ALFL1_ARATH
ID ALFL1_ARATH Reviewed; 241 AA.
AC Q9FFF5;
DT 21-SEP-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 25-MAY-2022, entry version 131.
DE RecName: Full=PHD finger protein ALFIN-LIKE 1;
DE Short=Protein AL1;
GN Name=AL1; OrderedLocusNames=At5g05610; ORFNames=MOP10.15;
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=9330910; DOI=10.1093/dnares/4.3.215;
RA Sato S., Kotani H., Nakamura Y., Kaneko T., Asamizu E., Fukami M.,
RA Miyajima N., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. I. Sequence
RT features of the 1.6 Mb regions covered by twenty physically assigned P1
RT clones.";
RL DNA Res. 4:215-230(1997).
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;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (SEP-2004) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Shinn P., Chen H., Kim C.J., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (FEB-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
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 [6]
RP GENE FAMILY, DOMAIN PHD-TYPE ZINC-FINGER, SUBCELLULAR LOCATION, INTERACTION
RP WITH HISTONES H3K4ME3 AND H3K4ME2, 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 [7]
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:0000269|PubMed:19154204}.
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:0000269|PubMed:19154204}.
CC -!- SIMILARITY: Belongs to the Alfin family. {ECO:0000305}.
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DR EMBL; AB005241; BAB11550.1; -; Genomic_DNA.
DR EMBL; CP002688; AED90898.1; -; Genomic_DNA.
DR EMBL; CP002688; AED90899.1; -; Genomic_DNA.
DR EMBL; AK176462; BAD44225.1; -; mRNA.
DR EMBL; AK176806; BAD44569.1; -; mRNA.
DR EMBL; BT024471; ABD19652.1; -; mRNA.
DR EMBL; AY084560; AAM61127.1; -; mRNA.
DR RefSeq; NP_196180.1; NM_120643.2.
DR RefSeq; NP_850775.1; NM_180444.3.
DR PDB; 5Y20; X-ray; 2.41 A; A=185-236.
DR PDBsum; 5Y20; -.
DR AlphaFoldDB; Q9FFF5; -.
DR SMR; Q9FFF5; -.
DR BioGRID; 15723; 6.
DR STRING; 3702.AT5G05610.1; -.
DR iPTMnet; Q9FFF5; -.
DR PaxDb; Q9FFF5; -.
DR PRIDE; Q9FFF5; -.
DR ProteomicsDB; 244937; -.
DR EnsemblPlants; AT5G05610.1; AT5G05610.1; AT5G05610.
DR EnsemblPlants; AT5G05610.2; AT5G05610.2; AT5G05610.
DR GeneID; 830444; -.
DR Gramene; AT5G05610.1; AT5G05610.1; AT5G05610.
DR Gramene; AT5G05610.2; AT5G05610.2; AT5G05610.
DR KEGG; ath:AT5G05610; -.
DR Araport; AT5G05610; -.
DR TAIR; locus:2169707; AT5G05610.
DR eggNOG; KOG1632; Eukaryota.
DR HOGENOM; CLU_058315_1_0_1; -.
DR InParanoid; Q9FFF5; -.
DR OMA; KFYSLCD; -.
DR OrthoDB; 1370179at2759; -.
DR PhylomeDB; Q9FFF5; -.
DR PRO; PR:Q9FFF5; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9FFF5; baseline and differential.
DR Genevisible; Q9FFF5; AT.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0035064; F:methylated histone binding; IDA:TAIR.
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 INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CHAIN 2..241
FT /note="PHD finger protein ALFIN-LIKE 1"
FT /id="PRO_0000412929"
FT ZN_FING 185..237
FT /note="PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 142..182
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT SITE 195
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT SITE 201
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT SITE 205
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT SITE 210
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT MOD_RES 2
FT /note="N-acetylalanine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT TURN 189..191
FT /evidence="ECO:0007829|PDB:5Y20"
FT STRAND 201..203
FT /evidence="ECO:0007829|PDB:5Y20"
FT TURN 205..207
FT /evidence="ECO:0007829|PDB:5Y20"
FT STRAND 210..212
FT /evidence="ECO:0007829|PDB:5Y20"
FT HELIX 213..216
FT /evidence="ECO:0007829|PDB:5Y20"
FT HELIX 220..224
FT /evidence="ECO:0007829|PDB:5Y20"
FT TURN 232..235
FT /evidence="ECO:0007829|PDB:5Y20"
SQ SEQUENCE 241 AA; 27223 MW; 972D2F7084A787A9 CRC64;
MAAESSNPRT VEEIFKDFSG RRSGFLRALS VDVDKFYSLC DPEMENLCLY GHPNGTWEVN
LPAEEVPPEL PEPALGINFA RDGMQRKDWL SLVAVHSDCW LLSVSSYFGA RLNRNERKRL
FSLINDLPTL FEVVTGRKPI KDGKPSMDLG SKSRNGVKRS IEGQTKSTPK LMEESYEDED
DEHGDTLCGS CGGNYTNDEF WICCDVCERW YHGKCVKITP AKAESIKQYK CPSCCTKKGR
Q
