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ATXR2_ARATH
ID   ATXR2_ARATH             Reviewed;         473 AA.
AC   Q5PP37; Q9LSY2;
DT   02-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT   04-JAN-2005, sequence version 1.
DT   03-AUG-2022, entry version 109.
DE   RecName: Full=Histone-lysine N-methyltransferase ATXR2 {ECO:0000303|PubMed:11691919};
DE            EC=2.1.1.- {ECO:0000255|PROSITE-ProRule:PRU00190};
DE   AltName: Full=Protein SET DOMAIN GROUP 36;
DE   AltName: Full=Trithorax-related protein 2 {ECO:0000303|PubMed:11691919};
DE            Short=TRX-related protein 2 {ECO:0000303|PubMed:11691919};
GN   Name=ATXR2 {ECO:0000303|PubMed:11691919}; Synonyms=SDG36, SET36;
GN   OrderedLocusNames=At3g21820 {ECO:0000312|Araport:AT3G21820};
GN   ORFNames=MSD21.13 {ECO:0000312|EMBL:BAB02844.1};
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=10819329; DOI=10.1093/dnares/7.2.131;
RA   Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.;
RT   "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence
RT   features of the regions of 4,504,864 bp covered by sixty P1 and TAC
RT   clones.";
RL   DNA Res. 7:131-135(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., Cheuk R.F., Kim C.J., Ecker J.R.;
RT   "Arabidopsis ORF clones.";
RL   Submitted (FEB-2005) 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 (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN   [5]
RP   NOMENCLATURE.
RX   PubMed=11691919; DOI=10.1093/nar/29.21.4319;
RA   Baumbusch L.O., Thorstensen T., Krauss V., Fischer A., Naumann K.,
RA   Assalkhou R., Schulz I., Reuter G., Aalen R.B.;
RT   "The Arabidopsis thaliana genome contains at least 29 active genes encoding
RT   SET domain proteins that can be assigned to four evolutionarily conserved
RT   classes.";
RL   Nucleic Acids Res. 29:4319-4333(2001).
RN   [6]
RP   FUNCTION, DISRUPTION PHENOTYPE, INTERACTION WITH ARF7 AND ARF19, AND
RP   SUBCELLULAR LOCATION.
RC   STRAIN=cv. Columbia;
RX   PubMed=29184030; DOI=10.1126/scisignal.aan0316;
RA   Lee K., Park O.S., Seo P.J.;
RT   "Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD genes to
RT   facilitate cellular dedifferentiation.";
RL   Sci. Signal. 10:0-0(2017).
RN   [7]
RP   FUNCTION, AND DISRUPTION PHENOTYPE.
RC   STRAIN=cv. Columbia;
RX   PubMed=29517958; DOI=10.1080/15592324.2018.1449543;
RA   Lee K., Park O.-S., Seo P.J.;
RT   "ATXR2 as a core regulator of de novo root organogenesis.";
RL   Plant Signal. Behav. 13:e1449543-e1449543(2018).
RN   [8]
RP   FUNCTION, DISRUPTION PHENOTYPE, AND INTERACTION WITH JMJ30.
RC   STRAIN=cv. Columbia;
RX   PubMed=29923261; DOI=10.1111/tpj.14002;
RA   Lee K., Park O.-S., Seo P.J.;
RT   "JMJ30-mediated demethylation of H3K9me3 drives tissue identity changes to
RT   promote callus formation in Arabidopsis.";
RL   Plant J. 95:961-975(2018).
CC   -!- FUNCTION: Histone methyltransferase that methylates 'Lys-36' (H3K36me)
CC       of histone H3 to produce H3K36me3 (PubMed:29184030). Promotes early
CC       stages of cellular dedifferentiation through H3K36me3-dependent, and to
CC       a lesser degree H3K4me3-dependent, activation of Lateral organ
CC       Boundaries-Domain (LBD) (e.g. LBD16 and LBD29) genes (PubMed:29184030).
CC       Positive regulator of root organogenesis including lateral root
CC       formation as well as adventitious root formation from wounded leaf
CC       tissues (PubMed:29517958). Recruited by JMJ30/ARF (e.g. ARF7 and ARF19)
CC       complexes to promote the deposition of H3K36me3 and, to a lower extent,
CC       H3K4me3 at LBD genes promoters, thus ensuring their stable activation
CC       during callus formation on callus-inducing medium (CIM)
CC       (PubMed:29923261, PubMed:29184030). {ECO:0000269|PubMed:29184030,
CC       ECO:0000269|PubMed:29517958, ECO:0000269|PubMed:29923261}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=L-lysyl-[histone] + S-adenosyl-L-methionine = H(+) + N(6)-
CC         methyl-L-lysyl-[histone] + S-adenosyl-L-homocysteine;
CC         Xref=Rhea:RHEA:10024, Rhea:RHEA-COMP:9845, Rhea:RHEA-COMP:9846,
CC         ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856,
CC         ChEBI:CHEBI:59789, ChEBI:CHEBI:61929;
CC         Evidence={ECO:0000250|UniProtKB:Q8VZJ1};
CC   -!- SUBUNIT: Interacts with JMJ30 (PubMed:29923261). Binds to ARF7 and
CC       ARF19 in the nucleus (PubMed:29184030). {ECO:0000269|PubMed:29184030,
CC       ECO:0000269|PubMed:29923261}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:29184030}.
