AGDP1_ARATH
ID AGDP1_ARATH Reviewed; 517 AA.
AC Q500V5; Q67YH5; Q9ZPZ3;
DT 05-JUN-2019, integrated into UniProtKB/Swiss-Prot.
DT 07-JUN-2005, sequence version 1.
DT 03-AUG-2022, entry version 115.
DE RecName: Full=Protein AGENET DOMAIN (AGD)-CONTAINING P1 {ECO:0000303|PubMed:30382101};
DE AltName: Full=Protein ONE AGENET DOMAIN-CONTAINING PROTEIN {ECO:0000303|PubMed:30425322};
GN Name=AGDP1 {ECO:0000303|PubMed:30382101};
GN Synonyms=ADCP1 {ECO:0000303|PubMed:30425322};
GN OrderedLocusNames=At1g09320 {ECO:0000312|Araport:AT1G09320};
GN ORFNames=T31J12.4 {ECO:0000312|EMBL:AAD18097.1};
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(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 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., Cheuk R.F., Kim C.J., Ecker J.R.;
RT "Arabidopsis cDNA clones.";
RL Submitted (MAY-2005) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP GENE FAMILY.
RX PubMed=12575993; DOI=10.1016/s0968-0004(03)00004-5;
RA Maurer-Stroh S., Dickens N.J., Hughes-Davies L., Kouzarides T.,
RA Eisenhaber F., Ponting C.P.;
RT "The tudor domain 'Royal Family': Tudor, plant agenet, chromo, PWWP and MBT
RT domains.";
RL Trends Biochem. Sci. 28:69-74(2003).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 198-364, FUNCTION, DISRUPTION
RP PHENOTYPE, DOMAIN, AND SUBCELLULAR LOCATION.
RC STRAIN=cv. Columbia;
RX PubMed=30382101; DOI=10.1038/s41467-018-06965-w;
RA Zhang C., Du X., Tang K., Yang Z., Pan L., Zhu P., Luo J., Jiang Y.,
RA Zhang H., Wan H., Wang X., Wu F., Tao W.A., He X.-J., Zhang H.,
RA Bressan R.A., Du J., Zhu J.-K.;
RT "Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin.";
RL Nat. Commun. 9:4547-4547(2018).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 201-355 IN COMPLEX WITH H3K9ME2
RP PEPTIDES, FUNCTION, MUTAGENESIS OF TYR-129; TRP-134; TYR-301; TRP-306;
RP TYR-461 AND TRP-466, DISRUPTION PHENOTYPE, DOMAIN, SUBCELLULAR LOCATION,
RP AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia;
RX PubMed=30425322; DOI=10.1038/s41422-018-0104-9;
RA Zhao S., Cheng L., Gao Y., Zhang B., Zheng X., Wang L., Li P., Sun Q.,
RA Li H.;
RT "Plant HP1 protein ADCP1 links multivalent H3K9 methylation readout to
RT heterochromatin formation.";
RL Cell Res. 29:54-66(2019).
CC -!- FUNCTION: Heterochromatin-binding protein that preferentially occupies
CC long transposons and specifically recognizes the histone H3 'Lys-9'
CC methylation (H3K9me) marks, with a stronger affinity for dimethylated
CC H3K9 (H3K9me2) (PubMed:30382101, PubMed:30425322). Required for
CC transcriptional silencing, non-CG DNA methylation (e.g. CHG and CHH
CC regions), and H3K9 dimethylation (H3K9me2) at some loci
CC (PubMed:30382101, PubMed:30425322). Mediates heterochromatin phase
CC separation and chromocenter formation (PubMed:30425322).
CC {ECO:0000269|PubMed:30382101, ECO:0000269|PubMed:30425322}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:30382101,
CC ECO:0000269|PubMed:30425322}. Note=Enriched in heterochromatin,
CC concentrated in centromeric and pericentromeric regions.
CC {ECO:0000269|PubMed:30382101, ECO:0000269|PubMed:30425322}.
CC -!- TISSUE SPECIFICITY: Expressed ubiquitously during vegetative stage, in
CC meristems (e.g. root tips and shoot apical meristem), and in ovules and
CC young seeds during reproductive stage. {ECO:0000269|PubMed:30425322}.
CC -!- DOMAIN: The tandem Agenet domains (AGDs) mediate the specific
CC recognition of the histone 3 lysine 9 dimethylation (H3K9me2) mark.
CC {ECO:0000269|PubMed:30382101, ECO:0000269|PubMed:30425322}.
CC -!- DISRUPTION PHENOTYPE: Abnormal transcription up-regulation of some
CC transposable elements (TEs) and of hypermethylated loci (including MU1,
CC GP1, SN1 and ERT7) (PubMed:30382101, PubMed:30425322). Hypomethylated
CC DNA CHG and CHH regions (PubMed:30382101, PubMed:30425322). Reduced
CC H3K9me2 levels (PubMed:30382101). Increased ratio of decondensed nuclei
CC (PubMed:30425322). {ECO:0000269|PubMed:30382101,
CC ECO:0000269|PubMed:30425322}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD18097.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AC006416; AAD18097.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE28429.1; -; Genomic_DNA.
