Reviewed, UniProtKB/Swiss-Prot Q84LH8 (PIF5_ARATH)

Names and origin

Protein names

Recommended name:
    Phytochrome-interacting factor 5
Alternative name(s):
    Basic helix-loop-helix protein 65
      Short name=bHLH 65
      Short name=AtbHLH065
    Phytochrome interacting factor-like 6

Gene names

Name:	PIF5
Synonyms:	PIL6
Ordered Locus Names:	At3g59060
ORF Names:	F17J16.110

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	444 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Transcription factor acting negatively in the phytochrome B signaling pathway to promote the shade-avoidance response. Regulates PHYB abundance at the post-transcriptional level, possibly via the ubiquitin-proteasome pathway. Promotes ethylene activity in the dark. May regulate the expression of a subset of genes by binding to the G-box motif. Might be involved in the integration of light-signals to control both circadian and photomorphogenic processes.
Subunit structure	Interacts specifically with the Pfr form of phytochrome B and with TOC1/APRR1. May form a heterodimer with PIF3.
Subcellular location	NucleusBy similarity.
Developmental stage	Circadian-controlled expression.
Induction	Up-regulated by white light. Rapid degradation after red light exposure (at protein level). Accumulates to high levels in the dark, is selectively degraded in response to red light and remains at high levels under shade-mimicking conditions.
Domain	The active phytochrome binding (APB) motif (26-39) is involved in interaction with PHYB and is required for proteasome-mediated degradation.
Post-translational modification	Phosphorylated. Additional phosphorylations induced within 60 seconds following phytochrome B photoactivation.
Sequence similarities	Contains 1 basic helix-loop-helix (bHLH) domain.

Ontologies

Keywords
Biological process	Phytochrome signaling pathway Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Ligand	DNA-binding
PTM	Phosphoprotein
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	red or far red light signaling pathway Inferred from electronic annotation. Source: UniProtKB-KW red, far-red light phototransduction Inferred from electronic annotation. Source: UniProtKB-KW regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	nucleus Inferred from electronic annotation. Source: InterPro
Molecular function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Ref.5 Inferred from physical interaction. Source: IntAct transcription regulator activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
PHYB	P14713	1	EBI-631622,EBI-300727

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q84LH8-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Notes: No experimental confirmation available.

Isoform 2 (identifier: Q84LH8-2)

The sequence of this isoform differs from the canonical sequence as follows:
     405-406: Missing.

Notes: No experimental confirmation available.

Isoform 3 (identifier: Q84LH8-3)

The sequence of this isoform differs from the canonical sequence as follows:
     289-300: TDKASILDEAID → IKLRYWMKQLIT
     301-444: Missing.

