ATXR5_RICCO
ID ATXR5_RICCO Reviewed; 374 AA.
AC B9RU15;
DT 14-MAY-2014, integrated into UniProtKB/Swiss-Prot.
DT 24-MAR-2009, sequence version 1.
DT 03-AUG-2022, entry version 60.
DE RecName: Full=Probable Histone-lysine N-methyltransferase ATXR5;
DE EC=2.1.1.369 {ECO:0000250|UniProtKB:Q8VZJ1};
DE Flags: Precursor;
GN Name=ATXR5; ORFNames=RCOM_1460410;
OS Ricinus communis (Castor bean).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; fabids; Malpighiales; Euphorbiaceae; Acalyphoideae; Acalypheae;
OC Ricinus.
OX NCBI_TaxID=3988;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Hale;
RX PubMed=20729833; DOI=10.1038/nbt.1674;
RA Chan A.P., Crabtree J., Zhao Q., Lorenzi H., Orvis J., Puiu D.,
RA Melake-Berhan A., Jones K.M., Redman J., Chen G., Cahoon E.B., Gedil M.,
RA Stanke M., Haas B.J., Wortman J.R., Fraser-Liggett C.M., Ravel J.,
RA Rabinowicz P.D.;
RT "Draft genome sequence of the oilseed species Ricinus communis.";
RL Nat. Biotechnol. 28:951-956(2010).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 146-374 IN COMPLEX WITH HTR1
RP PEPTIDE AND S-ADENOSYL-L-METHIONINE, AND SUBUNIT.
RX PubMed=24626927; DOI=10.1126/science.1248357;
RA Jacob Y., Bergamin E., Donoghue M.T., Mongeon V., LeBlanc C., Voigt P.,
RA Underwood C.J., Brunzelle J.S., Michaels S.D., Reinberg D., Couture J.F.,
RA Martienssen R.A.;
RT "Selective methylation of histone H3 variant H3.1 regulates heterochromatin
RT replication.";
RL Science 343:1249-1253(2014).
CC -!- FUNCTION: Histone methyltransferase that specifically monomethylates
CC 'Lys-27' of histone H3 (H3K27me1). Has much higher activity on
CC nucleosomes containing H3.1 than H3.3. Involved in the formation of
CC constitutive heterochromatin and the silencing of heterochromatic
CC elements. {ECO:0000250|UniProtKB:Q8VZJ1}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-lysyl(27)-[histone H3] + S-adenosyl-L-methionine = H(+) +
CC N(6)-methyl-L-lysyl(27)-[histone H3] + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:60296, Rhea:RHEA-COMP:15544, Rhea:RHEA-COMP:15548,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856,
CC ChEBI:CHEBI:59789, ChEBI:CHEBI:61929; EC=2.1.1.369;
CC Evidence={ECO:0000250|UniProtKB:Q8VZJ1};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:24626927}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000250}. Nucleus
CC {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the class V-like SAM-binding methyltransferase
CC superfamily. {ECO:0000255|PROSITE-ProRule:PRU00190}.
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DR EMBL; EQ973815; EEF45134.1; -; Genomic_DNA.
DR RefSeq; XP_002517234.1; XM_002517188.2.
DR PDB; 4O30; X-ray; 2.10 A; A/B=146-374.
DR PDB; 5VA6; X-ray; 2.40 A; A/B=146-374.
DR PDB; 5VAC; X-ray; 1.95 A; A=146-374.
DR PDB; 5VAH; X-ray; 2.40 A; A/B=146-374.
DR PDB; 5VBC; X-ray; 2.10 A; A/B=146-374.
DR PDBsum; 4O30; -.
DR PDBsum; 5VA6; -.
DR PDBsum; 5VAC; -.
DR PDBsum; 5VAH; -.
DR PDBsum; 5VBC; -.
DR AlphaFoldDB; B9RU15; -.
DR SMR; B9RU15; -.
DR DIP; DIP-61672N; -.
DR STRING; 3988.XP_002517234.1; -.
DR PRIDE; B9RU15; -.
DR GeneID; 8259125; -.
DR KEGG; rcu:8259125; -.
DR eggNOG; KOG1083; Eukaryota.
DR InParanoid; B9RU15; -.
DR OrthoDB; 1014608at2759; -.
DR BRENDA; 2.1.1.369; 1204.
DR Proteomes; UP000008311; Unassembled WGS sequence.
DR GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0042393; F:histone binding; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008168; F:methyltransferase activity; IEA:UniProtKB-KW.
DR GO; GO:0003712; F:transcription coregulator activity; IBA:GO_Central.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0032259; P:methylation; IEA:UniProtKB-KW.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IBA:GO_Central.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR Gene3D; 2.170.270.10; -; 1.
