NIT3_YEAST
ID NIT3_YEAST Reviewed; 291 AA.
AC P49954; D6VYY9; Q71SP9;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 1.
DT 03-AUG-2022, entry version 162.
DE RecName: Full=Omega-amidase NIT3 {ECO:0000303|PubMed:28373563};
DE EC=3.5.1.3 {ECO:0000269|PubMed:28373563};
DE AltName: Full=Nitrilase homolog 2;
GN Name=NIT3; OrderedLocusNames=YLR351C; ORFNames=L9638.5;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169871;
RA Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W.,
RA Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A.,
RA Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K.,
RA Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K., Koetter P., Louis E.J.,
RA Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S.,
RA Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D.,
RA Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M.,
RA Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P.,
RA Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M.,
RA Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K.,
RA Zollner A., Hani J., Hoheisel J.D.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
RL Nature 387:87-90(1997).
RN [3]
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 [4]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [5]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-34, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [6]
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 [7]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS), AND SUBUNIT.
RX PubMed=12833551; DOI=10.1002/prot.10417;
RA Kumaran D., Eswaramoorthy S., Gerchman S.E., Kycia H., Studier F.W.,
RA Swaminathan S.;
RT "Crystal structure of a putative CN hydrolase from yeast.";
RL Proteins 52:283-291(2003).
CC -!- FUNCTION: Possesses omega-amidase activity (PubMed:28373563). The role
CC of omega-amidase is to remove potentially toxic intermediates by
CC converting 2-oxoglutaramate and 2-oxosuccinamate to biologically useful
CC 2-oxoglutarate and oxaloacetate, respectively.
CC {ECO:0000269|PubMed:28373563}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a monoamide of a dicarboxylate + H2O = a dicarboxylate +
CC NH4(+); Xref=Rhea:RHEA:11716, ChEBI:CHEBI:15377, ChEBI:CHEBI:28938,
CC ChEBI:CHEBI:28965, ChEBI:CHEBI:77450; EC=3.5.1.3;
CC Evidence={ECO:0000269|PubMed:28373563};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.6 mM for 2-oxoglutaramate (at pH 8.5)
CC {ECO:0000269|PubMed:28373563};
CC Vmax=40.2 umol/min/mg enzyme with 2-oxoglutaramate as substrate (at
CC pH 8.5) {ECO:0000269|PubMed:28373563};
CC Note=kcat is 23.5 sec(-1) with 2-oxoglutaramate as substrate.
CC {ECO:0000269|PubMed:28373563};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:12833551}.
CC -!- MISCELLANEOUS: Present with 4510 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the carbon-nitrogen hydrolase superfamily.
CC NIT1/NIT2 family. {ECO:0000305}.
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DR EMBL; AF284572; AAF87101.1; -; Genomic_DNA.
DR EMBL; U19102; AAB67751.1; -; Genomic_DNA.
DR EMBL; BK006945; DAA09655.1; -; Genomic_DNA.
DR PIR; S51459; S51459.
DR RefSeq; NP_013455.1; NM_001182240.1.
DR PDB; 1F89; X-ray; 2.40 A; A/B=1-291.
DR PDBsum; 1F89; -.
DR AlphaFoldDB; P49954; -.
DR SMR; P49954; -.
DR BioGRID; 31613; 32.
DR DIP; DIP-4666N; -.
DR IntAct; P49954; 1.
DR STRING; 4932.YLR351C; -.
DR iPTMnet; P49954; -.
DR MaxQB; P49954; -.
DR PaxDb; P49954; -.
DR PRIDE; P49954; -.
DR EnsemblFungi; YLR351C_mRNA; YLR351C; YLR351C.
DR GeneID; 851065; -.
DR KEGG; sce:YLR351C; -.
DR SGD; S000004343; NIT3.
DR VEuPathDB; FungiDB:YLR351C; -.
DR eggNOG; KOG0806; Eukaryota.
DR GeneTree; ENSGT00550000074838; -.
DR HOGENOM; CLU_030130_1_0_1; -.
DR InParanoid; P49954; -.
DR OMA; GNTYRES; -.
DR BioCyc; YEAST:YLR351C-MON; -.
DR Reactome; R-SCE-6798695; Neutrophil degranulation.
