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Probable acyl-CoA dehydrogenase IBR3 (EC 1.3.99.-) (Protein INDOLE-3-BUTYRIC ACID RESPONSE 3)

 IBR3_ARATH              Reviewed;         824 AA.
Q8RWZ3; Q0WM98; Q67ZU5; Q9M7Y6; Q9M7Y7;
01-APR-2015, integrated into UniProtKB/Swiss-Prot.
01-JUN-2002, sequence version 1.
23-MAY-2018, entry version 135.
RecName: Full=Probable acyl-CoA dehydrogenase IBR3 {ECO:0000305};
EC=1.3.99.- {ECO:0000305};
AltName: Full=Protein INDOLE-3-BUTYRIC ACID RESPONSE 3 {ECO:0000303|PubMed:17277896};
Name=IBR3 {ECO:0000303|PubMed:17277896};
OrderedLocusNames=At3g06810/At3g06800 {ECO:0000312|Araport:AT3G06810};
ORFNames=F3E22.5/F3E22.6 {ECO:0000312|EMBL:AAF63817.1,
ECO:0000312|EMBL:AAF63818.1};
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=11130713; DOI=10.1038/35048706;
Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M.,
Fartmann B., Valle G., Bloecker H., Perez-Alonso M., Obermaier B.,
Delseny M., Boutry M., Grivell L.A., Mache R., Puigdomenech P.,
De Simone V., Choisne N., Artiguenave F., Robert C., Brottier P.,
Wincker P., Cattolico L., Weissenbach J., Saurin W., Quetier F.,
Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Benes V.,
Wurmbach E., Drzonek H., Erfle H., Jordan N., Bangert S.,
Wiedelmann R., Kranz H., Voss H., Holland R., Brandt P., Nyakatura G.,
Vezzi A., D'Angelo M., Pallavicini A., Toppo S., Simionati B.,
Conrad A., Hornischer K., Kauer G., Loehnert T.-H., Nordsiek G.,
Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J., Climent J.,
Navarro P., Collado C., Perez-Perez A., Ottenwaelder B., Duchemin D.,
Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
Monfort A., Argiriou A., Flores M., Liguori R., Vitale D.,
Mannhaupt G., Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W.,
Mayer K.F.X., Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J.,
Rooney T., Rizzo M., Walts A., Utterback T., Fujii C.Y., Shea T.P.,
Creasy T.H., Haas B., Maiti R., Wu D., Peterson J., Van Aken S.,
Pai G., Militscher J., Sellers P., Gill J.E., Feldblyum T.V.,
Preuss D., Lin X., Nierman W.C., Salzberg S.L., White O., Venter J.C.,
Fraser C.M., Kaneko T., Nakamura Y., Sato S., Kato T., Asamizu E.,
Sasamoto S., Kimura T., Idesawa K., Kawashima K., Kishida Y.,
Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Muraki A.,
Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
Watanabe A., Yamada M., Yasuda M., Tabata S.;
"Sequence and analysis of chromosome 3 of the plant Arabidopsis
thaliana.";
Nature 408:820-822(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]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J.,
Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J.,
Hayashizaki Y., Shinozaki K.;
"Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
[5]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=cv. Landsberg erecta;
PubMed=17272265; DOI=10.1074/mcp.M600408-MCP200;
Maor R., Jones A., Nuehse T.S., Studholme D.J., Peck S.C., Shirasu K.;
"Multidimensional protein identification technology (MudPIT) analysis
of ubiquitinated proteins in plants.";
Mol. Cell. Proteomics 6:601-610(2007).
[6]
FUNCTION, MUTAGENESIS OF HIS-229, AND DISRUPTION PHENOTYPE.
PubMed=17277896; DOI=10.1007/s11103-007-9134-2;
Zolman B.K., Nyberg M., Bartel B.;
"IBR3, a novel peroxisomal acyl-CoA dehydrogenase-like protein
required for indole-3-butyric acid response.";
Plant Mol. Biol. 64:59-72(2007).
[7]
DISRUPTION PHENOTYPE.
PubMed=18725356; DOI=10.1534/genetics.108.090399;
Zolman B.K., Martinez N., Millius A., Adham A.R., Bartel B.;
"Identification and characterization of Arabidopsis indole-3-butyric
acid response mutants defective in novel peroxisomal enzymes.";
Genetics 180:237-251(2008).
[8]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=20562230; DOI=10.1104/pp.110.157461;
Strader L.C., Culler A.H., Cohen J.D., Bartel B.;
"Conversion of endogenous indole-3-butyric acid to indole-3-acetic
acid drives cell expansion in Arabidopsis seedlings.";
Plant Physiol. 153:1577-1586(2010).
