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Chalcone--flavonone isomerase 1 (Chalcone isomerase 1) (EC 5.5.1.6) (Protein TRANSPARENT TESTA 5)

 CFI1_ARATH              Reviewed;         246 AA.
P41088; Q8W532; Q9LE13; Q9LF74; Q9LF75;
01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
11-JUL-2002, sequence version 2.
25-APR-2018, entry version 135.
RecName: Full=Chalcone--flavonone isomerase 1;
Short=Chalcone isomerase 1;
EC=5.5.1.6;
AltName: Full=Protein TRANSPARENT TESTA 5;
Name=CHI1; Synonyms=CFI, TT5; OrderedLocusNames=At3g55120;
ORFNames=T15C9_120;
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 [GENOMIC DNA], AND FUNCTION.
STRAIN=cv. Columbia, and cv. Landsberg erecta;
PubMed=1354004; DOI=10.1105/tpc.4.3.333;
Shirley B.W., Hanley S., Goodman H.M.;
"Effects of ionizing radiation on a plant genome: analysis of two
Arabidopsis transparent testa mutations.";
Plant Cell 4:333-347(1992).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=cv. Gr-5, cv. Ita-0, cv. Mh-0, cv. Per-1, cv. Rv-1, and
cv. Wlp-2;
PubMed=10835405;
Kuittinen H., Aguade M.;
"Nucleotide variation at the chalcone isomerase locus in Arabidopsis
thaliana.";
Genetics 155:863-872(2000).
[3]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=cv. Gran-10, cv. Gran-2, cv. Gran-3, cv. Gran-4, cv. Gran-5,
cv. Gran-6, cv. Gran-7, cv. Gran-8, cv. Gran-9, cv. Lu-2, cv. Lu-3,
cv. Lu-4, cv. Lu-5, cv. Lu-6, cv. Lu-7, cv. Lu-8, cv. Rv-10, cv. Rv-2,
cv. Rv-3, cv. Rv-4, cv. Rv-5, cv. Rv-6, cv. Rv-7, cv. Rv-8, cv. Rv-9,
cv. Tv-10, cv. Tv-2, cv. Tv-3, cv. Tv-4, cv. Tv-5, cv. Tv-6, cv. Tv-7,
cv. Tv-8, cv. Tv-9, cv. Wlp-10, cv. Wlp-2, cv. Wlp-3, cv. Wlp-4,
cv. Wlp-5, cv. Wlp-6, cv. Wlp-7, cv. Wlp-8, and cv. Wlp-9;
PubMed=12411612; DOI=10.1093/oxfordjournals.molbev.a004027;
Kuittinen H., Salguero D., Aguade M.;
"Parallel patterns of sequence variation within and between
populations at three loci of Arabidopsis thaliana.";
Mol. Biol. Evol. 19:2030-2034(2002).
[4]
NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, AND INDUCTION BY
LIGHT.
STRAIN=cv. Columbia;
PubMed=15821875; DOI=10.1007/s11103-004-6910-0;
Hartmann U., Sagasser M., Mehrtens F., Stracke R., Weisshaar B.;
"Differential combinatorial interactions of cis-acting elements
recognized by R2R3-MYB, BZIP, and BHLH factors control light-
responsive and tissue-specific activation of phenylpropanoid
biosynthesis genes.";
Plant Mol. Biol. 57:155-171(2005).
[5]
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).
[6]
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).
[7]
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).
[8]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
Feldmann K.A.;
"Full-length cDNA from Arabidopsis thaliana.";
Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
[9]
REVIEW, AND NOMENCLATURE.
PubMed=23473981; DOI=10.1016/j.plaphy.2013.02.001;
Saito K., Yonekura-Sakakibara K., Nakabayashi R., Higashi Y.,
Yamazaki M., Tohge T., Fernie A.R.;
"The flavonoid biosynthetic pathway in Arabidopsis: Structural and
genetic diversity.";
Plant Physiol. Biochem. 72:21-34(2013).
[10]
X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS).
PubMed=22622584; DOI=10.1038/nature11009;
Ngaki M.N., Louie G.V., Philippe R.N., Manning G., Pojer F.,
Bowman M.E., Li L., Larsen E., Wurtele E.S., Noel J.P.;
"Evolution of the chalcone-isomerase fold from fatty-acid binding to
stereospecific catalysis.";
Nature 485:530-533(2012).
