CLF_ARATH
ID CLF_ARATH Reviewed; 902 AA.
AC P93831; O80455;
DT 16-MAY-2003, integrated into UniProtKB/Swiss-Prot.
DT 16-MAY-2003, sequence version 2.
DT 03-AUG-2022, entry version 168.
DE RecName: Full=Histone-lysine N-methyltransferase CLF {ECO:0000303|PubMed:9052779, ECO:0000303|PubMed:9736998};
DE EC=2.1.1.- {ECO:0000255|PROSITE-ProRule:PRU00909};
DE AltName: Full=Polycomb group protein CURLY LEAF {ECO:0000303|PubMed:9052779, ECO:0000303|PubMed:9736998};
DE AltName: Full=Protein INCURVATA 1 {ECO:0000303|PubMed:11063708};
DE AltName: Full=Protein SET DOMAIN GROUP 1 {ECO:0000303|PubMed:11691919};
DE AltName: Full=Protein photoperiod insensitive flowering;
GN Name=CLF {ECO:0000303|PubMed:9052779, ECO:0000303|PubMed:9736998};
GN Synonyms=ICU1 {ECO:0000303|PubMed:11063708}, PIF1, PIF2,
GN SDG1 {ECO:0000303|PubMed:11691919}, SET1 {ECO:0000303|PubMed:11691919};
GN OrderedLocusNames=At2g23380 {ECO:0000312|Araport:AT2G23380};
GN ORFNames=F26B6.3 {ECO:0000312|EMBL:AAC23781.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, AND TISSUE SPECIFICITY.
RC STRAIN=cv. Landsberg erecta; TISSUE=Flower;
RX PubMed=9052779; DOI=10.1038/386044a0;
RA Goodrich J., Puangsomlee P., Martin M., Long D., Meyerowitz E.M.,
RA Coupland G.;
RT "A Polycomb-group gene regulates homeotic gene expression in Arabidopsis.";
RL Nature 386:44-51(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP FUNCTION.
RX PubMed=9736998; DOI=10.1007/s004250050389;
RA Kim G.-T., Tsukaya H., Uchimiya H.;
RT "The CURLY LEAF gene controls both division and elongation of cells during
RT the expansion of the leaf blade in Arabidopsis thaliana.";
RL Planta 206:175-183(1998).
RN [5]
RP FUNCTION.
RX PubMed=11063708; DOI=10.1093/genetics/156.3.1363;
RA Serrano-Cartagena J., Candela H., Robles P., Ponce M.R., Perez-Perez J.M.,
RA Piqueras P., Micol J.L.;
RT "Genetic analysis of incurvata mutants reveals three independent genetic
RT operations at work in Arabidopsis leaf morphogenesis.";
RL Genetics 156:1363-1377(2000).
RN [6]
RP FUNCTION.
RX PubMed=11250158; DOI=10.1016/s0960-9822(01)00072-0;
RA Soerensen M.B., Chaudhury A.M., Robert H., Bancharel E., Berger F.;
RT "Polycomb group genes control pattern formation in plant seed.";
RL Curr. Biol. 11:277-281(2001).
RN [7]
RP SUBCELLULAR LOCATION.
RX PubMed=11691919; DOI=10.1093/nar/29.21.4319;
RA Baumbusch L.O., Thorstensen T., Krauss V., Fischer A., Naumann K.,
RA Assalkhou R., Schulz I., Reuter G., Aalen R.B.;
RT "The Arabidopsis thaliana genome contains at least 29 active genes encoding
RT SET domain proteins that can be assigned to four evolutionarily conserved
RT classes.";
RL Nucleic Acids Res. 29:4319-4333(2001).
RN [8]
RP INTERACTION WITH FIE.
RX PubMed=14871310; DOI=10.1111/j.1365-313x.2003.01996.x;
RA Katz A., Oliva M., Mosquna A., Hakim O., Ohad N.;
RT "FIE and CURLY LEAF polycomb proteins interact in the regulation of
RT homeobox gene expression during sporophyte development.";
RL Plant J. 37:707-719(2004).
RN [9]
RP FUNCTION, DISRUPTION PHENOTYPE, INTERACTION WITH ATX1, AND SUBCELLULAR
RP LOCATION.
RC STRAIN=cv. Wassilewskija;
RX PubMed=17881378; DOI=10.1093/nar/gkm464;
RA Saleh A., Al-Abdallat A., Ndamukong I., Alvarez-Venegas R., Avramova Z.;
RT "The Arabidopsis homologs of trithorax (ATX1) and enhancer of zeste (CLF)
RT establish 'bivalent chromatin marks' at the silent AGAMOUS locus.";
RL Nucleic Acids Res. 35:6290-6296(2007).
RN [10]
RP INTERACTION WITH RING1A.
RX PubMed=19097900; DOI=10.1016/j.cub.2008.11.019;
RA Xu L., Shen W.H.;
RT "Polycomb silencing of KNOX genes confines shoot stem cell niches in
RT Arabidopsis.";
RL Curr. Biol. 18:1966-1971(2008).
RN [11]
RP INTERACTION WITH BLI.
RX PubMed=20647345; DOI=10.1105/tpc.109.073403;
RA Schatlowski N., Stahl Y., Hohenstatt M.L., Goodrich J., Schubert D.;
RT "The CURLY LEAF interacting protein BLISTER controls expression of
RT polycomb-group target genes and cellular differentiation of Arabidopsis
RT thaliana.";
RL Plant Cell 22:2291-2305(2010).
RN [12]
RP INTERACTION WITH ALP1.
RX PubMed=26642436; DOI=10.1371/journal.pgen.1005660;
RA Liang S.C., Hartwig B., Perera P., Mora-Garcia S., de Leau E., Thornton H.,
RA de Lima Alves F., de Alves F.L., Rappsilber J., Rapsilber J., Yang S.,
RA James G.V., Schneeberger K., Finnegan E.J., Turck F., Goodrich J.;
RT "Kicking against the PRCs - A domesticated transposase antagonises
RT silencing mediated by polycomb group proteins and is an accessory component
RT of polycomb repressive complex 2.";
RL PLoS Genet. 11:E1005660-E1005660(2015).
RN [13]
RP INTERACTION WITH EOL1.
RC STRAIN=cv. Columbia;
RX PubMed=28428341; DOI=10.1073/pnas.1620955114;
RA Zhou Y., Tergemina E., Cui H., Foerderer A., Hartwig B.,
RA Velikkakam James G., Schneeberger K., Turck F.;
RT "Ctf4-related protein recruits LHP1-PRC2 to maintain H3K27me3 levels in
RT dividing cells in Arabidopsis thaliana.";
RL Proc. Natl. Acad. Sci. U.S.A. 114:4833-4838(2017).
RN [14]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=30307069; DOI=10.1111/tpj.14125;
RA Liu C., Cheng J., Zhuang Y., Ye L., Li Z., Wang Y., Qi M., Xu L., Zhang Y.;
RT "Polycomb repressive complex 2 attenuates ABA-induced senescence in
RT Arabidopsis.";
RL Plant J. 97:368-377(2019).
RN [15]
RP REVIEW.
RX PubMed=33170267; DOI=10.1042/bst20200660;
RA Shu J., Chen C., Li C., Cui Y.;
RT "The complexity of PRC2 catalysts CLF and SWN in plants.";
RL Biochem. Soc. Trans. 48:2779-2789(2020).
CC -!- FUNCTION: Polycomb group (PcG) protein. Catalytic subunit of some PcG
CC multiprotein complex, which methylates 'Lys-27' of histone H3, leading
CC to transcriptional repression of the affected target genes, mainly
CC abscisic acid (ABA) responsive elements (PubMed:17881378,
CC PubMed:30307069). Required to regulate floral development by repressing
CC the AGAMOUS homeotic gene in leaves, inflorescence stems and flowers
CC (PubMed:17881378). Together with ATX1, modulates AG nucleosome
CC methylation statement (PubMed:17881378). Regulates the antero-posterior
CC organization of the endosperm, as well as the division and elongation
CC rates of leaf cells. PcG proteins act by forming multiprotein
CC complexes, which are required to maintain the transcriptionally
CC repressive state of homeotic genes throughout development. PcG proteins
CC are not required to initiate repression, but to maintain it during
CC later stages of development. {ECO:0000269|PubMed:11063708,
CC ECO:0000269|PubMed:11250158, ECO:0000269|PubMed:17881378,
CC ECO:0000269|PubMed:30307069, ECO:0000269|PubMed:9052779,
CC ECO:0000269|PubMed:9736998}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-lysyl-[histone] + S-adenosyl-L-methionine = H(+) + N(6)-
CC methyl-L-lysyl-[histone] + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:10024, Rhea:RHEA-COMP:9845, Rhea:RHEA-COMP:9846,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856,
CC ChEBI:CHEBI:59789, ChEBI:CHEBI:61929; Evidence={ECO:0000255|PROSITE-
CC ProRule:PRU00909};
CC -!- SUBUNIT: Probable component of a PcG complex. In plants, PcG complexes
CC are probably composed of a member of the EZ family (CLF or MEA), FIE,
CC and a member of the VEFS family (FIS2, VRN2 or EMF2) (By similarity).
CC Interacts with FIE (PubMed:14871310). Interacts with RING1A
CC (PubMed:19097900). Binds to ALP1 (PubMed:26642436). Interacts with BLI
CC (PubMed:20647345). Binds to ATX1 in the nucleus (PubMed:17881378).
CC Interacts with EOL1 (PubMed:28428341). {ECO:0000250,
CC ECO:0000269|PubMed:14871310, ECO:0000269|PubMed:17881378,
CC ECO:0000269|PubMed:19097900, ECO:0000269|PubMed:20647345,
CC ECO:0000269|PubMed:26642436, ECO:0000269|PubMed:28428341}.
CC -!- INTERACTION:
CC P93831; Q9SHY1: At1g65740; NbExp=2; IntAct=EBI-307155, EBI-15923123;
CC P93831; Q8L6Y4: EMF2; NbExp=4; IntAct=EBI-307155, EBI-2128696;
CC P93831; Q9LT47: FIE; NbExp=4; IntAct=EBI-307155, EBI-307146;
CC P93831; O22607: MSI4; NbExp=3; IntAct=EBI-307155, EBI-9661079;
CC P93831; Q8W5B1: VRN2; NbExp=3; IntAct=EBI-307155, EBI-2128880;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:11691919,
CC ECO:0000269|PubMed:17881378}.
CC -!- TISSUE SPECIFICITY: Strongly expressed throughout the apical meristem,
CC leaf primordia, and leaves of 7-8 day-old seedling. Weakly expressed in
CC the vasculature of hypocotyl. Strongly expressed throughout the young
CC stages 1 and 2 floral meristems that arose on the flanks of the apex.
CC In stage 3 and 4 flowers, it is expressed in the emerging sepal
CC primordia and in the dome of the floral meristem. During stages 6 and
CC 7, it is strongly expressed in developing petal and stamen, and weakly
CC expressed in the sepals. Late in floral development, at stage 12, it is
CC weakly expressed in all floral whorls, and expressed at intermediate
CC level in petals and ovules. {ECO:0000269|PubMed:9052779}.
CC -!- DEVELOPMENTAL STAGE: Expressed in all four whorls throughout flower
CC development.
CC -!- DISRUPTION PHENOTYPE: Misexpression of AGAMOUS, recognizable phenotypes
CC (e.g. curly leaves, and early flowering time) and loss of H3K27me3
CC histone H3-tail marks (PubMed:17881378). Double mutant plants atx1 clf
CC exhibits normal leaf-phenotype and flowering time (PubMed:17881378).
CC The double mutant clf-50 swn-1 is hypersensitive to abscisic acid (ABA)
CC associated with reduced ABA-responsive genes repression by histone H3
CC 'Lys-27' methylation (H3K27me3) (PubMed:30307069).
CC {ECO:0000269|PubMed:17881378, ECO:0000269|PubMed:30307069}.
CC -!- SIMILARITY: Belongs to the class V-like SAM-binding methyltransferase
CC superfamily. Histone-lysine methyltransferase family. EZ subfamily.
CC {ECO:0000255|PROSITE-ProRule:PRU00909}.
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DR EMBL; Y10580; CAA71599.1; -; mRNA.
DR EMBL; AC003040; AAC23781.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC07449.1; -; Genomic_DNA.
DR PIR; T01127; T01127.
