Histone-lysine N-methyltransferase CLF - Arabidopsis thaliana (Mouse-ear cress)

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P93831 (CLF_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified December 14, 2011. Version 94. History...

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Histone-lysine N-methyltransferase CLF
EC=2.1.1.43

Alternative name(s):
Polycomb group protein CURLY LEAF
Protein INCURVATA 1
Protein SET DOMAIN GROUP 1
Protein photoperiod insensitive flowering

Gene names

Name:	CLF
Synonyms:	ICU1, PIF1, PIF2, SDG1, SET1
Ordered Locus Names:	At2g23380
ORF Names:	F26B6.3

Organism

Arabidopsis thaliana (Mouse-ear cress)

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	902 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Polycomb group (PcG) protein. Catalytic subunit of some PcG multiprotein complex, which methylates 'Lys-27' of histone H3, leading to transcriptional repression of the affected target genes. Required to regulate floral development by repressing the AGAMOUS homeotic gene in leaves, influorescence stems and flowers. Regulates the antero-posterior organization of the endosperm, as well as the division and elongation rates of leaf cells. PcG proteins act by forming multiprotein complexes, which are required to maintain the transcriptionally repressive state of homeotic genes throughout development. PcG proteins are not required to initiate repression, but to maintain it during later stages of development. Ref.1 Ref.4 Ref.5 Ref.6
Catalytic activity	S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
Subunit structure	Probable component of a PcG complex. In plants, PcG complexes are probably composed of a member of the EZ family (CLF or MEA), FIE, and a member of the VEFS family (FIS2, VRN2 or EMF2) By similarity. Interacts with RING1A. Ref.8 Ref.9
Subcellular location	Nucleus Ref.7.
Tissue specificity	Strongly expressed throughout the apical meristem, leaf primordia, and leaves of 7-8 day-old seedling. Weakly expressed in the vasculature of hypocotyl. Strongly expressed throughout the young stages 1 and 2 floral meristems that arose on the flanks of the apex. In stage 3 and 4 flowers, it is expressed in the emerging sepal primordia and in the dome of the floral meristem. During stages 6 and 7, it is strongly expressed in developing petal and stamen, and weakly expressed in the sepals. Late in floral development, at stage 12, it is weakly expressed in all floral whorls, and expressed at intermediate level in petals and ovules. Ref.1
Developmental stage	Expressed in all four whorls throughout flower development.
Sequence similarities	Belongs to the histone-lysine methyltransferase family. EZ subfamily. Contains 1 SANT domain. Contains 1 SET domain.

Ontologies

Keywords
Biological process	Differentiation Flowering Transcription Transcription regulation
Cellular component	Nucleus
Ligand	S-adenosyl-L-methionine
Molecular function	Developmental protein Methyltransferase Repressor Transferase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	DNA mediated transformation Inferred from mutant phenotype. Source: TAIR cell differentiation Inferred from electronic annotation. Source: UniProtKB-KW flower development Inferred from electronic annotation. Source: UniProtKB-KW leaf morphogenesis Inferred from mutant phenotype Ref.5. Source: TAIR negative regulation of molecular function, epigenetic Inferred from mutant phenotype. Source: TAIR regulation of gene expression by genetic imprinting Inferred from mutant phenotype. Source: TAIR regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW vegetative to reproductive phase transition of meristem Inferred from mutant phenotype. Source: TAIR
Cellular component	nucleus Inferred from direct assay. Source: TAIR
Molecular function	histone-lysine N-methyltransferase activity Inferred from electronic annotation. Source: EC protein binding Inferred from physical interaction. Source: IntAct single-stranded RNA binding Inferred from direct assay. Source: TAIR
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
EMF2	Q8L6Y4	4	EBI-307155,EBI-2128696
FIE	Q9LT47	4	EBI-307155,EBI-307146

