ALFL2_ARATH
ID ALFL2_ARATH Reviewed; 246 AA.
AC Q9SRM4;
DT 21-SEP-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 25-MAY-2022, entry version 141.
DE RecName: Full=PHD finger protein ALFIN-LIKE 2;
DE Short=Protein AL2;
DE Contains:
DE RecName: Full=PHD finger protein ALFIN-LIKE 2, N-terminally processed;
GN Name=AL2; OrderedLocusNames=At3g11200; ORFNames=F11B9.12, F9F8.2;
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [5]
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 [6]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [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 -!- SUBUNIT: Interacts with H3K4me3 and to a lesser extent with H3K4me2.
CC {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:19154204}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=Q9SRM4-1; Sequence=Displayed;
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}.
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DR EMBL; AC009991; AAF01506.1; -; Genomic_DNA.
DR EMBL; AC073395; AAG50986.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE75012.1; -; Genomic_DNA.
DR EMBL; AY058833; AAL24221.1; -; mRNA.
DR EMBL; AY143832; AAN28771.1; -; mRNA.
DR EMBL; AY085138; AAM61691.1; -; mRNA.
DR RefSeq; NP_187729.1; NM_111955.3. [Q9SRM4-1]
DR PDB; 5XVL; X-ray; 1.63 A; A=10-142.
DR PDB; 5XVW; X-ray; 1.85 A; A/B/C/E=10-142.
DR PDB; 5Y21; X-ray; 1.77 A; A/B=10-142.
DR PDB; 5Y53; X-ray; 1.60 A; A/B/C/E=10-142.
DR PDBsum; 5XVL; -.
DR PDBsum; 5XVW; -.
DR PDBsum; 5Y21; -.
DR PDBsum; 5Y53; -.
DR AlphaFoldDB; Q9SRM4; -.
DR SMR; Q9SRM4; -.
DR BioGRID; 5624; 8.
DR IntAct; Q9SRM4; 6.
DR STRING; 3702.AT3G11200.1; -.
DR iPTMnet; Q9SRM4; -.
DR PaxDb; Q9SRM4; -.
DR PRIDE; Q9SRM4; -.
DR ProteomicsDB; 244838; -. [Q9SRM4-1]
DR EnsemblPlants; AT3G11200.1; AT3G11200.1; AT3G11200. [Q9SRM4-1]
DR GeneID; 820290; -.
DR Gramene; AT3G11200.1; AT3G11200.1; AT3G11200. [Q9SRM4-1]
DR KEGG; ath:AT3G11200; -.
DR Araport; AT3G11200; -.
DR TAIR; locus:2074663; AT3G11200.
DR eggNOG; KOG1632; Eukaryota.
DR HOGENOM; CLU_058315_1_0_1; -.
DR InParanoid; Q9SRM4; -.
DR OMA; TIKFYKC; -.
DR PhylomeDB; Q9SRM4; -.
DR PRO; PR:Q9SRM4; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9SRM4; baseline and differential.
DR Genevisible; Q9SRM4; 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; IBA:GO_Central.
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; Alternative splicing; Chromatin regulator;
KW Metal-binding; Nucleus; Reference proteome; Transcription;
KW Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..246
FT /note="PHD finger protein ALFIN-LIKE 2"
FT /id="PRO_0000425789"
FT INIT_MET 1
FT /note="Removed; alternate"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CHAIN 2..246
FT /note="PHD finger protein ALFIN-LIKE 2, N-terminally
FT processed"
FT /id="PRO_0000412930"
FT ZN_FING 190..242
FT /note="PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 140..190
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 151..173
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT SITE 200
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT SITE 206
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT SITE 210
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT SITE 215
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0000250|UniProtKB:O81488"
FT MOD_RES 2
FT /note="N-acetylalanine; in PHD finger protein ALFIN-LIKE 2,
FT N-terminally processed"
FT /evidence="ECO:0007744|PubMed:22223895"
FT HELIX 13..31
FT /evidence="ECO:0007829|PDB:5Y53"
FT TURN 32..34
FT /evidence="ECO:0007829|PDB:5Y53"
FT HELIX 35..41
FT /evidence="ECO:0007829|PDB:5Y53"
FT STRAND 50..53
FT /evidence="ECO:0007829|PDB:5Y53"
FT STRAND 59..62
FT /evidence="ECO:0007829|PDB:5Y53"
FT STRAND 66..69
FT /evidence="ECO:0007829|PDB:5Y53"
FT HELIX 79..85
FT /evidence="ECO:0007829|PDB:5Y53"
FT HELIX 88..110
FT /evidence="ECO:0007829|PDB:5Y53"
FT HELIX 111..113
FT /evidence="ECO:0007829|PDB:5Y53"
FT HELIX 116..127
FT /evidence="ECO:0007829|PDB:5Y53"
FT HELIX 132..137
FT /evidence="ECO:0007829|PDB:5Y53"
SQ SEQUENCE 246 AA; 27832 MW; FAA4AA0E6CB2599F CRC64;
MAAAAVSSNP RTVEEIFKDY SARRAALLRA LTKDVDDFYS QCDPEKENLC LYGHPNESWE
VNLPAEEVPP ELPEPALGIN FARDGMQRKD WLSLVAVHSD CWLLSVSFYF GARLNRNERK
RLFSLINDLP TLFDVVTGRK AMKDNKPSSD SGSKSRNGTK RSIDGQTKSS TPKLMEESYE
EEEEEDEHGD TLCGSCGGHY TNEEFWICCD VCERWYHGKC VKITPAKAES IKQYKCPPCC
AKKGRQ