DR Gene3D; 3.30.40.10; -; 1.
DR InterPro; IPR001214; SET_dom.
DR InterPro; IPR046341; SET_dom_sf.
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 Pfam; PF00628; PHD; 1.
DR Pfam; PF00856; SET; 1.
DR SMART; SM00249; PHD; 1.
DR SMART; SM00317; SET; 1.
DR SUPFAM; SSF57903; SSF57903; 1.
DR SUPFAM; SSF82199; SSF82199; 1.
DR PROSITE; PS50280; SET; 1.
DR PROSITE; PS01359; ZF_PHD_1; 1.
DR PROSITE; PS50016; ZF_PHD_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Chloroplast; Chromatin regulator; Metal-binding;
KW Methyltransferase; Nucleus; Plastid; Reference proteome;
KW S-adenosyl-L-methionine; Transferase; Transit peptide; Zinc; Zinc-finger.
FT TRANSIT 1..46
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 47..374
FT /note="Probable Histone-lysine N-methyltransferase ATXR5"
FT /id="PRO_0000429174"
FT DOMAIN 240..362
FT /note="SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT ZN_FING 59..109
FT /note="PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 16..38
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 216
FT /ligand="substrate"
FT BINDING 250..252
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 312..316
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 334
FT /ligand="substrate"
FT BINDING 364..365
FT /ligand="substrate"
FT BINDING 368
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190,
FT ECO:0000269|PubMed:24626927"
FT BINDING 374
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190,
FT ECO:0000269|PubMed:24626927"
FT HELIX 170..186
FT /evidence="ECO:0007829|PDB:5VAC"
FT STRAND 193..196
FT /evidence="ECO:0007829|PDB:4O30"
FT TURN 199..201
FT /evidence="ECO:0007829|PDB:5VAC"
FT HELIX 204..206
FT /evidence="ECO:0007829|PDB:5VAC"
FT HELIX 209..211
FT /evidence="ECO:0007829|PDB:5VAC"
FT HELIX 221..236
FT /evidence="ECO:0007829|PDB:5VAC"
FT STRAND 241..247
FT /evidence="ECO:0007829|PDB:5VAC"
FT TURN 248..250
FT /evidence="ECO:0007829|PDB:5VAC"
FT STRAND 251..258
FT /evidence="ECO:0007829|PDB:5VAC"
FT STRAND 264..268
FT /evidence="ECO:0007829|PDB:5VAC"
FT STRAND 271..275
FT /evidence="ECO:0007829|PDB:5VAC"
FT HELIX 276..278
FT /evidence="ECO:0007829|PDB:5VAC"
FT STRAND 287..291
FT /evidence="ECO:0007829|PDB:5VAC"
FT STRAND 293..295
FT /evidence="ECO:0007829|PDB:5VAC"
FT HELIX 296..298
FT /evidence="ECO:0007829|PDB:5VAC"
FT STRAND 300..303
FT /evidence="ECO:0007829|PDB:5VAC"
FT STRAND 305..308
FT /evidence="ECO:0007829|PDB:5VAC"
FT HELIX 310..313
FT /evidence="ECO:0007829|PDB:5VAC"
FT STRAND 319..323
FT /evidence="ECO:0007829|PDB:4O30"
FT HELIX 324..327
FT /evidence="ECO:0007829|PDB:5VAC"
FT STRAND 330..337
FT /evidence="ECO:0007829|PDB:5VAC"
FT STRAND 340..349
FT /evidence="ECO:0007829|PDB:5VAC"
FT STRAND 362..364
FT /evidence="ECO:0007829|PDB:5VAC"
SQ SEQUENCE 374 AA; 42515 MW; 4506A8C135E308A1 CRC64;
MAPASITTTT TVARRIVGSR RRTKATSPPD SPPPKKLKPI SEILAKAQYA VVERADYGDV
SCMQCGSGER AEELLLCDKC DKGFHMKCVR PIVVRVPIGS WLCPKCSGQR RVRRLSQRKI
IDFFRIQKCN HKTDKCSSPQ DIRKHRRRSG SLVYQKRRRR LLPFVSSEDP AQRLKQMGTL
ASALTELQME FSDDLTYSSG MAPRSANQAR FEEGGMQVLT KEDIETLEQC RAMCKRGDCP
PLLVVFDSRE GFTVEADGQI KDMTFIAEYT GDVDYIRNRE HDDCDSMMTL LLAKDPSKSL
VICPDKRGNI ARFISGINNH TLDGKKKQNC KCVRYSVNGE CRVFLVATRD IAKGERLYYD
YNGYEHEYPT QHFV
