dGSH amidase {ECO:0000303|PubMed:28373563};
DE EC=3.5.1.128 {ECO:0000269|PubMed:28373563};
DE AltName: Full=Nitrilase homolog 1;
GN Name=NIT2; OrderedLocusNames=YJL126W; ORFNames=J0706;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=10959838; DOI=10.1016/s0960-9822(00)00621-7;
RA Pace H.C., Hodawadekar S.C., Draganescu A., Huang J., Bieganowski P.,
RA Pekarsky Y., Croce C.M., Brenner C.;
RT "Crystal structure of the worm NitFhit Rosetta stone protein reveals a Nit
RT tetramer binding two Fhit dimers.";
RL Curr. Biol. 10:907-917(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 96604 / S288c / FY1679;
RX PubMed=8948101;
RX DOI=10.1002/(sici)1097-0061(199611)12:14<1471::aid-yea30>3.0.co;2-4;
RA Cziepluch C., Kordes E., Pujol A., Jauniaux J.-C.;
RT "Sequencing analysis of a 40.2 kb fragment of yeast chromosome X reveals 19
RT open reading frames including URA2 (5' end), TRK1, PBS2, SPT10, GCD14,
RT RPE1, PHO86, NCA3, ASF1, CCT7, GZF3, two tRNA genes, three remnant delta
RT elements and a Ty4 transposon.";
RL Yeast 12:1471-1474(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8641269; DOI=10.1002/j.1460-2075.1996.tb00557.x;
RA Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C.,
RA Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D.,
RA Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J.,
RA Heumann K., Hilger F., Hollenberg C.P., Huang M.-E., Jacq C.,
RA Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E.,
RA Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T.,
RA Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B.,
RA Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R.,
RA Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N.,
RA To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H.,
RA von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.;
RT "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X.";
RL EMBO J. 15:2031-2049(1996).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=28373563; DOI=10.1073/pnas.1613736114;
RA Peracchi A., Veiga-da-Cunha M., Kuhara T., Ellens K.W., Paczia N.,
RA Stroobant V., Seliga A.K., Marlaire S., Jaisson S., Bommer G.T., Sun J.,
RA Huebner K., Linster C.L., Cooper A.J.L., Van Schaftingen E.;
RT "Nit1 is a metabolite repair enzyme that hydrolyzes deaminated
RT glutathione.";
RL Proc. Natl. Acad. Sci. U.S.A. 114:E3233-E3242(2017).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.91 ANGSTROMS) IN COMPLEXES WITH 2-OXOGLUTARATE AND
RP OXALOACETATE, ACTIVE SITE, SUBUNIT, MUTAGENESIS OF CYS-169, AND FUNCTION.
RX PubMed=23897470; DOI=10.1107/s0907444913009347;
RA Liu H., Gao Y., Zhang M., Qiu X., Cooper A.J., Niu L., Teng M.;
RT "Structures of enzyme-intermediate complexes of yeast Nit2: insights into
RT its catalytic mechanism and different substrate specificity compared with
RT mammalian Nit2.";
RL Acta Crystallogr. D 69:1470-1481(2013).
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:28373563). Possesses amidase activity toward deaminated
CC ophthalmate in vitro (PubMed:28373563). {ECO:0000269|PubMed:28373563}.
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:28373563};
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:28373563};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:17126;
CC Evidence={ECO:0000269|PubMed:28373563};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=45 uM for N-(4-oxoglutarate)-L-cysteinylglycine (at pH 8.5)
CC {ECO:0000269|PubMed:28373563};
CC Vmax=5.8 umol/min/mg enzyme with N-(4-oxoglutarate)-L-
CC cysteinylglycine as substrate (at pH 8.5)
CC {ECO:0000269|PubMed:28373563};
CC Note=kcat is 3.6 sec(-1) with N-(4-oxoglutarate)-L-cysteinylglycine
CC as substrate. {ECO:0000269|PubMed:28373563};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:23897470}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:Q8VDK1}.
CC Mitochondrion {ECO:0000250|UniProtKB:Q8VDK1}.
CC -!- SIMILARITY: Belongs to the carbon-nitrogen hydrolase superfamily.
CC NIT1/NIT2 family. {ECO:0000305}.
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DR EMBL; AF284571; AAF87100.1; -; Genomic_DNA.
DR EMBL; Z49401; CAA89421.1; -; Genomic_DNA.
DR EMBL; BK006943; DAA08676.1; -; Genomic_DNA.
DR PIR; S56907; S56907.
DR RefSeq; NP_012409.1; NM_001181559.1.
DR PDB; 4H5U; X-ray; 1.92 A; A/B/C/D=1-307.
DR PDB; 4HG3; X-ray; 1.93 A; A/B/C/D=1-307.
DR PDB; 4HG5; X-ray; 1.91 A; A/B/C/D=1-307.
DR PDB; 4HGD; X-ray; 2.04 A; A/B/C/D=1-307.
DR PDBsum; 4H5U; -.
DR PDBsum; 4HG3; -.
DR PDBsum; 4HG5; -.
DR PDBsum; 4HGD; -.
DR AlphaFoldDB; P47016; -.
DR SMR; P47016; -.
DR BioGRID; 33630; 40.
DR STRING; 4932.YJL126W; -.
DR MaxQB; P47016; -.
DR PaxDb; P47016; -.
DR PRIDE; P47016; -.
DR EnsemblFungi; YJL126W_mRNA; YJL126W; YJL126W.
DR GeneID; 853316; -.