-!- FUNCTION: Catalyzes the intramolecular cyclization of bicyclic
chalcones into tricyclic (S)-flavanones. Responsible for the
isomerization of 4,2',4',6'-tetrahydroxychalcone (also termed
chalcone) into naringenin. {ECO:0000269|PubMed:1354004}.
-!- CATALYTIC ACTIVITY: A chalcone = a flavanone.
-!- PATHWAY: Secondary metabolite biosynthesis; flavonoid
biosynthesis.
-!- INTERACTION:
P13114:CHS; NbExp=4; IntAct=EBI-1546761, EBI-1546775;
-!- TISSUE SPECIFICITY: Mostly expressed in siliques and flowers, and,
to a lower extent, in leaves. {ECO:0000269|PubMed:15821875}.
-!- INDUCTION: By light. {ECO:0000269|PubMed:15821875}.
-!- MISCELLANEOUS: Part of the biosynthetic pathway for all classes of
flavonoids, a large class of secondary plant metabolites, many of
which are brightly colored.
-!- SIMILARITY: Belongs to the chalcone isomerase family.
{ECO:0000305}.
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EMBL; M86358; AAA32766.1; -; Genomic_DNA.
EMBL; AJ287299; CAB94969.1; -; Genomic_DNA.
EMBL; AJ287300; CAB94970.1; -; Genomic_DNA.
EMBL; AJ287301; CAB94971.1; -; Genomic_DNA.
EMBL; AJ287302; CAB94972.1; -; Genomic_DNA.
EMBL; AJ287303; CAB94973.1; -; Genomic_DNA.
EMBL; AJ287304; CAB94974.1; -; Genomic_DNA.
EMBL; AJ287305; CAB94975.1; -; Genomic_DNA.
EMBL; AJ287306; CAB94976.1; -; Genomic_DNA.
EMBL; AJ287307; CAB94977.1; -; Genomic_DNA.
EMBL; AJ287308; CAB94978.1; -; Genomic_DNA.
EMBL; AJ287309; CAB94979.1; -; Genomic_DNA.
EMBL; AJ287310; CAB94980.1; -; Genomic_DNA.
EMBL; AJ287311; CAB94981.1; -; Genomic_DNA.
EMBL; AJ287312; CAB94982.1; -; Genomic_DNA.
EMBL; AJ287313; CAB94983.1; -; Genomic_DNA.
EMBL; AJ287314; CAB94984.1; -; Genomic_DNA.
EMBL; AJ287315; CAB94985.1; -; Genomic_DNA.
EMBL; AJ287316; CAB94986.1; -; Genomic_DNA.
EMBL; AJ287317; CAB94987.1; -; Genomic_DNA.
EMBL; AJ287318; CAB94988.1; -; Genomic_DNA.
EMBL; AJ287319; CAB94989.1; -; Genomic_DNA.
EMBL; AJ287320; CAB94990.1; -; Genomic_DNA.
EMBL; AJ287321; CAB94991.1; -; Genomic_DNA.
EMBL; AJ492461; CAD42187.1; -; Genomic_DNA.
EMBL; AJ492462; CAD42188.1; -; Genomic_DNA.
EMBL; AJ492463; CAD42189.1; -; Genomic_DNA.
EMBL; AJ492464; CAD42190.1; -; Genomic_DNA.
EMBL; AJ492465; CAD42191.1; -; Genomic_DNA.
EMBL; AJ492466; CAD42192.1; -; Genomic_DNA.
EMBL; AJ492467; CAD42193.1; -; Genomic_DNA.
EMBL; AJ492468; CAD42194.1; -; Genomic_DNA.
EMBL; AJ492469; CAD42195.1; -; Genomic_DNA.
EMBL; AJ492470; CAD42196.1; -; Genomic_DNA.
EMBL; AJ492471; CAD42197.1; -; Genomic_DNA.
EMBL; AJ492472; CAD42198.1; -; Genomic_DNA.
EMBL; AJ492473; CAD42199.1; -; Genomic_DNA.
EMBL; AJ492474; CAD42200.1; -; Genomic_DNA.
EMBL; AJ492475; CAD42201.1; -; Genomic_DNA.
EMBL; AJ492476; CAD42202.1; -; Genomic_DNA.
EMBL; AJ492477; CAD42203.1; -; Genomic_DNA.
EMBL; AJ492478; CAD42204.1; -; Genomic_DNA.
EMBL; AJ492479; CAD42205.1; -; Genomic_DNA.