DR EMBL; AK176493; BAD44256.1; -; mRNA.
DR EMBL; BT022112; AAY34173.1; -; mRNA.
DR PIR; C86226; C86226.
DR RefSeq; NP_172403.3; NM_100802.5.
DR PDB; 5ZWZ; X-ray; 2.00 A; A=198-364.
DR PDB; 6IE4; X-ray; 2.70 A; A/C=31-177.
DR PDB; 6IE5; X-ray; 2.30 A; A=201-355.
DR PDB; 6IE6; X-ray; 1.70 A; A=201-355.
DR PDB; 6IE7; X-ray; 2.70 A; A/B/C/D=31-177.
DR PDBsum; 5ZWZ; -.
DR PDBsum; 6IE4; -.
DR PDBsum; 6IE5; -.
DR PDBsum; 6IE6; -.
DR PDBsum; 6IE7; -.
DR AlphaFoldDB; Q500V5; -.
DR SMR; Q500V5; -.
DR STRING; 3702.AT1G09320.1; -.
DR iPTMnet; Q500V5; -.
DR PaxDb; Q500V5; -.
DR PRIDE; Q500V5; -.
DR ProteomicsDB; 185476; -.
DR EnsemblPlants; AT1G09320.1; AT1G09320.1; AT1G09320.
DR GeneID; 837453; -.
DR Gramene; AT1G09320.1; AT1G09320.1; AT1G09320.
DR KEGG; ath:AT1G09320; -.
DR Araport; AT1G09320; -.
DR TAIR; locus:2203018; AT1G09320.
DR eggNOG; ENOG502QW7Z; Eukaryota.
DR HOGENOM; CLU_028776_0_0_1; -.
DR InParanoid; Q500V5; -.
DR OMA; WIASSKV; -.
DR OrthoDB; 561474at2759; -.
DR PhylomeDB; Q500V5; -.
DR PRO; PR:Q500V5; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q500V5; baseline and differential.
DR GO; GO:0000775; C:chromosome, centromeric region; IDA:UniProtKB.
DR GO; GO:0000792; C:heterochromatin; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0042393; F:histone binding; IDA:UniProtKB.
DR GO; GO:0035064; F:methylated histone binding; IDA:TAIR.
DR GO; GO:0006346; P:DNA methylation-dependent heterochromatin assembly; IMP:UniProtKB.
DR GO; GO:0036123; P:histone H3-K9 dimethylation; IDA:UniProtKB.
DR GO; GO:0044030; P:regulation of DNA methylation; IMP:UniProtKB.
DR InterPro; IPR008395; Agenet-like_dom.
DR InterPro; IPR014002; Agenet_dom_plant.
DR Pfam; PF05641; Agenet; 3.
DR SMART; SM00743; Agenet; 6.
PE 1: Evidence at protein level;
KW 3D-structure; Chromatin regulator; Nucleus; Reference proteome.
FT CHAIN 1..517
FT /note="Protein AGENET DOMAIN (AGD)-CONTAINING P1"
FT /id="PRO_0000447324"
FT REGION 1..35
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 37..111
FT /note="Plant Agenet, chromatin-binding"
FT /evidence="ECO:0000305|PubMed:30425322"
FT REGION 117..173
FT /note="Plant Agenet, chromatin-binding"
FT /evidence="ECO:0000305|PubMed:30425322"
FT REGION 177..202
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 219..287
FT /note="Plant Agenet, chromatin-binding"
FT /evidence="ECO:0000305|PubMed:30425322"
FT REGION 289..345
FT /note="Plant Agenet, chromatin-binding"
FT /evidence="ECO:0000305|PubMed:30425322"
FT REGION 378..446
FT /note="Plant Agenet, chromatin-binding"
FT /evidence="ECO:0000305|PubMed:30425322"
FT REGION 449..505
FT /note="Plant Agenet, chromatin-binding"
FT /evidence="ECO:0000305|PubMed:30425322"
FT COMPBIAS 180..202
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 129
FT /note="Y->A: Impaired H3K9me2 binding; when associated with
FT A-134. Disrupted H3K9me2 binding; when associated with A-
FT 134; A-301; A-306; A-461 and A-466."
FT /evidence="ECO:0000269|PubMed:30425322"
FT MUTAGEN 134
FT /note="W->A: Impaired H3K9me2 binding; when associated with
FT A-129. Disrupted H3K9me2 binding; when associated with A-
FT 129; A-301; A-306; A-461 and A-466."
FT /evidence="ECO:0000269|PubMed:30425322"
FT MUTAGEN 301
FT /note="Y->A: Impaired H3K9me2 binding; when associated with
FT A-306. Disrupted H3K9me2 binding; when associated with A-
FT 129; A-134; A-306; A-461 and A-466."
FT /evidence="ECO:0000269|PubMed:30425322"
FT MUTAGEN 306
FT /note="W->A: Impaired H3K9me2 binding; when associated with
FT A-301. Disrupted H3K9me2 binding; when associated with A-
FT 129; A-134; A-301; A-461 and A-466."
