DIM1A_ARATH
ID DIM1A_ARATH Reviewed; 353 AA.
AC O22268;
DT 24-JUN-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 144.
DE RecName: Full=Ribosomal RNA small subunit methyltransferase {ECO:0000305};
DE EC=2.1.1.- {ECO:0000269|PubMed:22829145};
DE AltName: Full=18S nuclear rRNA (adenine(1785)-N(6)/adenine(1786)-N(6))-dimethyltransferase {ECO:0000305};
DE AltName: Full=Adenosine dimethyl transferase 1A {ECO:0000305};
DE AltName: Full=Dimethyladenosine transferase 1A {ECO:0000303|PubMed:19929881};
GN Name=DIM1A {ECO:0000303|PubMed:19929881};
GN OrderedLocusNames=At2g47420 {ECO:0000312|Araport:AT2G47420};
GN ORFNames=T30B22.28 {ECO:0000312|EMBL:AAC62868.1};
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 {ECO:0000312|Proteomes:UP000006548};
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
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;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RC STRAIN=cv. Columbia;
RX PubMed=19929881; DOI=10.1111/j.1365-313x.2009.04079.x;
RA Richter U., Kuhn K., Okada S., Brennicke A., Weihe A., Borner T.;
RT "A mitochondrial rRNA dimethyladenosine methyltransferase in Arabidopsis.";
RL Plant J. 61:558-569(2010).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF GLY-66, TISSUE SPECIFICITY,
RP AND SUBCELLULAR LOCATION.
RX PubMed=22829145; DOI=10.1105/tpc.112.101022;
RA Wieckowski Y., Schiefelbein J.;
RT "Nuclear ribosome biogenesis mediated by the DIM1A rRNA dimethylase is
RT required for organized root growth and epidermal patterning in
RT Arabidopsis.";
RL Plant Cell 24:2839-2856(2012).
CC -!- FUNCTION: N6-adenine methyltransferase which modifies the AA
CC dinucleotide at the plant nuclear 18S rRNA nucleotides A1785 and A1786
CC (PubMed:22829145). Required for generating appropriate patterns of gene
CC expression during root development, including the cell-specific
CC expression of transcriptional regulators involved in root hair and non-
CC hair cells patterning (PubMed:22829145). {ECO:0000269|PubMed:22829145,
CC ECO:0000305|PubMed:19929881}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=adenosine(1785)/adenosine(1786) in 18S rRNA + 4 S-adenosyl-L-
CC methionine = 4 H(+) + N(6)-dimethyladenosine(1785)/N(6)-
CC dimethyladenosine(1786) in 18S rRNA + 4 S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:47640, Rhea:RHEA-COMP:11866, Rhea:RHEA-COMP:11867,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74411, ChEBI:CHEBI:74493;
CC Evidence={ECO:0000269|PubMed:22829145};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:19929881,
CC ECO:0000269|PubMed:22829145}. Nucleus, nucleolus
CC {ECO:0000269|PubMed:19929881, ECO:0000269|PubMed:22829145}.
CC -!- TISSUE SPECIFICITY: Expressed in rapidly dividing tissues, including
CC root meristems and lateral root primordia, developing cotyledons and
CC leaves, petals, anther, pollen grains and silique abscission zone.
CC {ECO:0000269|PubMed:22829145}.
CC -!- MISCELLANEOUS: The inability to isolate a null mutant suggests that
CC DIM1A is essential for viability. {ECO:0000305|PubMed:22829145}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. rRNA adenine N(6)-methyltransferase family. {ECO:0000305}.
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DR EMBL; AC002535; AAC62868.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC10839.1; -; Genomic_DNA.
DR EMBL; AY039949; AAK64053.1; -; mRNA.
DR EMBL; AY113864; AAM44912.1; -; mRNA.
DR PIR; T00442; T00442.
DR RefSeq; NP_182264.1; NM_130310.3.
DR AlphaFoldDB; O22268; -.
DR SMR; O22268; -.
DR STRING; 3702.AT2G47420.1; -.
DR PaxDb; O22268; -.
DR PRIDE; O22268; -.
DR ProteomicsDB; 224397; -.
DR DNASU; 819355; -.
DR EnsemblPlants; AT2G47420.1; AT2G47420.1; AT2G47420.
DR GeneID; 819355; -.
DR Gramene; AT2G47420.1; AT2G47420.1; AT2G47420.
DR KEGG; ath:AT2G47420; -.
DR Araport; AT2G47420; -.
DR TAIR; locus:2061982; AT2G47420.
DR eggNOG; KOG0820; Eukaryota.
DR HOGENOM; CLU_041220_2_0_1; -.
DR InParanoid; O22268; -.
DR OMA; VNAQMWA; -.
DR OrthoDB; 963506at2759; -.
DR PhylomeDB; O22268; -.
DR PRO; PR:O22268; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; O22268; baseline and differential.
DR Genevisible; O22268; AT.
DR GO; GO:0005730; C:nucleolus; IDA:TAIR.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0000179; F:rRNA (adenine-N6,N6-)-dimethyltransferase activity; IMP:TAIR.
DR GO; GO:0051301; P:cell division; IMP:TAIR.
DR GO; GO:0001708; P:cell fate specification; IMP:TAIR.
DR GO; GO:0031167; P:rRNA methylation; IBA:GO_Central.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR001737; KsgA/Erm.
DR InterPro; IPR020596; rRNA_Ade_Mease_Trfase_CS.
DR InterPro; IPR020598; rRNA_Ade_methylase_Trfase_N.
DR InterPro; IPR011530; rRNA_adenine_dimethylase.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR PANTHER; PTHR11727; PTHR11727; 1.
DR Pfam; PF00398; RrnaAD; 1.
DR SMART; SM00650; rADc; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR TIGRFAMs; TIGR00755; ksgA; 1.
DR PROSITE; PS01131; RRNA_A_DIMETH; 1.
DR PROSITE; PS51689; SAM_RNA_A_N6_MT; 1.
PE 1: Evidence at protein level;
KW Methyltransferase; Nucleus; Reference proteome; RNA-binding;
KW rRNA processing; S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..353
FT /note="Ribosomal RNA small subunit methyltransferase"
FT /id="PRO_0000433250"
FT REGION 1..23
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 270..313
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..15
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 282..305
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 35
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01026"
FT BINDING 37
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01026"
FT BINDING 62
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01026"
FT BINDING 83
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01026"
FT BINDING 111
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01026"
FT BINDING 126
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01026"
FT MUTAGEN 66
FT /note="G->E: In dim1A; loss of adenine methylation, but no
FT effect on pre-rRNA processing."
FT /evidence="ECO:0000269|PubMed:22829145"
SQ SEQUENCE 353 AA; 39687 MW; 7BF9B910CF184DD4 CRC64;
MAGGKIRKEK PKASNRAPSN HYQGGISFHK SKGQHILKNP LLVDSIVQKA GIKSTDVILE
IGPGTGNLTK KLLEAGKEVI AVELDSRMVL ELQRRFQGTP FSNRLKVIQG DVLKTELPRF
DICVANIPYQ ISSPLTFKLL FHPTSFRCAV IMYQREFAMR LVAQPGDNLY CRLSVNTQLY
ARVSHLLKVG KNNFRPPPKV DSSVVRIEPR RPGPQVNKKE WDGFLRVCFI RKNKTLGSIF
KQKSVLSMLE KNFKTLQAVL ASLQNNGEPA LNTTSMDLGD QSMGMEDDDN EMDDDDMEMD
EGEGDGGETS EFKEKVMNVL KEGGFEEKRS SKLSQQEFLY LLSLFNKSGI HFT