EMBL; AJ492480; CAD42206.1; -; Genomic_DNA.
EMBL; AJ492481; CAD42207.1; -; Genomic_DNA.
EMBL; AJ492482; CAD42208.1; -; Genomic_DNA.
EMBL; AJ492483; CAD42209.1; -; Genomic_DNA.
EMBL; AJ492484; CAD42210.1; -; Genomic_DNA.
EMBL; AJ492485; CAD42211.1; -; Genomic_DNA.
EMBL; AJ492486; CAD42212.1; -; Genomic_DNA.
EMBL; AJ492487; CAD42213.1; -; Genomic_DNA.
EMBL; AJ492488; CAD42214.1; -; Genomic_DNA.
EMBL; AJ492489; CAD42215.1; -; Genomic_DNA.
EMBL; AJ492490; CAD42216.1; -; Genomic_DNA.
EMBL; AJ492491; CAD42217.1; -; Genomic_DNA.
EMBL; AJ492492; CAD42218.1; -; Genomic_DNA.
EMBL; AJ492493; CAD42219.1; -; Genomic_DNA.
EMBL; AJ492494; CAD42220.1; -; Genomic_DNA.
EMBL; AJ492495; CAD42221.1; -; Genomic_DNA.
EMBL; AJ492496; CAD42222.1; -; Genomic_DNA.
EMBL; AJ492497; CAD42223.1; -; Genomic_DNA.
EMBL; AJ492498; CAD42224.1; -; Genomic_DNA.
EMBL; AJ492499; CAD42225.1; -; Genomic_DNA.
EMBL; AJ492500; CAD42226.1; -; Genomic_DNA.
EMBL; AJ492501; CAD42227.1; -; Genomic_DNA.
EMBL; AJ492502; CAD42228.1; -; Genomic_DNA.
EMBL; AJ492503; CAD42229.1; -; Genomic_DNA.
EMBL; AJ418046; CAD10782.1; -; mRNA.
EMBL; AF439537; AAL35225.1; -; Genomic_DNA.
EMBL; AL132970; CAB82707.2; -; Genomic_DNA.
EMBL; CP002686; AEE79342.1; -; Genomic_DNA.
EMBL; BT004265; AAO42267.1; -; mRNA.
EMBL; BT005528; AAO63948.1; -; mRNA.
EMBL; AY086088; AAM63295.1; -; mRNA.
PIR; JQ1687; JQ1687.
PIR; T47651; T47651.
RefSeq; NP_191072.1; NM_115370.4.
UniGene; At.27425; -.
PDB; 4DOI; X-ray; 1.55 A; A/B=1-246.
PDBsum; 4DOI; -.
ProteinModelPortal; P41088; -.
SMR; P41088; -.
IntAct; P41088; 3.
STRING; 3702.AT3G55120.1; -.
iPTMnet; P41088; -.
PaxDb; P41088; -.
PRIDE; P41088; -.
EnsemblPlants; AT3G55120.1; AT3G55120.1; AT3G55120.
GeneID; 824678; -.
Gramene; AT3G55120.1; AT3G55120.1; AT3G55120.
KEGG; ath:AT3G55120; -.
Araport; AT3G55120; -.
TAIR; locus:2097228; AT3G55120.
eggNOG; ENOG410IJZH; Eukaryota.
eggNOG; ENOG410YEUK; LUCA.
HOGENOM; HOG000006208; -.
InParanoid; P41088; -.
KO; K01859; -.
OMA; ENCVAFW; -.
OrthoDB; EOG09360OSC; -.
PhylomeDB; P41088; -.
BioCyc; ARA:AT3G55120-MONOMER; -.
UniPathway; UPA00154; -.
PRO; PR:P41088; -.
Proteomes; UP000006548; Chromosome 3.
ExpressionAtlas; P41088; baseline and differential.
Genevisible; P41088; AT.
GO; GO:0005783; C:endoplasmic reticulum; IDA:TAIR.
GO; GO:0042406; C:extrinsic component of endoplasmic reticulum membrane; IDA:TAIR.
GO; GO:0005634; C:nucleus; IDA:TAIR.
GO; GO:0009705; C:plant-type vacuole membrane; IDA:TAIR.
GO; GO:0045430; F:chalcone isomerase activity; IEA:UniProtKB-EC.
GO; GO:0009813; P:flavonoid biosynthetic process; IMP:TAIR.