DR EvolutionaryTrace; P49954; -.
DR PRO; PR:P49954; -.
DR Proteomes; UP000002311; Chromosome XII.
DR RNAct; P49954; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005739; C:mitochondrion; HDA:SGD.
DR GO; GO:0016811; F:hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides; IDA:SGD.
DR GO; GO:0050152; F:omega-amidase activity; IBA:GO_Central.
DR GO; GO:0006528; P:asparagine metabolic process; IBA:GO_Central.
DR GO; GO:0043605; P:cellular amide catabolic process; IDA:SGD.
DR GO; GO:0006541; P:glutamine metabolic process; IBA:GO_Central.
DR GO; GO:0006107; P:oxaloacetate metabolic process; IBA:GO_Central.
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; Hydrolase; Phosphoprotein; Reference proteome.
FT CHAIN 1..291
FT /note="Omega-amidase NIT3"
FT /id="PRO_0000213256"
FT DOMAIN 11..264
FT /note="CN hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00054"
FT ACT_SITE 53
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00054"
FT ACT_SITE 128
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 MOD_RES 34
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT STRAND 4..9
FT /evidence="ECO:0007829|PDB:1F89"
FT STRAND 11..17
FT /evidence="ECO:0007829|PDB:1F89"
FT HELIX 25..42
FT /evidence="ECO:0007829|PDB:1F89"
FT STRAND 46..50
FT /evidence="ECO:0007829|PDB:1F89"
FT TURN 53..56
FT /evidence="ECO:0007829|PDB:1F89"
FT HELIX 61..67
FT /evidence="ECO:0007829|PDB:1F89"
FT STRAND 73..75
FT /evidence="ECO:0007829|PDB:1F89"
FT HELIX 78..89
FT /evidence="ECO:0007829|PDB:1F89"
FT STRAND 93..95
FT /evidence="ECO:0007829|PDB:1F89"
FT STRAND 99..102
FT /evidence="ECO:0007829|PDB:1F89"
FT TURN 104..106
FT /evidence="ECO:0007829|PDB:1F89"
FT STRAND 109..116
FT /evidence="ECO:0007829|PDB:1F89"
FT STRAND 122..127
FT /evidence="ECO:0007829|PDB:1F89"
FT HELIX 143..146
FT /evidence="ECO:0007829|PDB:1F89"
FT STRAND 155..159
FT /evidence="ECO:0007829|PDB:1F89"
FT STRAND 162..166
FT /evidence="ECO:0007829|PDB:1F89"
FT HELIX 169..173
FT /evidence="ECO:0007829|PDB:1F89"
FT HELIX 175..183
FT /evidence="ECO:0007829|PDB:1F89"
FT STRAND 186..192
FT /evidence="ECO:0007829|PDB:1F89"
FT HELIX 199..215
FT /evidence="ECO:0007829|PDB:1F89"
FT STRAND 217..222
FT /evidence="ECO:0007829|PDB:1F89"
FT STRAND 230..232
FT /evidence="ECO:0007829|PDB:1F89"
FT STRAND 239..241
FT /evidence="ECO:0007829|PDB:1F89"
FT STRAND 247..250
FT /evidence="ECO:0007829|PDB:1F89"
FT STRAND 253..262
FT /evidence="ECO:0007829|PDB:1F89"
FT HELIX 264..273
FT /evidence="ECO:0007829|PDB:1F89"
SQ SEQUENCE 291 AA; 32549 MW; A813744120088827 CRC64;
MSASKILSQK IKVALVQLSG SSPDKMANLQ RAATFIERAM KEQPDTKLVV LPECFNSPYS
TDQFRKYSEV INPKEPSTSV QFLSNLANKF KIILVGGTIP ELDPKTDKIY NTSIIFNEDG
KLIDKHRKVH LFDVDIPNGI SFHESETLSP GEKSTTIDTK YGKFGVGICY DMRFPELAML
SARKGAFAMI YPSAFNTVTG PLHWHLLARS RAVDNQVYVM LCSPARNLQS SYHAYGHSIV
VDPRGKIVAE AGEGEEIIYA ELDPEVIESF RQAVPLTKQR RFDVYSDVNA H
