NILP3_ARATH
ID NILP3_ARATH Reviewed; 369 AA.
AC Q8RUF8; F4JZF7; Q9LYH1;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 1.
DT 03-AUG-2022, entry version 126.
DE RecName: Full=Omega-amidase, chloroplastic {ECO:0000305};
DE EC=3.5.1.3 {ECO:0000269|PubMed:24461228};
DE AltName: Full=Nitrilase-like protein 3 {ECO:0000303|PubMed:12435743};
DE Flags: Precursor;
GN Name=NLP3 {ECO:0000303|PubMed:12435743};
GN OrderedLocusNames=At5g12040 {ECO:0000312|Araport:AT5G12040};
GN ORFNames=F14F18.210 {ECO:0000312|EMBL:CAB87677.1};
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] (ISOFORM 1).
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 8-294 (ISOFORM 2).
RC STRAIN=cv. Columbia;
RX PubMed=14993207; DOI=10.1101/gr.1515604;
RA Castelli V., Aury J.-M., Jaillon O., Wincker P., Clepet C., Menard M.,
RA Cruaud C., Quetier F., Scarpelli C., Schaechter V., Temple G., Caboche M.,
RA Weissenbach J., Salanoubat M.;
RT "Whole genome sequence comparisons and 'full-length' cDNA sequences: a
RT combined approach to evaluate and improve Arabidopsis genome annotation.";
RL Genome Res. 14:406-413(2004).
RN [5]
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 [6]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-64, CLEAVAGE OF TRANSIT PEPTIDE
RP [LARGE SCALE ANALYSIS] AFTER MET-63, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [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 [7]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, DISRUPTION
RP PHENOTYPE, AND INDUCTION BY ASPARAGINE.
RX PubMed=24461228; DOI=10.1016/j.phytochem.2013.12.020;
RA Zhang Q., Marsolais F.;
RT "Identification and characterization of omega-amidase as an enzyme
RT metabolically linked to asparagine transamination in Arabidopsis.";
RL Phytochemistry 99:36-43(2014).
CC -!- FUNCTION: Omega-amidase involved in the metabolism of asparagine.
CC Probably also closely coupled with glutamine transamination in the
CC methionine salvage cycle. Can use alpha-ketosuccinamate and alpha-
CC hydroxysuccinamate as substrates, producing respectively oxaloacetate
CC and malate, or alpha-ketoglutaramate, producing alpha-ketoglutarate.
CC {ECO:0000269|PubMed:24461228}.
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:24461228};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:11717;
CC Evidence={ECO:0000269|PubMed:24461228};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=6.13 mM for alpha-ketosuccinamate {ECO:0000269|PubMed:24461228};
CC KM=4.43 mM for alpha-ketoglutaramate {ECO:0000269|PubMed:24461228};
CC KM=5.58 mM for alpha-hydroxysuccinamate
CC {ECO:0000269|PubMed:24461228};
CC Vmax=0.785 umol/sec/mg enzyme with alpha-ketosuccinamate as substrate
CC {ECO:0000269|PubMed:24461228};
CC Vmax=0.836 umol/sec/mg enzyme with alpha-ketoglutaramate as substrate
CC {ECO:0000269|PubMed:24461228};
CC Vmax=0.865 umol/sec/mg enzyme with alpha-hydroxysuccinamate as
CC substrate {ECO:0000269|PubMed:24461228};
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q8RUF8-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8RUF8-2; Sequence=VSP_053942, VSP_053943;
CC -!- INDUCTION: Down-regulated in roots after treatment with asparagine.
CC {ECO:0000269|PubMed:24461228}.
CC -!- DISRUPTION PHENOTYPE: 2-fold higher levels of alpha-ketosuccinamate and
CC 3-fold higher levels of alpha-hydroxysuccinamate.
CC {ECO:0000269|PubMed:24461228}.
CC -!- SIMILARITY: Belongs to the nitrilase superfamily. NIT1/NIT2 family.
CC {ECO:0000305}.
CC -!- CAUTION: The T-DNA insertion may still allow the production of a
CC functional cytosolic form of the protein, if translation is initiated
CC from the second initiation codon, encoding Met-63 in the full-length
CC protein. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB87677.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB87677.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AL163812; CAB87677.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED91753.1; -; Genomic_DNA.
DR EMBL; CP002688; AED91754.1; -; Genomic_DNA.