DR RefSeq; NP_179919.1; NM_127902.6.
DR AlphaFoldDB; P93831; -.
DR SMR; P93831; -.
DR BioGRID; 2222; 17.
DR DIP; DIP-31377N; -.
DR IntAct; P93831; 14.
DR STRING; 3702.AT2G23380.1; -.
DR iPTMnet; P93831; -.
DR PaxDb; P93831; -.
DR PRIDE; P93831; -.
DR ProteomicsDB; 246546; -.
DR EnsemblPlants; AT2G23380.1; AT2G23380.1; AT2G23380.
DR GeneID; 816870; -.
DR Gramene; AT2G23380.1; AT2G23380.1; AT2G23380.
DR KEGG; ath:AT2G23380; -.
DR Araport; AT2G23380; -.
DR TAIR; locus:2005501; AT2G23380.
DR eggNOG; KOG1079; Eukaryota.
DR HOGENOM; CLU_011060_0_0_1; -.
DR InParanoid; P93831; -.
DR OMA; DESICRQ; -.
DR OrthoDB; 875190at2759; -.
DR PhylomeDB; P93831; -.
DR BRENDA; 2.1.1.356; 399.
DR PRO; PR:P93831; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; P93831; baseline and differential.
DR Genevisible; P93831; AT.
DR GO; GO:0005677; C:chromatin silencing complex; IEA:EnsemblPlants.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0031519; C:PcG protein complex; IEA:EnsemblPlants.
DR GO; GO:0003682; F:chromatin binding; IBA:GO_Central.
DR GO; GO:0046976; F:histone methyltransferase activity (H3-K27 specific); IBA:GO_Central.
DR GO; GO:0018024; F:histone-lysine N-methyltransferase activity; IDA:TAIR.
DR GO; GO:0003727; F:single-stranded RNA binding; IDA:TAIR.
DR GO; GO:0009738; P:abscisic acid-activated signaling pathway; IEA:UniProtKB-KW.
DR GO; GO:1990110; P:callus formation; IGI:TAIR.
DR GO; GO:0030154; P:cell differentiation; IEA:UniProtKB-KW.
DR GO; GO:0006338; P:chromatin remodeling; IEA:InterPro.
DR GO; GO:0009294; P:DNA-mediated transformation; IMP:TAIR.
DR GO; GO:0009908; P:flower development; IEA:UniProtKB-KW.
DR GO; GO:0031507; P:heterochromatin assembly; IBA:GO_Central.
DR GO; GO:0070734; P:histone H3-K27 methylation; IMP:UniProtKB.
DR GO; GO:0098532; P:histone H3-K27 trimethylation; IBA:GO_Central.
DR GO; GO:0016571; P:histone methylation; IMP:TAIR.
DR GO; GO:0009965; P:leaf morphogenesis; IMP:TAIR.
DR GO; GO:0009909; P:regulation of flower development; IMP:UniProtKB.
DR GO; GO:0006349; P:regulation of gene expression by genomic imprinting; IMP:TAIR.
DR GO; GO:1900055; P:regulation of leaf senescence; IGI:TAIR.
DR GO; GO:0048586; P:regulation of long-day photoperiodism, flowering; IEA:EnsemblPlants.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IMP:UniProtKB.
DR GO; GO:0009737; P:response to abscisic acid; IGI:TAIR.
DR GO; GO:0010228; P:vegetative to reproductive phase transition of meristem; IMP:TAIR.
DR GO; GO:0010048; P:vernalization response; IMP:TAIR.
DR Gene3D; 2.170.270.10; -; 1.
DR InterPro; IPR026489; CXC_dom.
DR InterPro; IPR045318; EZH1/2-like.
DR InterPro; IPR025778; Hist-Lys_N-MeTrfase_plant.
DR InterPro; IPR041355; Pre-SET_CXC.
DR InterPro; IPR001214; SET_dom.
DR InterPro; IPR046341; SET_dom_sf.
DR InterPro; IPR033467; Tesmin/TSO1-like_CXC.
DR PANTHER; PTHR45747; PTHR45747; 1.
DR Pfam; PF18264; preSET_CXC; 1.
DR Pfam; PF00856; SET; 1.
