Reviewed, UniProtKB/Swiss-Prot P41088 (CFI1_ARATH)

Names and origin

Protein names

Recommended name:
    Chalcone--flavonone isomerase 1
      Short name=Chalcone isomerase 1
    EC=5.5.1.6
Alternative name(s):
    Protein TRANSPARENT TESTA 5

Gene names

Name:	CHI1
Synonyms:	CFI, TT5
Ordered Locus Names:	At3g55120
ORF Names:	T15C9_120

Organism

Arabidopsis thaliana (Mouse-ear cress) [Complete proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › eurosids II › Brassicales › Brassicaceae › Arabidopsis

Protein attributes

Sequence length	246 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at transcript level.

General annotation (Comments)

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. Ref.1
Catalytic activity	A chalcone = a flavanone.
Pathway	Secondary metabolite biosynthesis; flavonoid biosynthesis.
Tissue specificity	Mostly expressed in siliques and flowers, and, to a lower extent, in leaves. Ref.4
Induction	By light. Ref.4
Miscellaneous	Part of the biosynthetic pathway for all classes of flavonoids, a large class of secondary plant metabolites, many of which are brightly colored.
Sequence similarities	Belongs to the chalcone isomerase family.

Ontologies

Keywords
Biological process	Flavonoid biosynthesis
Molecular function	Isomerase
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	flavonoid biosynthetic process Inferred from mutant phenotype. Source: TAIR response to UV-B Inferred from mutant phenotype. Source: TAIR
Cellular component	extrinsic to endoplasmic reticulum membrane Inferred from direct assay. Source: TAIR nucleus Inferred from direct assay. Source: TAIR plant-type vacuole membrane Inferred from direct assay. Source: TAIR
Molecular function	chalcone isomerase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 246	246	Chalcone--flavonone isomerase 1		PRO_0000166428
Sites
	Binding site	59	1	Substrate By similarity
	Binding site	124	1	Substrate By similarity
	Binding site	201	1	Substrate By similarity
	Site	117	1	Important for catalytic activity By similarity
Natural variations
	Natural variant	202	1	I → V in strain: cv. Cha-0.
	Natural variant	238	1	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.
	Natural variant	246	1	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.

Sequences

	Sequence		Length	Mass (Da)
	P41088-1 [UniParc]. Last modified July 11, 2002. Version 2. Checksum: 2EB68BF68D576B98	FASTA	246	26,596
	10 20 30 40 50 60 MSSSNACASP SPFPAVTKLH VDSVTFVPSV KSPASSNPLF LGGAGVRGLD IQGKFVIFTV 70 80 90 100 110 120 IGVYLEGNAV PSLSVKWKGK TTEELTESIP FFREIVTGAF EKFIKVTMKL PLTGQQYSEK 130 140 150 160 170 180 VTENCVAIWK QLGLYTDCEA KAVEKFLEIF KEETFPPGSS ILFALSPTGS LTVAFSKDDS 190 200 210 220 230 240 IPETGIAVIE NKLLAEAVLE SIIGKNGVSP GTRLSVAERL SQLMMKNKDE KEVSDHSVEE KLAKEN