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 902

902

Histone-lysine N-methyltransferase CLF

PRO_0000213995

Regions

Domain

531 – 581

SANT

Domain

751 – 871

121

SET

Compositional bias

649 – 720

Cys-rich

Experimental info

Sequence conflict

225

S → N in CAA71599. Ref.2

Sequence conflict

332

T → P in CAA71599. Ref.2

Sequence conflict

415

K → N in CAA71599. Ref.2

Sequence conflict

658

K → Q in CAA71599. Ref.2

Sequence conflict

674

C → Y in CAA71599. Ref.2

Sequence conflict

761

V → I in CAA71599. Ref.2

Sequences

Sequence

Length

Mass (Da)

Tools

P93831 [UniParc].

Last modified May 16, 2003. Version 2.
Checksum: 90B45ED27D219D64
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FASTA

902

100,370

        10         20         30         40         50         60 
MASEASPSSS ATRSEPPKDS PAEERGPASK EVSEVIESLK KKLAADRCIS IKKRIDENKK 

        70         80         90        100        110        120 
NLFAITQSFM RSSMERGGSC KDGSDLLVKR QRDSPGMKSG IDESNNNRYV EDGPASSGMV 

       130        140        150        160        170        180 
QGSSVPVKIS LRPIKMPDIK RLSPYTTWVF LDRNQRMTED QSVVGRRRIY YDQTGGEALI 

       190        200        210        220        230        240 
CSDSEEEAID DEEEKRDFLE PEDYIIRMTL EQLGLSDSVL AELASFLSRS TSEIKARHGV 

       250        260        270        280        290        300 
LMKEKEVSES GDNQAESSLL NKDMEGALDS FDNLFCRRCL VFDCRLHGCS QDLIFPAEKP 

       310        320        330        340        350        360 
APWCPPVDEN LTCGANCYKT LLKSGRFPGY GTIEGKTGTS SDGAGTKTTP TKFSSKLNGR 

       370        380        390        400        410        420 
KPKTFPSESA SSNEKCALET SDSENGLQQD TNSDKVSSSP KVKGSGRRVG RKRNKNRVAE 

       430        440        450        460        470        480 
RVPRKTQKRQ KKTEASDSDS IASGSCSPSD AKHKDNEDAT SSSQKHVKSG NSGKSRKNGT 

       490        500        510        520        530        540 
PAEVSNNSVK DDVPVCQSNE VASELDAPGS DESLRKEEFM GETVSRGRLA TNKLWRPLEK 

       550        560        570        580        590        600 
SLFDKGVEIF GMNSCLIARN LLSGFKSCWE VFQYMTCSEN KASFFGGDGL NPDGSSKFDI 

       610        620        630        640        650        660 
NGNMVNNQVR RRSRFLRRRG KVRRLKYTWK SAAYHSIRKR ITEKKDQPCR QFNPCNCKIA 

       670        680        690        700        710        720 
CGKECPCLLN GTCCEKYCGC PKSCKNRFRG CHCAKSQCRS RQCPCFAADR ECDPDVCRNC 

       730        740        750        760        770        780 
WVIGGDGSLG VPSQRGDNYE CRNMKLLLKQ QQRVLLGISD VSGWGAFLKN SVSKHEYLGE 

       790        800        810        820        830        840 
YTGELISHKE ADKRGKIYDR ENCSFLFNLN DQFVLDAYRK GDKLKFANHS PEPNCYAKVI 

       850        860        870        880        890        900 
MVAGDHRVGI FAKERILAGE ELFYDYRYEP DRAPAWAKKP EAPGSKKDEN VTPSVGRPKK 