DR KEGG; sce:YJL126W; -.
DR SGD; S000003662; NIT2.
DR VEuPathDB; FungiDB:YJL126W; -.
DR eggNOG; KOG0807; Eukaryota.
DR GeneTree; ENSGT00550000075099; -.
DR HOGENOM; CLU_030130_1_2_1; -.
DR InParanoid; P47016; -.
DR OMA; MTCYDVR; -.
DR BioCyc; YEAST:YJL126W-MON; -.
DR BRENDA; 3.5.1.128; 984.
DR PRO; PR:P47016; -.
DR Proteomes; UP000002311; Chromosome X.
DR RNAct; P47016; protein.
DR GO; GO:0005739; C:mitochondrion; IEA:UniProtKB-SubCell.
DR GO; GO:0050406; F:[acetyl-CoA carboxylase]-phosphatase activity; IEA:RHEA.
DR GO; GO:0110050; F:deaminated glutathione amidase activity; IDA:SGD.
DR GO; GO:0043605; P:cellular amide catabolic process; IDA:SGD.
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 InterPro; IPR001110; UPF0012_CS.
DR Pfam; PF00795; CN_hydrolase; 1.
DR SUPFAM; SSF56317; SSF56317; 1.
DR PROSITE; PS50263; CN_HYDROLASE; 1.
DR PROSITE; PS01227; UPF0012; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Hydrolase; Mitochondrion; Reference proteome.
FT CHAIN 1..307
FT /note="Deaminated glutathione amidase"
FT /id="PRO_0000213255"
FT DOMAIN 6..285
FT /note="CN hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00054"
FT ACT_SITE 45
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00054"
FT ACT_SITE 127
FT /note="Proton donor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00054"
FT ACT_SITE 169
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00054,
FT ECO:0000269|PubMed:23897470"
FT BINDING 173
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23897470"
FT BINDING 199
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:23897470"
FT MUTAGEN 169
FT /note="C->S: Abolishes enzyme activity."
FT /evidence="ECO:0000269|PubMed:23897470"
FT STRAND 5..13
FT /evidence="ECO:0007829|PDB:4HG5"
FT HELIX 19..35
FT /evidence="ECO:0007829|PDB:4HG5"
FT STRAND 39..42
FT /evidence="ECO:0007829|PDB:4HG5"
FT HELIX 54..61
FT /evidence="ECO:0007829|PDB:4HG5"
FT HELIX 64..82
FT /evidence="ECO:0007829|PDB:4HG5"
FT STRAND 87..94
FT /evidence="ECO:0007829|PDB:4HG5"
FT HELIX 98..102
FT /evidence="ECO:0007829|PDB:4HG5"
FT STRAND 108..115
FT /evidence="ECO:0007829|PDB:4HG5"
FT STRAND 121..126
FT /evidence="ECO:0007829|PDB:4HG5"
FT STRAND 132..134
FT /evidence="ECO:0007829|PDB:4HG5"
FT STRAND 140..142
FT /evidence="ECO:0007829|PDB:4HG5"
FT HELIX 143..145
FT /evidence="ECO:0007829|PDB:4HG5"
FT STRAND 157..159
FT /evidence="ECO:0007829|PDB:4HG5"
FT STRAND 162..166
FT /evidence="ECO:0007829|PDB:4HG5"
FT HELIX 171..173
FT /evidence="ECO:0007829|PDB:4HG5"
FT HELIX 175..184
FT /evidence="ECO:0007829|PDB:4HG5"
FT STRAND 187..190
FT /evidence="ECO:0007829|PDB:4HG5"
FT HELIX 197..215
FT /evidence="ECO:0007829|PDB:4HG5"
FT STRAND 218..221
FT /evidence="ECO:0007829|PDB:4HG5"
FT STRAND 223..227
FT /evidence="ECO:0007829|PDB:4HG5"
FT HELIX 233..238
FT /evidence="ECO:0007829|PDB:4HG5"
FT TURN 243..246
FT /evidence="ECO:0007829|PDB:4HG5"
FT STRAND 251..253
FT /evidence="ECO:0007829|PDB:4HG5"
FT STRAND 257..259
FT /evidence="ECO:0007829|PDB:4HG5"
FT STRAND 265..268
FT /evidence="ECO:0007829|PDB:4HG5"
FT STRAND 277..284
FT /evidence="ECO:0007829|PDB:4HG5"
FT HELIX 285..294
FT /evidence="ECO:0007829|PDB:4HG5"
FT HELIX 297..299
FT /evidence="ECO:0007829|PDB:4HG5"
FT TURN 303..305
FT /evidence="ECO:0007829|PDB:4HG5"
SQ SEQUENCE 307 AA; 34693 MW; 48787C43B10A828E CRC64;
MTSKLKRVAV AQLCSSADLT KNLKVVKELI SEAIQKKADV VFLPEASDYL SQNPLHSRYL
AQKSPKFIRQ LQSSITDLVR DNSRNIDVSI GVHLPPSEQD LLEGNDRVRN VLLYIDHEGK
ILQEYQKLHL FDVDVPNGPI LKESKSVQPG KAIPDIIESP LGKLGSAICY DIRFPEFSLK
LRSMGAEILC FPSAFTIKTG EAHWELLGRA RAVDTQCYVL MPGQVGMHDL SDPEWEKQSH
MSALEKSSRR ESWGHSMVID PWGKIIAHAD PSTVGPQLIL ADLDRELLQE IRNKMPLWNQ
RRDDLFH