[9]
ACETYLATION [LARGE SCALE ANALYSIS] AT GLY-2, CLEAVAGE OF INITIATOR
METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS
SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=22223895; DOI=10.1074/mcp.M111.015131;
Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C.,
Meinnel T., Giglione C.;
"Comparative large-scale characterisation of plant vs. mammal proteins
reveals similar and idiosyncratic N-alpha acetylation features.";
Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
[10]
FUNCTION, AND INDUCTION.
PubMed=23906045; DOI=10.1111/j.1438-8677.2012.00685.x;
Huang T.Y., Desclos-Theveniau M., Chien C.T., Zimmerli L.;
"Arabidopsis thaliana transgenics overexpressing IBR3 show enhanced
susceptibility to the bacterium Pseudomonas syringae.";
Plant Biol. 15:832-840(2013).
-!- FUNCTION: Involved with IBR1 and IBR10 in the peroxisomal beta-
oxidation of indole-3-butyric acid (IBA) to form indole-3-acetic
acid (IAA), a biologically active auxin (PubMed:20562230). May be
responsible for catalyzing the first step in IBA-CoA beta-
oxidation (PubMed:17277896). May play a role in defense response
to pathogenic bacteria (PubMed:23906045).
{ECO:0000269|PubMed:17277896, ECO:0000269|PubMed:20562230,
ECO:0000269|PubMed:23906045}.
-!- CATALYTIC ACTIVITY: Acyl-CoA + acceptor = 2,3-dehydroacyl-CoA +
reduced acceptor. {ECO:0000305}.
-!- COFACTOR:
Name=FAD; Xref=ChEBI:CHEBI:57692;
Evidence={ECO:0000250|UniProtKB:Q709F0};
-!- SUBCELLULAR LOCATION: Peroxisome {ECO:0000305}.
-!- INDUCTION: By infection with the bacterial pathogen P.syringae pv.
tomato strain DC3000. {ECO:0000269|PubMed:23906045}.
-!- DISRUPTION PHENOTYPE: Defective in root hair expansion
(PubMed:20562230). Mutant plants are resistant to the inhibitory
effect of intermediate levels of indole-3-butyric acid (IBA) and
2,4-DB on root elongation (PubMed:17277896, PubMed:18725356).
{ECO:0000269|PubMed:17277896, ECO:0000269|PubMed:18725356,
ECO:0000269|PubMed:20562230}.
-!- MISCELLANEOUS: Plants over-expressing IBR3 exhibit enhanced
susceptibility to the bacterial pathogen P.syringae pv. tomato
strain DC3000. {ECO:0000269|PubMed:23906045}.
-!- SIMILARITY: Belongs to the acyl-CoA dehydrogenase family.
{ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=AAF63817.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to two different genes At3g06800 and At3g06810.; Evidence={ECO:0000305};
Sequence=AAF63818.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to two different genes At3g06800 and At3g06810.; Evidence={ECO:0000305};
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EMBL; AC023912; AAF63817.1; ALT_SEQ; Genomic_DNA.
EMBL; AC023912; AAF63818.1; ALT_SEQ; Genomic_DNA.
EMBL; CP002686; AEE74461.1; -; Genomic_DNA.
EMBL; AY091014; AAM14036.1; -; mRNA.
EMBL; BT002365; AAN86198.1; -; mRNA.
EMBL; AK176022; BAD43785.1; -; mRNA.
EMBL; AK229932; BAF01758.1; -; mRNA.
RefSeq; NP_187337.2; NM_111561.5.
UniGene; At.43455; -.
ProteinModelPortal; Q8RWZ3; -.
SMR; Q8RWZ3; -.
IntAct; Q8RWZ3; 3.
STRING; 3702.AT3G06810.1; -.
iPTMnet; Q8RWZ3; -.
PaxDb; Q8RWZ3; -.
PRIDE; Q8RWZ3; -.
EnsemblPlants; AT3G06810.1; AT3G06810.1; AT3G06810.
GeneID; 819865; -.
Gramene; AT3G06810.1; AT3G06810.1; AT3G06810.
KEGG; ath:AT3G06810; -.
Araport; AT3G06810; -.
TAIR; locus:2083328; AT3G06810.
eggNOG; KOG1469; Eukaryota.
eggNOG; ENOG410XNTS; LUCA.
KO; K00249; -.
OMA; AHLCELM; -.
OrthoDB; EOG093601TO; -.
PhylomeDB; Q8RWZ3; -.
BioCyc; ARA:AT3G06810-MONOMER; -.
Reactome; R-ATH-77289; Mitochondrial Fatty Acid Beta-Oxidation.
PRO; PR:Q8RWZ3; -.
Proteomes; UP000006548; Chromosome 3.
ExpressionAtlas; Q8RWZ3; differential.
Genevisible; Q8RWZ3; AT.
GO; GO:0005777; C:peroxisome; IEA:UniProtKB-SubCell.
GO; GO:0050660; F:flavin adenine dinucleotide binding; IBA:GO_Central.
GO; GO:0016627; F:oxidoreductase activity, acting on the CH-CH group of donors; IEA:InterPro.