DR EMBL; AY075592; AAL91613.1; -; mRNA.
DR EMBL; AY093711; AAM10335.1; -; mRNA.
DR EMBL; BX829894; -; NOT_ANNOTATED_CDS; mRNA.
DR PIR; T48563; T48563.
DR RefSeq; NP_196765.2; NM_121242.5. [Q8RUF8-1]
DR RefSeq; NP_974769.1; NM_203040.1. [Q8RUF8-2]
DR AlphaFoldDB; Q8RUF8; -.
DR SMR; Q8RUF8; -.
DR BioGRID; 16355; 25.
DR STRING; 3702.AT5G12040.1; -.
DR iPTMnet; Q8RUF8; -.
DR PaxDb; Q8RUF8; -.
DR PRIDE; Q8RUF8; -.
DR ProteomicsDB; 249390; -. [Q8RUF8-1]
DR EnsemblPlants; AT5G12040.1; AT5G12040.1; AT5G12040. [Q8RUF8-1]
DR EnsemblPlants; AT5G12040.2; AT5G12040.2; AT5G12040. [Q8RUF8-2]
DR GeneID; 831077; -.
DR Gramene; AT5G12040.1; AT5G12040.1; AT5G12040. [Q8RUF8-1]
DR Gramene; AT5G12040.2; AT5G12040.2; AT5G12040. [Q8RUF8-2]
DR KEGG; ath:AT5G12040; -.
DR Araport; AT5G12040; -.
DR TAIR; locus:2143039; AT5G12040.
DR eggNOG; KOG0806; Eukaryota.
DR InParanoid; Q8RUF8; -.
DR OMA; LFDSGYC; -.
DR PhylomeDB; Q8RUF8; -.
DR BioCyc; ARA:AT5G12040-MON; -.
DR BRENDA; 3.5.1.3; 399.
DR SABIO-RK; Q8RUF8; -.
DR PRO; PR:Q8RUF8; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q8RUF8; baseline and differential.
DR Genevisible; Q8RUF8; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0009536; C:plastid; HDA:TAIR.
DR GO; GO:0050152; F:omega-amidase activity; IDA:UniProtKB.
DR GO; GO:0008270; F:zinc ion binding; HDA:TAIR.
DR GO; GO:0006528; P:asparagine metabolic process; IBA:GO_Central.
DR GO; GO:0006541; P:glutamine metabolic process; IBA:GO_Central.
DR GO; GO:0006108; P:malate metabolic process; IDA:UniProtKB.
DR GO; GO:0006107; P:oxaloacetate metabolic process; IDA:UniProtKB.
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 Acetylation; Alternative splicing; Chloroplast; Hydrolase; Plastid;
KW Reference proteome; Transit peptide.
FT TRANSIT 1..63
FT /note="Chloroplast"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CHAIN 64..369
FT /note="Omega-amidase, chloroplastic"
FT /id="PRO_0000426706"
FT DOMAIN 88..337
FT /note="CN hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00054"
FT ACT_SITE 127
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00054"
FT ACT_SITE 201
FT /note="Proton donor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00054"
FT ACT_SITE 242
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00054"
FT MOD_RES 64
FT /note="N-acetylalanine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT VAR_SEQ 290..294
FT /note="LYVAT -> VHEPS (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14993207"
FT /id="VSP_053942"
FT VAR_SEQ 295..369
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14993207"
FT /id="VSP_053943"
SQ SEQUENCE 369 AA; 40330 MW; D22D910AEFB93040 CRC64;
MKSAISSSLF FNSKNLLNPN PLSRFISLKS NFLPKLSPRS ITSHTLKLPS SSTSALRSIS
SSMASSFNPE QARVPSALPL PAPPLTKFNI GLCQLSVTSD KKRNISHAKK AIEEAASKGA
KLVLLPEIWN SPYSNDSFPV YAEEIDAGGD ASPSTAMLSE VSKRLKITII GGSIPERVGD
RLYNTCCVFG SDGELKAKHR KIHLFDIDIP GKITFMESKT LTAGETPTIV DTDVGRIGIG
ICYDIRFQEL AMIYAARGAH LLCYPGAFNM TTGPLHWELL QRARATDNQL YVATCSPARD
SGAGYTAWGH STLVGPFGEV LATTEHEEAI IIAEIDYSIL EQRRTSLPLN RQRRGDLYQL
VDVQRLDSK