LA

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"A Polycomb-group gene regulates homeotic gene expression in Arabidopsis." Goodrich J., Puangsomlee P., Martin M., Long D., Meyerowitz E.M., Coupland G. Nature 386:44-51(1997) [PubMed: 9052779] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY. Strain: cv. Landsberg erecta. Tissue: Flower.
[2]	"Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana." Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D., Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V., Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S., Cronin L.A. Venter J.C. Nature 402:761-768(1999) [PubMed: 10617197] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[3]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[4]	"The CURLY LEAF gene controls both division and elongation of cells during the expansion of the leaf blade in Arabidopsis thaliana." Kim G.-T., Tsukaya H., Uchimiya H. Planta 206:175-183(1998) [PubMed: 9736998] [Abstract] Cited for: FUNCTION.
[5]	"Genetic analysis of incurvata mutants reveals three independent genetic operations at work in Arabidopsis leaf morphogenesis." Serrano-Cartagena J., Candela H., Robles P., Ponce M.R., Perez-Perez J.M., Piqueras P., Micol J.L. Genetics 156:1363-1377(2000) [PubMed: 11063708] [Abstract] Cited for: FUNCTION.
[6]	"Polycomb group genes control pattern formation in plant seed." Soerensen M.B., Chaudhury A.M., Robert H., Bancharel E., Berger F. Curr. Biol. 11:277-281(2001) [PubMed: 11250158] [Abstract] Cited for: FUNCTION.
[7]	"The Arabidopsis thaliana genome contains at least 29 active genes encoding SET domain proteins that can be assigned to four evolutionarily conserved classes." Baumbusch L.O., Thorstensen T., Krauss V., Fischer A., Naumann K., Assalkhou R., Schulz I., Reuter G., Aalen R.B. Nucleic Acids Res. 29:4319-4333(2001) [PubMed: 11691919] [Abstract] Cited for: SUBCELLULAR LOCATION.
[8]	"FIE and CURLY LEAF polycomb proteins interact in the regulation of homeobox gene expression during sporophyte development." Katz A., Oliva M., Mosquna A., Hakim O., Ohad N. Plant J. 37:707-719(2004) [PubMed: 14871310] [Abstract] Cited for: INTERACTION WITH FIE.
[9]	"Polycomb silencing of KNOX genes confines shoot stem cell niches in Arabidopsis." Xu L., Shen W.H. Curr. Biol. 18:1966-1971(2008) [PubMed: 19097900] [Abstract] Cited for: INTERACTION WITH RING1A.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	Y10580 mRNA. Translation: CAA71599.1. AC003040 Genomic DNA. Translation: AAC23781.1. CP002685 Genomic DNA. Translation: AEC07449.1.
IPI	IPI00534983.
PIR	T01127.
RefSeq	NP_179919.1. NM_127902.5.
UniGene	At.22.
3D structure databases
ProteinModelPortal	P93831.
SMR	P93831. Positions 651-872.
ModBase	Search...
Protein-protein interaction databases
IntAct	P93831. 6 interactions.
STRING	P93831.
Proteomic databases
PRIDE	P93831.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT2G23380.1; AT2G23380.1; AT2G23380.
GeneID	816870.
GenomeReviews	Gene locus AT2G23380 in contig CT485783_GR.
KEGG	ath:AT2G23380.
NMPDR	fig\|3702.1.peg.9364.
Organism-specific databases
GeneFarm	2273.
TAIR	At2g23380.
Phylogenomic databases
eggNOG	KOG1079.
GeneTree	EPGT00070000028476.
HOGENOM	HBG633142.
InParanoid	P93831.
OMA	KVIMVAG.
PhylomeDB	P93831.
ProtClustDB	CLSN2683888.
Gene expression databases
ArrayExpress	P93831.
Genevestigator	P93831.
GermOnline	AT2G23380. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR001214. SET_dom. [Graphical view]
KO	K11430.
Pfam	PF00856. SET. 1 hit. [Graphical view]
SMART	SM00317. SET. 1 hit. [Graphical view]
PROSITE	PS51293. SANT. False negative. PS50280. SET. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

CLF_ARATH

Accession

Primary (citable) accession number: P93831
Secondary accession number(s): O80455

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 16, 2003
Last sequence update:	May 16, 2003
Last modified:	December 14, 2011
This is version 94 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program

Relevant documents

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents