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Probable indole-3-pyruvate monooxygenase YUCCA4 (EC 1.14.13.168) (Flavin-containing monooxygenase YUCCA4)

 YUC4_ARATH              Reviewed;         411 AA.
Q9LFM5; Q3E9I6;
02-NOV-2010, integrated into UniProtKB/Swiss-Prot.
01-OCT-2000, sequence version 1.
05-DEC-2018, entry version 126.
RecName: Full=Probable indole-3-pyruvate monooxygenase YUCCA4;
EC=1.14.13.168;
AltName: Full=Flavin-containing monooxygenase YUCCA4;
Name=YUC4; Synonyms=THREAD, YUCCA4; OrderedLocusNames=At5g11320;
ORFNames=F2I11_210;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=11130714; DOI=10.1038/35048507;
Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K.,
Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S.,
Nakazaki N., Naruo K., Okumura S., Shinpo S., Takeuchi C., Wada T.,
Watanabe A., Yamada M., Yasuda M., Sato S., de la Bastide M.,
Huang E., Spiegel L., Gnoj L., O'Shaughnessy A., Preston R.,
Habermann K., Murray J., Johnson D., Rohlfing T., Nelson J.,
Stoneking T., Pepin K., Spieth J., Sekhon M., Armstrong J., Becker M.,
Belter E., Cordum H., Cordes M., Courtney L., Courtney W., Dante M.,
Du H., Edwards J., Fryman J., Haakensen B., Lamar E., Latreille P.,
Leonard S., Meyer R., Mulvaney E., Ozersky P., Riley A., Strowmatt C.,
Wagner-McPherson C., Wollam A., Yoakum M., Bell M., Dedhia N.,
Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D., Baker J.,
Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S.,
Langham S.-A., McCullagh B., Robben J., Grymonprez B., Zimmermann W.,
Ramsperger U., Wedler H., Balke K., Wedler E., Peters S.,
van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R.,
Weitzenegger T., Bothe G., Rose M., Hauf J., Berneiser S., Hempel S.,
Feldpausch M., Lamberth S., Villarroel R., Gielen J., Ardiles W.,
Bents O., Lemcke K., Kolesov G., Mayer K.F.X., Rudd S., Schoof H.,
Schueller C., Zaccaria P., Mewes H.-W., Bevan M., Fransz P.F.;
"Sequence and analysis of chromosome 5 of the plant Arabidopsis
thaliana.";
Nature 408:823-826(2000).
[2]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[3]
FUNCTION, TISSUE SPECIFICITY, GENE FAMILY, NOMENCLATURE, AND
DISRUPTION PHENOTYPE.
PubMed=16818609; DOI=10.1101/gad.1415106;
Cheng Y., Dai X., Zhao Y.;
"Auxin biosynthesis by the YUCCA flavin monooxygenases controls the
formation of floral organs and vascular tissues in Arabidopsis.";
Genes Dev. 20:1790-1799(2006).
[4]
INDUCTION BY STY1.
PubMed=16740145; DOI=10.1111/j.1365-313X.2006.02775.x;
Sohlberg J.J., Myrenaas M., Kuusk S., Lagercrantz U., Kowalczyk M.,
Sandberg G., Sundberg E.;
"STY1 regulates auxin homeostasis and affects apical-basal patterning
of the Arabidopsis gynoecium.";
Plant J. 47:112-123(2006).
[5]
FUNCTION, AND DEVELOPMENTAL STAGE.
PubMed=17704214; DOI=10.1105/tpc.107.053009;
Cheng Y., Dai X., Zhao Y.;
"Auxin synthesized by the YUCCA flavin monooxygenases is essential for
embryogenesis and leaf formation in Arabidopsis.";
Plant Cell 19:2430-2439(2007).
[6]
GENE FAMILY.
STRAIN=cv. Columbia;
PubMed=17461789; DOI=10.1111/j.1365-313X.2007.03101.x;
Hansen B.G., Kliebenstein D.J., Halkier B.A.;
"Identification of a flavin-monooxygenase as the S-oxygenating enzyme
in aliphatic glucosinolate biosynthesis in Arabidopsis.";
Plant J. 50:902-910(2007).
[7]
INDUCTION BY LEC2.
PubMed=18287041; DOI=10.1073/pnas.0712364105;
Stone S.L., Braybrook S.A., Paula S.L., Kwong L.W., Meuser J.,
Pelletier J., Hsieh T.-F., Fischer R.L., Goldberg R.B., Harada J.J.;
"Arabidopsis LEAFY COTYLEDON2 induces maturation traits and auxin
activity: implications for somatic embryogenesis.";
Proc. Natl. Acad. Sci. U.S.A. 105:3151-3156(2008).
[8]
INDUCTION BY NGA3.
PubMed=19435937; DOI=10.1105/tpc.109.065508;
Trigueros M., Navarrete-Gomez M., Sato S., Christensen S.K., Pelaz S.,
Weigel D., Yanofsky M.F., Ferrandiz C.;
"The NGATHA genes direct style development in the Arabidopsis
gynoecium.";
Plant Cell 21:1394-1409(2009).
