ALFL3_ARATH
ID ALFL3_ARATH Reviewed; 250 AA.
AC Q9M2B4;
DT 21-SEP-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 25-MAY-2022, entry version 130.
DE RecName: Full=PHD finger protein ALFIN-LIKE 3;
DE Short=Protein AL3;
GN Name=AL3; OrderedLocusNames=At3g42790; ORFNames=T21C14_10;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP GENE FAMILY, SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
RX PubMed=19154204; DOI=10.1111/j.1365-313x.2009.03795.x;
RA Lee W.Y., Lee D., Chung W.I., Kwon C.S.;
RT "Arabidopsis ING and Alfin1-like protein families localize to the nucleus
RT and bind to H3K4me3/2 via plant homeodomain fingers.";
RL Plant J. 58:511-524(2009).
RN [5]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
CC -!- FUNCTION: Histone-binding component that specifically recognizes H3
CC tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription
CC start sites of virtually all active genes. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:19154204}.
CC -!- TISSUE SPECIFICITY: Ubiquitously expressed.
CC {ECO:0000269|PubMed:19154204}.
CC -!- DOMAIN: The PHD-type zinc finger mediates the binding to H3K4me3.
CC {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the Alfin family. {ECO:0000305}.
CC -!- CAUTION: Lacks the Tyr (here Asp-204), a conserved feature of the
CC aromatic cage required for the interaction with histone H3K4me3/2.
CC {ECO:0000305}.
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DR EMBL; AL138639; CAB87196.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE77752.1; -; Genomic_DNA.
DR EMBL; AY062851; AAL32929.1; -; mRNA.
DR EMBL; AY114574; AAM47893.1; -; mRNA.
DR PIR; T47337; T47337.
DR RefSeq; NP_189865.1; NM_114147.5.
DR PDB; 5YC3; X-ray; 2.60 A; A=191-245.
DR PDB; 5YC4; X-ray; 2.70 A; A=191-245.
DR PDBsum; 5YC3; -.
DR PDBsum; 5YC4; -.
DR AlphaFoldDB; Q9M2B4; -.
DR SMR; Q9M2B4; -.
DR BioGRID; 8641; 4.
DR STRING; 3702.AT3G42790.1; -.
DR iPTMnet; Q9M2B4; -.
DR PaxDb; Q9M2B4; -.
DR PRIDE; Q9M2B4; -.
DR ProteomicsDB; 245043; -.
DR EnsemblPlants; AT3G42790.1; AT3G42790.1; AT3G42790.
DR GeneID; 823316; -.
DR Gramene; AT3G42790.1; AT3G42790.1; AT3G42790.
DR KEGG; ath:AT3G42790; -.
DR Araport; AT3G42790; -.
DR TAIR; locus:2099321; AT3G42790.
DR eggNOG; KOG1632; Eukaryota.
DR HOGENOM; CLU_058315_1_0_1; -.
DR InParanoid; Q9M2B4; -.
DR OMA; CCDACEI; -.
DR OrthoDB; 1275921at2759; -.
DR PhylomeDB; Q9M2B4; -.
DR PRO; PR:Q9M2B4; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9M2B4; baseline and differential.
DR Genevisible; Q9M2B4; AT.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0042393; F:histone binding; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000976; F:transcription cis-regulatory region binding; IPI:TAIR.
DR GO; GO:0003712; F:transcription coregulator activity; IBA:GO_Central.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR CDD; cd15613; PHD_AL_plant; 1.
DR Gene3D; 3.30.40.10; -; 1.
DR InterPro; IPR045104; Alfin.
DR InterPro; IPR021998; Alfin_N.
DR InterPro; IPR044104; PHD_AL_plant.
DR InterPro; IPR019786; Zinc_finger_PHD-type_CS.
DR InterPro; IPR011011; Znf_FYVE_PHD.
DR InterPro; IPR001965; Znf_PHD.
DR InterPro; IPR019787; Znf_PHD-finger.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR PANTHER; PTHR12321; PTHR12321; 1.
DR Pfam; PF12165; Alfin; 1.
DR Pfam; PF00628; PHD; 1.
DR SMART; SM00249; PHD; 1.
DR SUPFAM; SSF57903; SSF57903; 1.
DR PROSITE; PS01359; ZF_PHD_1; 1.
DR PROSITE; PS50016; ZF_PHD_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Chromatin regulator; Metal-binding; Nucleus;
KW Reference proteome; Transcription; Transcription regulation; Zinc;
KW Zinc-finger.
FT CHAIN 1..250
FT /note="PHD finger protein ALFIN-LIKE 3"
FT /id="PRO_0000412931"
FT ZN_FING 194..246
FT /note="PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 146..192
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 146..162
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 163..180
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT SITE 210
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT SITE 214
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT SITE 219
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT TURN 198..200
FT /evidence="ECO:0007829|PDB:5YC3"
FT STRAND 209..212
FT /evidence="ECO:0007829|PDB:5YC3"
FT TURN 214..216
FT /evidence="ECO:0007829|PDB:5YC3"
FT STRAND 219..221
FT /evidence="ECO:0007829|PDB:5YC3"
FT TURN 222..226
FT /evidence="ECO:0007829|PDB:5YC3"
FT HELIX 229..232
FT /evidence="ECO:0007829|PDB:5YC3"
FT TURN 241..244
FT /evidence="ECO:0007829|PDB:5YC3"
SQ SEQUENCE 250 AA; 28215 MW; 2496EF9B764D894E CRC64;
MEGGAALYNP RTVEEVFKDF KGRRTAIVKA LTTDVQEFYQ QCDPEKENLC LYGLPNEEWE
VNLPAEEVPP ELPEPALGIN FARDGLSEKE WLSLVAIHSD AWLLSVSFYF GSRFSFHKEE
RKRLFNMIND VPTIFEVVTG MAKAKDKSSA ANQNGNKSKS NSKVRTSEGK SSKTKQPKEE
DEEIDEDDED DHGETLCGAC GDSDGADEFW ICCDLCEKWF HGKCVKITPA RAEHIKQYKC
PSCSNKRARA