GO; GO:0033539; P:fatty acid beta-oxidation using acyl-CoA dehydrogenase; IBA:GO_Central.
GO; GO:0048767; P:root hair elongation; IMP:TAIR.
Gene3D; 1.10.540.10; -; 1.
InterPro; IPR006091; Acyl-CoA_Oxase/DH_cen-dom.
InterPro; IPR036250; AcylCo_DH-like_C.
InterPro; IPR009075; AcylCo_DH/oxidase_C.
InterPro; IPR013786; AcylCoA_DH/ox_N.
InterPro; IPR037069; AcylCoA_DH/ox_N_sf.
InterPro; IPR009100; AcylCoA_DH/oxidase_NM_dom.
InterPro; IPR002575; Aminoglycoside_PTrfase.
InterPro; IPR011009; Kinase-like_dom_sf.
Pfam; PF00441; Acyl-CoA_dh_1; 1.
Pfam; PF02770; Acyl-CoA_dh_M; 1.
Pfam; PF02771; Acyl-CoA_dh_N; 1.
Pfam; PF01636; APH; 1.
SUPFAM; SSF47203; SSF47203; 1.
SUPFAM; SSF56112; SSF56112; 1.
SUPFAM; SSF56645; SSF56645; 1.
1: Evidence at protein level;
Acetylation; Complete proteome; FAD; Fatty acid metabolism;
Flavoprotein; Lipid metabolism; Oxidoreductase; Peroxisome;
Reference proteome.
INIT_MET 1 1 Removed. {ECO:0000244|PubMed:22223895}.
CHAIN 2 824 Probable acyl-CoA dehydrogenase IBR3.
/FTId=PRO_0000432488.
NP_BIND 555 565 FAD. {ECO:0000250|UniProtKB:Q709F0}.
NP_BIND 589 591 FAD. {ECO:0000250|UniProtKB:Q709F0}.
NP_BIND 776 780 FAD. {ECO:0000250|UniProtKB:Q709F0}.
MOTIF 822 824 Microbody targeting signal.
{ECO:0000305}.
BINDING 706 706 FAD. {ECO:0000250|UniProtKB:Q709F0}.
BINDING 776 776 FAD. {ECO:0000250|UniProtKB:Q709F0}.
MOD_RES 2 2 N-acetylglycine.
{ECO:0000244|PubMed:22223895}.
MUTAGEN 229 229 H->Y: In ibr3-11; resistance to the
inhibitory effect of intermediate levels
of indole-3-butyric acid (IBA) on root
elongation.
{ECO:0000269|PubMed:17277896}.
CONFLICT 246 246 V -> D (in Ref. 4; BAD43785).
{ECO:0000305}.
CONFLICT 558 558 T -> A (in Ref. 4; BAF01758).
{ECO:0000305}.
SEQUENCE 824 AA; 91713 MW; 8EB06907C448F263 CRC64;
MGSSTGDLVT RIQSAHRFDH DALFRFAADN VSGFPTNPSQ FKVSQFGHGQ SNPTFLIEVG
SGSSLKRYVL RKKPPGKLLQ SAHAVDREFQ VLRALGEHTQ VPVPKVFCLC TDPAVIGTAF
YIMEFMEGRI FIDPKLPNVA PERRNAIYRA TAKALASLHS ADVDAIGLEK YGRRGNYCKR
QIDRWFKQYL ASTSEGKPER NPKMFELVDW LRKNIPAEDS TGATSGLVHG DFRIDNLVFH
PSEDRVIGII DWELSTLGNQ MCDVAYSCMH YIVNVQLDKE HVSEGFETTG LPEGMLSMPE
FLLEYCSASG KPWPAANWKF YVAFSLFRAA SIYTGVYSRW LMGNASAGER ARNTGVQANE
LVESALGYIA RENVLPEHPP SVQRDVSPSY ESLVDGSGRF IPNRKVLELR QKLIKFMETH
IYPMENEFSK LAQSDMRWTV HPQEEKLKEM AKREGLWNLF VPVDSAARAR RELAATENKH
NLSGKSFDQL FGEGLTNLEY GYLCEIMGRS VWAPQVFNCG APDTGNMEVI LRYGNKEQIS
EWLIPLLEGR IRSGFAMTEP QVASSDATNI ECSIRRQGDS YVINGTKWWT SGAMDPRCRV
LILMGKTDFN APKHKQQSMI LVDMRTPGIS VKRPLTVFGF DDAPHGHAEI SFENVVVPAK
NILLGEGRGF EIAQGRLGPG RLHHCMRLIG AAERGMELMA QRALSRKTFG KFIAQHGSFV
SDLAKLRVEL EGTRLLVLEA ADHLDKFGNK KARGILAMAK VAAPNMALKV LDTAIQVHGA
AGVSSDTVLA HLWATARTLR IADGPDEVHL GTIGKLELQR ASKL


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