[9]
INDUCTION BY STY1.
PubMed=20154152; DOI=10.1105/tpc.108.064816;
Eklund D.M., Staaldal V., Valsecchi I., Cierlik I., Eriksson C.,
Hiratsu K., Ohme-Takagi M., Sundstroem J.F., Thelander M., Ezcurra I.,
Sundberg E.;
"The Arabidopsis thaliana STYLISH1 protein acts as a transcriptional
activator regulating auxin biosynthesis.";
Plant Cell 22:349-363(2010).
[10]
FUNCTION.
PubMed=22025721; DOI=10.1073/pnas.1108436108;
Won C., Shen X., Mashiguchi K., Zheng Z., Dai X., Cheng Y.,
Kasahara H., Kamiya Y., Chory J., Zhao Y.;
"Conversion of tryptophan to indole-3-acetic acid by TRYPTOPHAN
AMINOTRANSFERASES OF ARABIDOPSIS and YUCCAs in Arabidopsis.";
Proc. Natl. Acad. Sci. U.S.A. 108:18518-18523(2011).
[11]
FUNCTION, CATALYTIC ACTIVITY, ALTERNATIVE SPLICING, SUBCELLULAR
LOCATION, AND TISSUE SPECIFICITY.
PubMed=22233288; DOI=10.1111/j.1365-313X.2011.04866.x;
Kriechbaumer V., Wang P., Hawes C., Abell B.M.;
"Alternative splicing of the auxin biosynthesis gene YUCCA4 determines
its subcellular compartmentation.";
Plant J. 70:292-302(2012).
-!- FUNCTION: Involved in auxin biosynthesis. Both isoforms are
catalitically active. Involved during embryogenesis and seedling
development. Required for the formation of floral organs and
vascular tissues. Belongs to the set of redundant YUCCA genes
probably responsible for auxin biosynthesis in shoots.
{ECO:0000269|PubMed:16818609, ECO:0000269|PubMed:17704214,
ECO:0000269|PubMed:22025721, ECO:0000269|PubMed:22233288}.
-!- CATALYTIC ACTIVITY:
Reaction=H(+) + indole-3-pyruvate + NADPH + O2 = (indol-3-
yl)acetate + CO2 + H2O + NADP(+); Xref=Rhea:RHEA:34331,
ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:15379,
ChEBI:CHEBI:16526, ChEBI:CHEBI:17640, ChEBI:CHEBI:30854,
ChEBI:CHEBI:57783, ChEBI:CHEBI:58349; EC=1.14.13.168;
Evidence={ECO:0000269|PubMed:22233288};
-!- COFACTOR:
Name=FAD; Xref=ChEBI:CHEBI:57692; Evidence={ECO:0000250};
-!- PATHWAY: Plant hormone metabolism; auxin biosynthesis.
-!- SUBCELLULAR LOCATION: Isoform 1: Cytoplasm.
-!- SUBCELLULAR LOCATION: Isoform 2: Endoplasmic reticulum membrane;
Single-pass membrane protein; Cytoplasmic side.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q9LFM5-1; Sequence=Displayed;
Name=2;
IsoId=Q9LFM5-2; Sequence=VSP_039987, VSP_039988;
Note=May be due to an intron retention. Expressed only in
flowers. Contains a transmembrane at positions 334 - 354.;
-!- TISSUE SPECIFICITY: Expressed in leaves, stems, flowers, buds and
siliques. Detected in the apical gynoecium and in the developing
ovules. {ECO:0000269|PubMed:16818609,
ECO:0000269|PubMed:22233288}.
-!- DEVELOPMENTAL STAGE: Expression relatively broad during early
stages of embryogenesis and more restricted to apical region of
the cotyledons in the mature embryo.
{ECO:0000269|PubMed:17704214}.
-!- INDUCTION: Positively regulated by LEC2, by NGA3 and by STY1.
{ECO:0000269|PubMed:16740145, ECO:0000269|PubMed:18287041,
ECO:0000269|PubMed:19435937, ECO:0000269|PubMed:20154152}.
-!- DISRUPTION PHENOTYPE: No visible phenotype, due to the redundancy
with the other members of the YUCCA family.
{ECO:0000269|PubMed:16818609}.
-!- SIMILARITY: Belongs to the FMO family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AL360314; CAB96667.1; -; Genomic_DNA.
EMBL; CP002688; AED91659.1; -; Genomic_DNA.
EMBL; CP002688; AED91660.1; -; Genomic_DNA.
RefSeq; NP_196693.1; NM_121170.3. [Q9LFM5-1]
RefSeq; NP_850808.1; NM_180477.2. [Q9LFM5-2]
UniGene; At.32275; -.
ProteinModelPortal; Q9LFM5; -.
SMR; Q9LFM5; -.
STRING; 3702.AT5G11320.1; -.
PaxDb; Q9LFM5; -.