CC   -!- DISRUPTION PHENOTYPE: Reduced callus formation from somatic cells
CC       associated with an impaired reduction of H3K9me3 deposition and lower
CC       accumulation of H3K36me3 at LBD16 and LBD29 loci during leaf-to-callus
CC       transition (PubMed:29923261, PubMed:29184030). Lower lateral root
CC       formation and impaired ability to form adventitious root formation from
CC       wounded leaf tissues (PubMed:29517958). The double mutant jmj30-2
CC       atxr2-1 is strongly impaired in callus formation (PubMed:29923261).
CC       {ECO:0000269|PubMed:29184030, ECO:0000269|PubMed:29517958,
CC       ECO:0000269|PubMed:29923261}.
CC   -!- SIMILARITY: Belongs to the class V-like SAM-binding methyltransferase
CC       superfamily. Histone-lysine methyltransferase family. TRX/MLL
CC       subfamily. {ECO:0000255|PROSITE-ProRule:PRU00190}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=BAB02844.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; AB025634; BAB02844.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; CP002686; AEE76555.1; -; Genomic_DNA.
DR   EMBL; BT020260; AAV84481.1; -; mRNA.
DR   EMBL; BT021112; AAX12882.1; -; mRNA.
DR   EMBL; AK221711; BAD95436.1; -; mRNA.
DR   RefSeq; NP_188819.2; NM_113077.5.
DR   AlphaFoldDB; Q5PP37; -.
DR   STRING; 3702.AT3G21820.1; -.
DR   iPTMnet; Q5PP37; -.
DR   PaxDb; Q5PP37; -.
DR   PRIDE; Q5PP37; -.
DR   ProteomicsDB; 241102; -.
DR   EnsemblPlants; AT3G21820.1; AT3G21820.1; AT3G21820.
DR   GeneID; 821736; -.
DR   Gramene; AT3G21820.1; AT3G21820.1; AT3G21820.
DR   KEGG; ath:AT3G21820; -.
DR   Araport; AT3G21820; -.
DR   TAIR; locus:2093059; AT3G21820.
DR   eggNOG; KOG2084; Eukaryota.
DR   HOGENOM; CLU_034791_0_0_1; -.
DR   InParanoid; Q5PP37; -.
DR   OMA; TYHSLLC; -.
DR   OrthoDB; 1001347at2759; -.
DR   PhylomeDB; Q5PP37; -.
DR   PRO; PR:Q5PP37; -.
DR   Proteomes; UP000006548; Chromosome 3.
DR   ExpressionAtlas; Q5PP37; baseline and differential.
DR   GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR   GO; GO:0046975; F:histone methyltransferase activity (H3-K36 specific); IMP:UniProtKB.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:1990110; P:callus formation; IMP:TAIR.
DR   GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR   GO; GO:0010452; P:histone H3-K36 methylation; IMP:TAIR.
DR   GO; GO:0097198; P:histone H3-K36 trimethylation; IMP:UniProtKB.
DR   GO; GO:0010311; P:lateral root formation; IMP:UniProtKB.
DR   GO; GO:0062211; P:root regeneration; IMP:UniProtKB.
DR   Gene3D; 2.170.270.10; -; 1.
DR   InterPro; IPR044237; ATXR2-like.
DR   InterPro; IPR001214; SET_dom.
DR   InterPro; IPR046341; SET_dom_sf.
DR   InterPro; IPR002893; Znf_MYND.
DR   PANTHER; PTHR47436; PTHR47436; 1.
DR   Pfam; PF00856; SET; 1.
DR   Pfam; PF01753; zf-MYND; 1.
DR   SMART; SM00317; SET; 1.
DR   SUPFAM; SSF82199; SSF82199; 1.
DR   PROSITE; PS50280; SET; 1.
PE   1: Evidence at protein level;
KW   Chromatin regulator; Metal-binding; Methyltransferase; Nucleus;
KW   Reference proteome; S-adenosyl-L-methionine; Transferase; Zinc;
KW   Zinc-finger.
FT   CHAIN           1..473
FT                   /note="Histone-lysine N-methyltransferase ATXR2"
FT                   /id="PRO_0000233359"
FT   DOMAIN          33..441
FT                   /note="SET"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT   ZN_FING         134..203
FT                   /note="MYND-type; degenerate"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT   BINDING         176
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT   BINDING         180
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT   BINDING         199
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT   BINDING         203
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT   BINDING         440
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
SQ   SEQUENCE   473 AA;  52803 MW;  2EFE76512D6F74D7 CRC64;
     MDSVYKTDEN FAADVAALLA PLPTPQLQEY FNKLITSRRC NGIEVKNNGT IGKGVYANSE
     FDEDELILKD EILVGIQHSS NKVDCLVCSF CFRFIGSIEK QIGRKLYFKN LGVSGCCDDD
     SSEEDECVKY NGNEEQCGGS SSSHNTLPEG VVSSLMNGEM ALPHTDKFPL PSPLSCPGGC
     QEAFYCSESC AAADWESSHS LLCTGERSES ISREALGEFI KHANDTNDIF LLAAKAIAFT
     ILRYRKLKAE HVDKKAKQSE PKQSLLLEAW KPVSIGYKRR WWDCIALPDD VDPTDEGAFR
     MQIKNLACTS LELLKIAIFD KECEALFSLE IYGNIIGMFE LNNLDLVVAS PVEDYFLYID
     DLPDAEKEET EEITRPFLDA LGDEYSDCCQ GTAFFPLQSC MNHSCCPNAK AFKREEDRDG
     QAVIIALRRI SKNEEVTISY IDEELPYKER QALLADYGFS CKCSKCLEDS SSI
 
 
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