Notes: No experimental confirmation available.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 444	444	Phytochrome-interacting factor 5		PRO_0000328935
Regions
	Domain	278 – 306	29	Helix-loop-helix motif
	DNA binding	253 – 277	25	Basic motif
	Region	26 – 39	14	Involved in interaction with phyB
	Compositional bias	266 – 271	6	Poly-Arg
	Compositional bias	319 – 326	8	Poly-Ala
	Compositional bias	342 – 412	71	Gln-rich
Natural variations
	Alternative sequence	289 – 300	12	TDKAS…DEAID → IKLRYWMKQLIT in isoform 3.		VSP_032844
	Alternative sequence	301 – 444	144	Missing in isoform 3.		VSP_032845
	Alternative sequence	405 – 406	2	Missing in isoform 2.		VSP_032846
Experimental info
	Mutagenesis	31	1	E → A: Loss of binding to PHYB
	Mutagenesis	32	1	L → A: Loss of binding to PHYB
	Mutagenesis	37	1	G → A: Loss of binding to PHYB
	Mutagenesis	38	1	Q → A: Loss of binding to PHYB
	Sequence conflict	126	1	T → M in AAM10954. Ref.1
	Sequence conflict	174	1	S → N in AAN15368 and AAL91160. Ref.4
	Sequence conflict	371	1	Q → L in AAM10954. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified June 1, 2003. Version 1. Checksum: 593D72C1F2ED86C7	FASTA	444	49,302
	10 20 30 40 50 60 MEQVFADWNF EDNFHMSTNK RSIRPEDELV ELLWRDGQVV LQSQARREPS VQVQTHKQET 70 80 90 100 110 120 LRKPNNIFLD NQETVQKPNY AALDDQETVS WIQYPPDDVI DPFESEFSSH FFSSIDHLGG 130 140 150 160 170 180 PEKPRTIEET VKHEAQAMAP PKFRSSVITV GPSHCGSNQS TNIHQATTLP VSMSDRSKNV 190 200 210 220 230 240 EERLDTSSGG SSGCSYGRNN KETVSGTSVT IDRKRKHVMD ADQESVSQSD IGLTSTDDQT 250 260 270 280 290 300 MGNKSSQRSG STRRSRAAEV HNLSERRRRD RINERMKALQ ELIPHCSRTD KASILDEAID 310 320 330 340 350 360 YLKSLQMQLQ VMWMGSGMAA AAAAAASPMM FPGVQSSPYI NQMAMQSQMQ LSQFPVMNRS 370 380 390 400 410 420 APQNHPGLVC QNPVQLQLQA QNQILSEQLA RYMGGIPQMP PAGNQMQTVQ QQPADMLGFG 430 440 SPAGPQSQLS APATTDSLHM GKIG
	Isoform 2 [UniParc]. Checksum: 9C4AEBF44151A212		442	49,043
	10 20 30 40 50 60 MEQVFADWNF EDNFHMSTNK RSIRPEDELV ELLWRDGQVV LQSQARREPS VQVQTHKQET 70 80 90 100 110 120 LRKPNNIFLD NQETVQKPNY AALDDQETVS WIQYPPDDVI DPFESEFSSH FFSSIDHLGG 130 140 150 160 170 180 PEKPRTIEET VKHEAQAMAP PKFRSSVITV GPSHCGSNQS TNIHQATTLP VSMSDRSKNV 190 200 210 220 230 240 EERLDTSSGG SSGCSYGRNN KETVSGTSVT IDRKRKHVMD ADQESVSQSD IGLTSTDDQT 250 260 270 280 290 300 MGNKSSQRSG STRRSRAAEV HNLSERRRRD RINERMKALQ ELIPHCSRTD KASILDEAID 310 320 330 340 350 360 YLKSLQMQLQ VMWMGSGMAA AAAAAASPMM FPGVQSSPYI NQMAMQSQMQ LSQFPVMNRS 370 380 390 400 410 420 APQNHPGLVC QNPVQLQLQA QNQILSEQLA RYMGGIPQMP PAGNQTVQQQ PADMLGFGSP 430 440 AGPQSQLSAP ATTDSLHMGK IG
	Isoform 3 [UniParc]. Checksum: EBFE4AA76858DDF1		300	34,233
	10 20 30 40 50 60 MEQVFADWNF EDNFHMSTNK RSIRPEDELV ELLWRDGQVV LQSQARREPS VQVQTHKQET 70 80 90 100 110 120 LRKPNNIFLD NQETVQKPNY AALDDQETVS WIQYPPDDVI DPFESEFSSH FFSSIDHLGG 130 140 150 160 170 180 PEKPRTIEET VKHEAQAMAP PKFRSSVITV GPSHCGSNQS TNIHQATTLP VSMSDRSKNV 190 200 210 220 230 240 EERLDTSSGG SSGCSYGRNN KETVSGTSVT IDRKRKHVMD ADQESVSQSD IGLTSTDDQT 250 260 270 280 290 300 MGNKSSQRSG STRRSRAAEV HNLSERRRRD RINERMKALQ ELIPHCSRIK LRYWMKQLIT