EnsemblPlants; AT5G11320.1; AT5G11320.1; AT5G11320. [Q9LFM5-1]
EnsemblPlants; AT5G11320.2; AT5G11320.2; AT5G11320. [Q9LFM5-2]
GeneID; 831003; -.
Gramene; AT5G11320.1; AT5G11320.1; AT5G11320. [Q9LFM5-1]
Gramene; AT5G11320.2; AT5G11320.2; AT5G11320. [Q9LFM5-2]
KEGG; ath:AT5G11320; -.
Araport; AT5G11320; -.
TAIR; locus:2147962; AT5G11320.
eggNOG; KOG1399; Eukaryota.
eggNOG; COG2072; LUCA.
HOGENOM; HOG000240759; -.
InParanoid; Q9LFM5; -.
KO; K11816; -.
OMA; FSIHPRF; -.
OrthoDB; EOG09360AXT; -.
PhylomeDB; Q9LFM5; -.
BRENDA; 1.14.13.168; 399.
Reactome; R-ATH-217271; FMO oxidises nucleophiles.
UniPathway; UPA00151; -.
PRO; PR:Q9LFM5; -.
Proteomes; UP000006548; Chromosome 5.
ExpressionAtlas; Q9LFM5; baseline and differential.
Genevisible; Q9LFM5; AT.
GO; GO:0005829; C:cytosol; IDA:TAIR.
GO; GO:0005783; C:endoplasmic reticulum; IDA:TAIR.
GO; GO:0005789; C:endoplasmic reticulum membrane; IDA:TAIR.
GO; GO:0005794; C:Golgi apparatus; IDA:TAIR.
GO; GO:0000139; C:Golgi membrane; IDA:TAIR.
GO; GO:0005654; C:nucleoplasm; IDA:TAIR.
GO; GO:0050660; F:flavin adenine dinucleotide binding; IEA:InterPro.
GO; GO:0103075; F:indole-3-pyruvate monooxygenase activity; IEA:UniProtKB-EC.
GO; GO:0047434; F:indolepyruvate decarboxylase activity; IDA:TAIR.
GO; GO:0004499; F:N,N-dimethylaniline monooxygenase activity; IEA:InterPro.
GO; GO:0050661; F:NADP binding; IEA:InterPro.
GO; GO:0009851; P:auxin biosynthetic process; IDA:TAIR.
GO; GO:0048825; P:cotyledon development; IGI:TAIR.
GO; GO:0010229; P:inflorescence development; IGI:TAIR.
GO; GO:0048827; P:phyllome development; IGI:TAIR.
GO; GO:0009911; P:positive regulation of flower development; IGI:TAIR.
Gene3D; 3.50.50.60; -; 1.
InterPro; IPR036188; FAD/NAD-bd_sf.
InterPro; IPR000960; Flavin_mOase.
InterPro; IPR000103; Pyridine_nuc-diS_OxRdtase_2.
PIRSF; PIRSF000332; FMO; 1.
PRINTS; PR00469; PNDRDTASEII.
SUPFAM; SSF51905; SSF51905; 2.
1: Evidence at protein level;
Alternative splicing; Auxin biosynthesis; Complete proteome;
Cytoplasm; Endoplasmic reticulum; FAD; Flavoprotein; Membrane;
Monooxygenase; NADP; Oxidoreductase; Reference proteome.
CHAIN 1 411 Probable indole-3-pyruvate monooxygenase
YUCCA4.
/FTId=PRO_0000400071.
NP_BIND 21 26 FAD. {ECO:0000255}.
NP_BIND 183 188 NADP. {ECO:0000255}.
VAR_SEQ 334 357 ENSFFTKEGMPKTPFPNGWKGEKG -> VLLSIYYLSYSLS
CYIYVNVYMYM (in isoform 2).
{ECO:0000305}.
/FTId=VSP_039987.
VAR_SEQ 358 411 Missing (in isoform 2). {ECO:0000305}.
/FTId=VSP_039988.
SEQUENCE 411 AA; 45406 MW; 957AE2299820DBE2 CRC64;
MGTCRESEPT QIFVPGPIIV GAGPSGLAVA ACLSNRGVPS VILERTDCLA SLWQKRTYDR
LKLHLPKHFC ELPLMPFPKN FPKYPSKQLF ISYVESYAAR FNIKPVFNQT VEKAEFDDAS
GLWNVKTQDG VYTSTWLVVA TGENAEPVFP NIPGLKKFTG PVVHTSAYKS GSAFANRKVL
VVGCGNSGME VSLDLCRYNA LPHMVVRNSV HVLPRDFFGL STFGIAMTLL KWFPLKLVDK
FLLLLANSTL GNTDLLGLRR PKTGPIELKN VTGKTPVLDV GAISLIRSGQ IKVTQAVKEI
TRNGAKFLNG KEIEFDSIIL ATGYKSNVPD WLKENSFFTK EGMPKTPFPN GWKGEKGLYT
VGFTRRGLSG TAYDAVKIAE DITDQWMKFN GPLSCRNICS SHIIHLHFNK S


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