FT /evidence="ECO:0000269|PubMed:30425322"
FT MUTAGEN 461
FT /note="Y->A: Impaired H3K9me2 binding; when associated with
FT A-466. Disrupted H3K9me2 binding; when associated with A-
FT 129; A-134; A-301; A-306 and A-466."
FT /evidence="ECO:0000269|PubMed:30425322"
FT MUTAGEN 466
FT /note="W->A: Impaired H3K9me2 binding; when associated with
FT A-461. Disrupted H3K9me2 binding; when associated with A-
FT 129; A-134; A-301; A-306 and A-461."
FT /evidence="ECO:0000269|PubMed:30425322"
FT CONFLICT 105
FT /note="P -> S (in Ref. 3; BAD44256)"
FT /evidence="ECO:0000305"
FT HELIX 37..39
FT /evidence="ECO:0007829|PDB:6IE4"
FT STRAND 44..47
FT /evidence="ECO:0007829|PDB:6IE4"
FT STRAND 57..65
FT /evidence="ECO:0007829|PDB:6IE4"
FT STRAND 76..87
FT /evidence="ECO:0007829|PDB:6IE4"
FT STRAND 92..99
FT /evidence="ECO:0007829|PDB:6IE4"
FT HELIX 100..102
FT /evidence="ECO:0007829|PDB:6IE4"
FT HELIX 114..116
FT /evidence="ECO:0007829|PDB:6IE4"
FT STRAND 123..129
FT /evidence="ECO:0007829|PDB:6IE4"
FT STRAND 132..142
FT /evidence="ECO:0007829|PDB:6IE4"
FT TURN 143..145
FT /evidence="ECO:0007829|PDB:6IE4"
FT STRAND 146..151
FT /evidence="ECO:0007829|PDB:6IE4"
FT TURN 152..155
FT /evidence="ECO:0007829|PDB:6IE4"
FT STRAND 156..161
FT /evidence="ECO:0007829|PDB:6IE4"
FT HELIX 162..164
FT /evidence="ECO:0007829|PDB:6IE4"
FT STRAND 165..167
FT /evidence="ECO:0007829|PDB:6IE4"
FT STRAND 170..172
FT /evidence="ECO:0007829|PDB:6IE4"
FT STRAND 175..177
FT /evidence="ECO:0007829|PDB:6IE4"
FT TURN 205..207
FT /evidence="ECO:0007829|PDB:6IE6"
FT HELIX 210..220
FT /evidence="ECO:0007829|PDB:6IE6"
FT STRAND 226..229
FT /evidence="ECO:0007829|PDB:6IE6"
FT STRAND 239..249
FT /evidence="ECO:0007829|PDB:6IE6"
FT TURN 250..252
FT /evidence="ECO:0007829|PDB:6IE6"
FT STRAND 253..262
FT /evidence="ECO:0007829|PDB:6IE6"
FT STRAND 266..275
FT /evidence="ECO:0007829|PDB:6IE6"
FT STRAND 278..280
FT /evidence="ECO:0007829|PDB:6IE6"
FT STRAND 296..301
FT /evidence="ECO:0007829|PDB:6IE6"
FT STRAND 304..315
FT /evidence="ECO:0007829|PDB:6IE6"
FT STRAND 318..323
FT /evidence="ECO:0007829|PDB:6IE6"
FT TURN 324..327
FT /evidence="ECO:0007829|PDB:6IE6"
FT STRAND 328..333
FT /evidence="ECO:0007829|PDB:6IE6"
FT HELIX 334..336
FT /evidence="ECO:0007829|PDB:6IE6"
FT STRAND 337..339
FT /evidence="ECO:0007829|PDB:6IE6"
FT STRAND 342..344
FT /evidence="ECO:0007829|PDB:6IE6"
FT STRAND 347..349
FT /evidence="ECO:0007829|PDB:6IE6"
SQ SEQUENCE 517 AA; 59713 MW; 2F3890F10E977171 CRC64;
MLRPRRSLGV SSPAKQRKKA APKNSMATRA NRKRLPSYLK PGSAVEISSD EIGFRGSWYM
GKVITIPSSS DKDSVKCQVE YTTLFFDKEG TKPLKEVVDM SQLRPPAPPM SEIEKKKKIV
VGEEVDAFYN DGWWEGDVTE VLDDGKFSVF FRSSKEQIRF RKDELRFHRE WVDGAWKPPL
EETEEEEDES EEDKLDDSED EEDILARVDL ETTRAIAKQM FSSGTVVEVS SDEEGFQGCW
FAAKVVEPVG EDKFLVEYRD LREKDGIEPL KEETDFLHIR PPPPRDEDID FAVGDKINAF
YNDGWWVGVV IDGMKHGTVG IYFRQSQEKM RFGRQGLRLH KDWVDGTWQL PLKGGKIKRE
KTVSCNRNVR PKKATEKQAF SIGTPIEVSP EEEGFEDSWF LAKLIEYRGK DKCLVEYDNL
KAEDGKEPLR EEVNVSRIRP LPLESVMVSP FERHDKVNAL YNDGWWVGVI RKVLAKSSYL
VLFKNTQELL KFHHSQLRLH QEWIDGKWIT SFKSQKV