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity." Heim M.A., Jakoby M., Werber M., Martin C., Weisshaar B., Bailey P.C. Mol. Biol. Evol. 20:735-747(2003) [PubMed: 12679534] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), GENE FAMILY, NOMENCLATURE.
[2]	"A Link between circadian-controlled bHLH factors and the APRR1/TOC1 quintet in Arabidopsis thaliana." Yamashino T., Matsushika A., Fujimori T., Sato S., Kato T., Tabata S., Mizuno T. Plant Cell Physiol. 44:619-629(2003) [PubMed: 12826627] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM 1), FUNCTION, INDUCTION, INTERACTION WITH TOC1/APRR1. Strain: cv. Columbia.
[3]	"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.
[4]	"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] (ISOFORM 3). Strain: cv. Columbia.
[5]	"A novel molecular recognition motif necessary for targeting photoactivated phytochrome signaling to specific basic helix-loop-helix transcription factors." Khanna R., Huq E., Kikis E.A., Al-Sady B., Lanzatella C., Quail P.H. Plant Cell 16:3033-3044(2004) [PubMed: 15486100] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF GLU-31; LEU-32; GLY-37 AND GLN-38, INTERACTION WITH PHYB.
[6]	"Circadian-controlled basic/helix-loop-helix factor, PIL6, implicated in light-signal transduction in Arabidopsis thaliana." Fujimori T., Yamashino T., Kato T., Mizuno T. Plant Cell Physiol. 45:1078-1086(2004) [PubMed: 15356333] [Abstract] Cited for: FUNCTION, DEVELOPMENTAL STAGE, INTERACTION WITH TOC1/APRR1 AND PIF3.
[7]	"Rhythmic growth explained by coincidence between internal and external cues." Nozue K., Covington M.F., Duek P.D., Lorrain S., Fankhauser C., Harmer S.L., Maloof J.N. Nature 448:358-361(2007) [PubMed: 17589502] [Abstract] Cited for: FUNCTION, INDUCTION.
[8]	"The basic helix-loop-helix transcription factor PIF5 acts on ethylene biosynthesis and phytochrome signaling by distinct mechanisms." Khanna R., Shen Y., Marion C.M., Tsuchisaka A., Theologis A., Schaefer E., Quail P.H. Plant Cell 19:3915-3929(2007) [PubMed: 18065691] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF GLY-37.
[9]	"Phytochrome induces rapid PIF5 phosphorylation and degradation in response to red-light activation." Shen Y., Khanna R., Carle C.M., Quail P.H. Plant Physiol. 145:1043-1051(2007) [PubMed: 17827270] [Abstract] Cited for: PHOSPHORYLATION.
[10]	"Phytochrome-mediated inhibition of shade avoidance involves degradation of growth-promoting bHLH transcription factors." Lorrain S., Allen T., Duek P.D., Whitelam G.C., Fankhauser C. Plant J. 53:312-323(2008) [PubMed: 18047474] [Abstract] Cited for: FUNCTION, PHOSPHORYLATION, INDUCTION.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AF488598 mRNA. Translation: AAM10954.1. AB103112 pre-RNA. Translation: BAC56978.1. AL163527 Genomic DNA. Translation: CAB86934.1. AY081271 mRNA. Translation: AAL91160.1. BT000049 mRNA. Translation: AAN15368.1.
PIR	T47788.
RefSeq	NP_001030889.1. NP_001030890.1. NP_191465.3.
UniGene	At.43437 At.67329
3D structure databases
HSSP	HSSP built from PDB template 1AN4 based on UniProtKB P22415.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q84LH8.
Genome annotation databases
GeneID	825075.
GenomeReviews	Gene locus AT3G59060 in contig BA000014_GR.
KEGG	ath:AT3G59060.
NMPDR	fig|3702.1.peg.17252.
Organism-specific databases
TAIR	At3g59060.
Family and domain databases
InterPro	IPR001092. HLH_basic. IPR011598. HLH_DNA_bd. [Graphical view]
Gene3D	G3DSA:4.10.280.10. HLH_DNA_bd. 1 hit.
Pfam	PF00010. HLH. 1 hit. [Graphical view]
SMART	SM00353. HLH. 1 hit. [Graphical view]
PROSITE	PS50888. HLH. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

PIF5_ARATH

Accession

Primary (citable) accession number: Q84LH8
Secondary accession number(s): Q8RXG4, Q8S3D7, Q9LYT0

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 8, 2008
Last sequence update:	June 1, 2003
Last modified:	November 25, 2008
This is version 30 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)