ALFL4_ARATH
ID ALFL4_ARATH Reviewed; 255 AA.
AC O81488; Q0WWI3; Q2HIV6; Q8LBJ5;
DT 30-AUG-2005, integrated into UniProtKB/Swiss-Prot.
DT 30-AUG-2005, sequence version 2.
DT 25-MAY-2022, entry version 145.
DE RecName: Full=PHD finger protein ALFIN-LIKE 4;
DE Short=Protein AL4;
GN Name=AL4; OrderedLocusNames=At5g26210; ORFNames=F9D12.13, T19G15_60;
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=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(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;
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 [4]
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 (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Fujita M., Mizukado S., Seki M., Shinozaki K., Mitsuda N., Takiguchi Y.,
RA Takagi M.;
RT "ORF cloning and analysis of Arabidopsis transcription factor genes.";
RL Submitted (MAR-2009) to the EMBL/GenBank/DDBJ databases.
RN [6]
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 [7]
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).
RN [8]
RP STRUCTURE BY NMR OF 201-251.
RG RIKEN structural genomics initiative (RSGI);
RT "Solution structure of PHD domain in nucleic acid binding protein-like
RT NP_197993.";
RL Submitted (NOV-2004) to the PDB data bank.
RN [9]
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).
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC26230.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF077407; AAC26230.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED93537.1; -; Genomic_DNA.
DR EMBL; BT024475; ABD19656.1; -; mRNA.
DR EMBL; AK226367; BAE98515.1; -; mRNA.
DR EMBL; AB493760; BAH30598.1; -; mRNA.
DR EMBL; AY087173; AAM64729.1; -; mRNA.
DR PIR; T01840; T01840.
DR RefSeq; NP_197993.1; NM_122522.5.
DR PDB; 1WE9; NMR; -; A=201-251.
DR PDBsum; 1WE9; -.
DR AlphaFoldDB; O81488; -.
DR SMR; O81488; -.
DR BioGRID; 17965; 9.
DR STRING; 3702.AT5G26210.1; -.
DR iPTMnet; O81488; -.
DR PaxDb; O81488; -.
DR PRIDE; O81488; -.
DR ProteomicsDB; 244852; -.
DR EnsemblPlants; AT5G26210.1; AT5G26210.1; AT5G26210.
DR GeneID; 832690; -.
DR Gramene; AT5G26210.1; AT5G26210.1; AT5G26210.
DR KEGG; ath:AT5G26210; -.
DR Araport; AT5G26210; -.
DR TAIR; locus:2179709; AT5G26210.
DR eggNOG; KOG1632; Eukaryota.
DR HOGENOM; CLU_058315_1_0_1; -.
DR InParanoid; O81488; -.
DR OMA; CIKATET; -.
DR OrthoDB; 1275921at2759; -.
DR PhylomeDB; O81488; -.
DR EvolutionaryTrace; O81488; -.
DR PRO; PR:O81488; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; O81488; baseline and differential.
DR Genevisible; O81488; 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 CHAIN 1..255
FT /note="PHD finger protein ALFIN-LIKE 4"
FT /id="PRO_0000059336"
FT ZN_FING 199..251
FT /note="PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 145..200
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 145..162
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 163..179
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 180..200
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT SITE 209
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT SITE 215
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT SITE 219
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT SITE 224
FT /note="Histone H3K4me3 binding"
FT /evidence="ECO:0000250"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CONFLICT 186
FT /note="E -> G (in Ref. 4; BAE98515)"
FT /evidence="ECO:0000305"
FT STRAND 203..205
FT /evidence="ECO:0007829|PDB:1WE9"
FT STRAND 211..213
FT /evidence="ECO:0007829|PDB:1WE9"
FT STRAND 215..217
FT /evidence="ECO:0007829|PDB:1WE9"
FT STRAND 219..221
FT /evidence="ECO:0007829|PDB:1WE9"
FT STRAND 224..226
FT /evidence="ECO:0007829|PDB:1WE9"
FT TURN 227..231
FT /evidence="ECO:0007829|PDB:1WE9"
FT HELIX 236..239
FT /evidence="ECO:0007829|PDB:1WE9"
FT HELIX 246..249
FT /evidence="ECO:0007829|PDB:1WE9"
SQ SEQUENCE 255 AA; 28779 MW; 077571EBCB255BB0 CRC64;
MEAGGAYNPR TVEEVFRDFK GRRAGMIKAL TTDVQEFFRL CDPEKENLCL YGHPNEHWEV
NLPAEEVPPE LPEPVLGINF ARDGMAEKDW LSLVAVHSDA WLLAVAFFFG ARFGFDKADR
KRLFNMVNDL PTIFEVVAGT AKKQGKDKSS VSNNSSNRSK SSSKRGSESR AKFSKPEPKD
DEEEEEEGVE EEDEDEQGET QCGACGESYA ADEFWICCDL CEMWFHGKCV KITPARAEHI
KQYKCPSCSN KRARS