GO; GO:0009733; P:response to auxin; IEP:TAIR.
GO; GO:0080167; P:response to karrikin; IEP:TAIR.
GO; GO:0009411; P:response to UV; IMP:TAIR.
GO; GO:0010224; P:response to UV-B; IMP:TAIR.
Gene3D; 1.10.890.20; -; 1.
Gene3D; 3.50.70.10; -; 2.
InterPro; IPR016087; Chalcone_isomerase.
InterPro; IPR016088; Chalcone_isomerase_3-sand.
InterPro; IPR016089; Chalcone_isomerase_bundle_sf.
InterPro; IPR036298; Chalcone_isomerase_sf.
Pfam; PF02431; Chalcone; 1.
SUPFAM; SSF54626; SSF54626; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Flavonoid biosynthesis; Isomerase;
Reference proteome.
CHAIN 1 246 Chalcone--flavonone isomerase 1.
/FTId=PRO_0000166428.
BINDING 59 59 Substrate. {ECO:0000250}.
BINDING 124 124 Substrate. {ECO:0000250}.
BINDING 201 201 Substrate. {ECO:0000250}.
SITE 117 117 Important for catalytic activity.
{ECO:0000250}.
VARIANT 202 202 I -> V (in strain: cv. Cha-0).
VARIANT 238 238 V -> L (in strain: cv. Gr-5, cv. Gran-2,
cv. Gran-3, cv. Gran-5, cv. Gran-7, cv.
Gran-8, cv. Gran-10, cv. Ita-0, cv. Ler,
cv. Mh-0, cv. Per-1, cv. Rv-1, cv. Rv-3,
cv. Rv-4, cv. Rv-5, cv. Rv-8, cv. Wlp-1,
cv. Wlp-2, cv. Wlp-3, cv. Wlp-4, cv. Wlp-
5, cv. Wlp-6, cv. Wlp-7, cv. Wlp-8, cv.
Wlp-9 and cv. Wlp-10).
VARIANT 246 246 N -> NRE (in strain: cv. Rv-2, cv. Rv-9,
cv. Rv-10, cv. Tv-1, cv. Tv-2, cv. TV-6,
cv. Tv-7, cv. Tv-8, cv. Tv-9 and cv. Tv-
10).
STRAND 19 21 {ECO:0000244|PDB:4DOI}.
STRAND 24 26 {ECO:0000244|PDB:4DOI}.
STRAND 28 31 {ECO:0000244|PDB:4DOI}.
TURN 33 35 {ECO:0000244|PDB:4DOI}.
STRAND 38 51 {ECO:0000244|PDB:4DOI}.
STRAND 54 65 {ECO:0000244|PDB:4DOI}.
HELIX 69 77 {ECO:0000244|PDB:4DOI}.
HELIX 82 87 {ECO:0000244|PDB:4DOI}.
HELIX 89 97 {ECO:0000244|PDB:4DOI}.
STRAND 102 110 {ECO:0000244|PDB:4DOI}.
HELIX 114 121 {ECO:0000244|PDB:4DOI}.
TURN 122 124 {ECO:0000244|PDB:4DOI}.
HELIX 125 131 {ECO:0000244|PDB:4DOI}.
HELIX 137 150 {ECO:0000244|PDB:4DOI}.
STRAND 160 165 {ECO:0000244|PDB:4DOI}.
STRAND 169 179 {ECO:0000244|PDB:4DOI}.
STRAND 186 190 {ECO:0000244|PDB:4DOI}.
HELIX 192 203 {ECO:0000244|PDB:4DOI}.
HELIX 210 224 {ECO:0000244|PDB:4DOI}.
HELIX 227 230 {ECO:0000244|PDB:4DOI}.
SEQUENCE 246 AA; 26596 MW; 2EB68BF68D576B98 CRC64;
MSSSNACASP SPFPAVTKLH VDSVTFVPSV KSPASSNPLF LGGAGVRGLD IQGKFVIFTV
IGVYLEGNAV PSLSVKWKGK TTEELTESIP FFREIVTGAF EKFIKVTMKL PLTGQQYSEK
VTENCVAIWK QLGLYTDCEA KAVEKFLEIF KEETFPPGSS ILFALSPTGS LTVAFSKDDS
IPETGIAVIE NKLLAEAVLE SIIGKNGVSP GTRLSVAERL SQLMMKNKDE KEVSDHSVEE
KLAKEN


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