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Effects of ionizing radiation on a plant genome: analysis of two Arabidopsis transparent testa mutations." Shirley B.W., Hanley S., Goodman H.M. Plant Cell 4:333-347(1992) [PubMed: 1354004] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION. Strain: cv. Columbia and cv. Landsberg erecta.
[2]	"Nucleotide variation at the chalcone isomerase locus in Arabidopsis thaliana." Kuittinen H., Aguade M. Genetics 155:863-872(2000) [PubMed: 10835405] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: cv. Gr-5, cv. Ita-0, cv. Mh-0, cv. Per-1, cv. Rv-1 and cv. Wlp-2.
[3]	"Parallel patterns of sequence variation within and between populations at three loci of Arabidopsis thaliana." Kuittinen H., Salguero D., Aguade M. Mol. Biol. Evol. 19:2030-2034(2002) [PubMed: 12411612] [Abstract] Cited for: 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.
[4]	"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." Hartmann U., Sagasser M., Mehrtens F., Stracke R., Weisshaar B. Plant Mol. Biol. 57:155-171(2005) [PubMed: 15821875] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, INDUCTION BY LIGHT. Strain: cv. Columbia.
[5]	"Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana." 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. Nature 408:820-822(2000) [PubMed: 11130713] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[6]	"Empirical analysis of transcriptional activity in the Arabidopsis genome." 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. Science 302:842-846(2003) [PubMed: 14593172] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[7]	"Full-length cDNA from Arabidopsis thaliana." Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A. Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	M86358 Genomic DNA. Translation: AAA32766.1. AJ287299 Genomic DNA. Translation: CAB94969.1. AJ287300 Genomic DNA. Translation: CAB94970.1. AJ287301 Genomic DNA. Translation: CAB94971.1. AJ287302 Genomic DNA. Translation: CAB94972.1. AJ287303 Genomic DNA. Translation: CAB94973.1. AJ287304 Genomic DNA. Translation: CAB94974.1. AJ287305 Genomic DNA. Translation: CAB94975.1. AJ287306 Genomic DNA. Translation: CAB94976.1. AJ287307 Genomic DNA. Translation: CAB94977.1. AJ287308 Genomic DNA. Translation: CAB94978.1. AJ287309 Genomic DNA. Translation: CAB94979.1. AJ287310 Genomic DNA. Translation: CAB94980.1. AJ287311 Genomic DNA. Translation: CAB94981.1. AJ287312 Genomic DNA. Translation: CAB94982.1. AJ287313 Genomic DNA. Translation: CAB94983.1. AJ287314 Genomic DNA. Translation: CAB94984.1. AJ287315 Genomic DNA. Translation: CAB94985.1. AJ287316 Genomic DNA. Translation: CAB94986.1. AJ287317 Genomic DNA. Translation: CAB94987.1. AJ287318 Genomic DNA. Translation: CAB94988.1. AJ287319 Genomic DNA. Translation: CAB94989.1. AJ287320 Genomic DNA. Translation: CAB94990.1. AJ287321 Genomic DNA. Translation: CAB94991.1. AJ492461 Genomic DNA. Translation: CAD42187.1. AJ492462 Genomic DNA. Translation: CAD42188.1. AJ492463 Genomic DNA. Translation: CAD42189.1. AJ492464 Genomic DNA. Translation: CAD42190.1. AJ492465 Genomic DNA. Translation: CAD42191.1. AJ492466 Genomic DNA. Translation: CAD42192.1. AJ492467 Genomic DNA. Translation: CAD42193.1. AJ492468 Genomic DNA. Translation: CAD42194.1. AJ492469 Genomic DNA. Translation: CAD42195.1. AJ492470 Genomic DNA. Translation: CAD42196.1. AJ492471 Genomic DNA. Translation: CAD42197.1. AJ492472 Genomic DNA. Translation: CAD42198.1. AJ492473 Genomic DNA. Translation: CAD42199.1. AJ492474 Genomic DNA. Translation: CAD42200.1. AJ492475 Genomic DNA. Translation: CAD42201.1. AJ492476 Genomic DNA. Translation: CAD42202.1. AJ492477 Genomic DNA. Translation: CAD42203.1. AJ492478 Genomic DNA. Translation: CAD42204.1. AJ492479 Genomic DNA. Translation: CAD42205.1. AJ492480 Genomic DNA. Translation: CAD42206.1. AJ492481 Genomic DNA. Translation: CAD42207.1. AJ492482 Genomic DNA. Translation: CAD42208.1. AJ492483 Genomic DNA. Translation: CAD42209.1. AJ492484 Genomic DNA. Translation: CAD42210.1. AJ492485 Genomic DNA. Translation: CAD42211.1. AJ492486 Genomic DNA. Translation: CAD42212.1. AJ492487 Genomic DNA. Translation: CAD42213.1. AJ492488 Genomic DNA. Translation: CAD42214.1. AJ492489 Genomic DNA. Translation: CAD42215.1. AJ492490 Genomic DNA. Translation: CAD42216.1. AJ492491 Genomic DNA. Translation: CAD42217.1. AJ492492 Genomic DNA. Translation: CAD42218.1. AJ492493 Genomic DNA. Translation: CAD42219.1. AJ492494 Genomic DNA. Translation: CAD42220.1. AJ492495 Genomic DNA. Translation: CAD42221.1. AJ492496 Genomic DNA. Translation: CAD42222.1. AJ492497 Genomic DNA. Translation: CAD42223.1. AJ492498 Genomic DNA. Translation: CAD42224.1. AJ492499 Genomic DNA. Translation: CAD42225.1. AJ492500 Genomic DNA. Translation: CAD42226.1. AJ492501 Genomic DNA. Translation: CAD42227.1. AJ492502 Genomic DNA. Translation: CAD42228.1. AJ492503 Genomic DNA. Translation: CAD42229.1. AJ418046 mRNA. Translation: CAD10782.1. AF439537 Genomic DNA. Translation: AAL35225.1. AL132970 Genomic DNA. Translation: CAB82707.2. BT004265 mRNA. Translation: AAO42267.1. BT005528 mRNA. Translation: AAO63948.1. AY086088 mRNA. Translation: AAM63295.1.
IPI	IPI00534732.
PIR	JQ1687. T47651.
RefSeq	NP_191072.1.
UniGene	At.27425
3D structure databases
HSSP	HSSP built from PDB template 1JX1 based on UniProtKB P28012.
ModBase	Search...
Protein-protein interaction databases
IntAct	P41088. 3 interactions.
Proteomic databases
PRIDE	P41088.
Genome annotation databases
GeneID	824678.
GenomeReviews	Gene locus AT3G55120 in contig BA000014_GR.
KEGG	ath:AT3G55120.
NMPDR	fig|3702.1.peg.16826.
Organism-specific databases
TAIR	At3g55120.
Phylogenomic databases
OMA	P41088. VIENKLL.
Enzyme and pathway databases
BRENDA	5.5.1.6. 302.
Gene expression databases
ArrayExpress	P41088.
GermOnline	AT3G55120. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR016088. Chalcone_isomerase_3-sand. IPR003466. Chalcone_isomerase_subgr. [Graphical view]
Gene3D	G3DSA:3.50.70.10. Chalcone. 1 hit.
Pfam	PF02431. Chalcone. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

CFI1_ARATH

Accession

Primary (citable) accession number: P41088
Secondary accession number(s): Q8W532 , Q9LE13, Q9LF74, Q9LF75

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	July 11, 2002
Last modified:	June 16, 2009
This is version 72 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)