DR SMART; SM01114; CXC; 1.
DR SMART; SM00317; SET; 1.
DR SUPFAM; SSF82199; SSF82199; 1.
DR PROSITE; PS51633; CXC; 1.
DR PROSITE; PS51576; SAM_MT43_EZ; 1.
DR PROSITE; PS50280; SET; 1.
PE 1: Evidence at protein level;
KW Abscisic acid signaling pathway; Chromatin regulator;
KW Developmental protein; Differentiation; Flowering; Methyltransferase;
KW Nucleus; Reference proteome; Repressor; S-adenosyl-L-methionine;
KW Transcription; Transcription regulation; Transferase.
FT CHAIN 1..902
FT /note="Histone-lysine N-methyltransferase CLF"
FT /id="PRO_0000213995"
FT DOMAIN 531..581
FT /note="SANT"
FT /evidence="ECO:0000255"
FT DOMAIN 638..737
FT /note="CXC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00970"
FT DOMAIN 752..867
FT /note="SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT REGION 1..33
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 73..107
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 335..522
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 875..902
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..16
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 17..33
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 82..97
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 335..400
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 405..419
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 420..436
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 463..494
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 866
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT CONFLICT 225
FT /note="S -> N (in Ref. 2; CAA71599)"
FT /evidence="ECO:0000305"
FT CONFLICT 332
FT /note="T -> P (in Ref. 2; CAA71599)"
FT /evidence="ECO:0000305"
FT CONFLICT 415
FT /note="K -> N (in Ref. 2; CAA71599)"
FT /evidence="ECO:0000305"
FT CONFLICT 658
FT /note="K -> Q (in Ref. 2; CAA71599)"
FT /evidence="ECO:0000305"
FT CONFLICT 674
FT /note="C -> Y (in Ref. 2; CAA71599)"
FT /evidence="ECO:0000305"
FT CONFLICT 761
FT /note="V -> I (in Ref. 2; CAA71599)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 902 AA; 100370 MW; 90B45ED27D219D64 CRC64;
MASEASPSSS ATRSEPPKDS PAEERGPASK EVSEVIESLK KKLAADRCIS IKKRIDENKK
NLFAITQSFM RSSMERGGSC KDGSDLLVKR QRDSPGMKSG IDESNNNRYV EDGPASSGMV
QGSSVPVKIS LRPIKMPDIK RLSPYTTWVF LDRNQRMTED QSVVGRRRIY YDQTGGEALI
CSDSEEEAID DEEEKRDFLE PEDYIIRMTL EQLGLSDSVL AELASFLSRS TSEIKARHGV
LMKEKEVSES GDNQAESSLL NKDMEGALDS FDNLFCRRCL VFDCRLHGCS QDLIFPAEKP
APWCPPVDEN LTCGANCYKT LLKSGRFPGY GTIEGKTGTS SDGAGTKTTP TKFSSKLNGR
KPKTFPSESA SSNEKCALET SDSENGLQQD TNSDKVSSSP KVKGSGRRVG RKRNKNRVAE
RVPRKTQKRQ KKTEASDSDS IASGSCSPSD AKHKDNEDAT SSSQKHVKSG NSGKSRKNGT
PAEVSNNSVK DDVPVCQSNE VASELDAPGS DESLRKEEFM GETVSRGRLA TNKLWRPLEK
SLFDKGVEIF GMNSCLIARN LLSGFKSCWE VFQYMTCSEN KASFFGGDGL NPDGSSKFDI
NGNMVNNQVR RRSRFLRRRG KVRRLKYTWK SAAYHSIRKR ITEKKDQPCR QFNPCNCKIA
CGKECPCLLN GTCCEKYCGC PKSCKNRFRG CHCAKSQCRS RQCPCFAADR ECDPDVCRNC
WVIGGDGSLG VPSQRGDNYE CRNMKLLLKQ QQRVLLGISD VSGWGAFLKN SVSKHEYLGE
YTGELISHKE ADKRGKIYDR ENCSFLFNLN DQFVLDAYRK GDKLKFANHS PEPNCYAKVI
MVAGDHRVGI FAKERILAGE ELFYDYRYEP DRAPAWAKKP EAPGSKKDEN VTPSVGRPKK
LA
