DIM1_YEAST
ID DIM1_YEAST Reviewed; 318 AA.
AC P41819; D6W3A4;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1995, sequence version 1.
DT 03-AUG-2022, entry version 174.
DE RecName: Full=Dimethyladenosine transferase {ECO:0000303|PubMed:8064863};
DE EC=2.1.1.183 {ECO:0000255|PROSITE-ProRule:PRU01026};
DE AltName: Full=18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase;
DE AltName: Full=18S rRNA dimethylase;
DE AltName: Full=S-adenosylmethionine-6-N', N'-adenosyl(rRNA) dimethyltransferase;
GN Name=DIM1 {ECO:0000303|PubMed:8064863};
GN OrderedLocusNames=YPL266W {ECO:0000312|SGD:S000006187};
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, AND CATALYTIC ACTIVITY.
RC STRAIN=ATCC 28383 / FL100 / VTT C-80102;
RX PubMed=8064863; DOI=10.1006/jmbi.1994.1525;
RA Lafontaine D., Delcour J., Glasser A.L., Desgres J., Vandenhaute J.;
RT "The DIM1 gene responsible for the conserved m6(2)Am6(2)A dimethylation in
RT the 3'-terminal loop of 18 S rRNA is essential in yeast.";
RL J. Mol. Biol. 241:492-497(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169875;
RA Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W.,
RA Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D.,
RA Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E.,
RA Churcher C.M., Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H.,
RA DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N.,
RA Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K.,
RA Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M.,
RA Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A.,
RA Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S.,
RA Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D.,
RA Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S.,
RA Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B.,
RA Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A.,
RA Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R.,
RA Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A.,
RA Vo D.H., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.";
RL Nature 387:103-105(1997).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP SUBCELLULAR LOCATION.
RX PubMed=12628929; DOI=10.1093/emboj/cdg121;
RA Schaefer T., Strauss D., Petfalski E., Tollervey D., Hurt E.;
RT "The path from nucleolar 90S to cytoplasmic 40S pre-ribosomes.";
RL EMBO J. 22:1370-1380(2003).
RN [5]
RP IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=29897761; DOI=10.1021/acs.jproteome.8b00032;
RA He C., Jia C., Zhang Y., Xu P.;
RT "Enrichment-based proteogenomics identifies microproteins, missing
RT proteins, and novel smORFs in Saccharomyces cerevisiae.";
RL J. Proteome Res. 17:2335-2344(2018).
RN [6] {ECO:0007744|PDB:6RBD}
RP STRUCTURE BY ELECTRON MICROSCOPY (3.47 ANGSTROMS).
RX PubMed=31227701; DOI=10.1038/s41467-019-10678-z;
RA Mitterer V., Shayan R., Ferreira-Cerca S., Murat G., Enne T., Rinaldi D.,
RA Weigl S., Omanic H., Gleizes P.E., Kressler D., Plisson-Chastang C.,
RA Pertschy B.;
RT "Conformational proofreading of distant 40S ribosomal subunit maturation
RT events by a long-range communication mechanism.";
RL Nat. Commun. 10:2754-2754(2019).
RN [7] {ECO:0007744|PDB:6ZQD, ECO:0007744|PDB:6ZQE, ECO:0007744|PDB:6ZQF, ECO:0007744|PDB:6ZQG}
RP STRUCTURE BY ELECTRON MICROSCOPY (3.50 ANGSTROMS).
RX PubMed=32943521; DOI=10.1126/science.abb4119;
RA Cheng J., Lau B., La Venuta G., Ameismeier M., Berninghausen O., Hurt E.,
RA Beckmann R.;
RT "90S pre-ribosome transformation into the primordial 40S subunit.";
RL Science 369:1470-1476(2020).
RN [8] {ECO:0007744|PDB:7AJU}
RP STRUCTURE BY ELECTRON MICROSCOPY (3.80 ANGSTROMS).
RX PubMed=33326748; DOI=10.1016/j.molcel.2020.11.009;
RA Lau B., Cheng J., Flemming D., La Venuta G., Berninghausen O., Beckmann R.,
RA Hurt E.;
RT "Structure of the Maturing 90S Pre-ribosome in Association with the RNA
RT Exosome.";
RL Mol. Cell 81:293-303(2021).
CC -!- FUNCTION: Specifically dimethylates two adjacent adenosines in the loop
CC of a conserved hairpin near the 3'-end of 18S rRNA in the 40S particle.
CC {ECO:0000269|PubMed:8064863}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=adenosine(1779)/adenosine(1780) in 18S rRNA + 4 S-adenosyl-L-
CC methionine = 4 H(+) + N(6)-dimethyladenosine(1779)/N(6)-
CC dimethyladenosine(1780) in 18S rRNA + 4 S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:42780, Rhea:RHEA-COMP:10234, Rhea:RHEA-COMP:10236,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74411, ChEBI:CHEBI:74493; EC=2.1.1.183;
CC Evidence={ECO:0000305|PubMed:8064863};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:12628929}. Nucleus,
CC nucleolus {ECO:0000269|PubMed:12628929}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. rRNA adenine N(6)-methyltransferase family.
CC {ECO:0000255|PROSITE-ProRule:PRU01026}.
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DR EMBL; L26480; AAA57357.1; -; Genomic_DNA.
DR EMBL; Z73622; CAA98001.1; -; Genomic_DNA.
DR EMBL; BK006949; DAA11170.1; -; Genomic_DNA.
DR PIR; S47985; S47985.
DR RefSeq; NP_015057.1; NM_001184080.1.
DR PDB; 6RBD; EM; 3.47 A; y=1-318.
DR PDB; 6ZQD; EM; 3.80 A; JL=1-318.
DR PDB; 6ZQE; EM; 7.10 A; JL=1-318.
DR PDB; 6ZQF; EM; 4.90 A; JL=1-318.
DR PDB; 6ZQG; EM; 3.50 A; JL=1-318.
DR PDB; 7AJU; EM; 3.80 A; JL=1-318.
DR PDBsum; 6RBD; -.
DR PDBsum; 6ZQD; -.
DR PDBsum; 6ZQE; -.
DR PDBsum; 6ZQF; -.
DR PDBsum; 6ZQG; -.
DR PDBsum; 7AJU; -.
DR AlphaFoldDB; P41819; -.
DR SMR; P41819; -.
DR BioGRID; 35947; 291.
DR DIP; DIP-3924N; -.
DR IntAct; P41819; 20.
DR STRING; 4932.YPL266W; -.
DR iPTMnet; P41819; -.
DR MaxQB; P41819; -.
DR PaxDb; P41819; -.
DR PRIDE; P41819; -.
DR EnsemblFungi; YPL266W_mRNA; YPL266W; YPL266W.
DR GeneID; 855862; -.
DR KEGG; sce:YPL266W; -.
DR SGD; S000006187; DIM1.
DR VEuPathDB; FungiDB:YPL266W; -.
DR eggNOG; KOG0820; Eukaryota.
DR GeneTree; ENSGT00950000183142; -.
DR HOGENOM; CLU_041220_2_0_1; -.
DR InParanoid; P41819; -.
DR OMA; VNAQMWA; -.
DR BioCyc; YEAST:G3O-34149-MON; -.
DR PRO; PR:P41819; -.
DR Proteomes; UP000002311; Chromosome XVI.
DR RNAct; P41819; protein.
DR GO; GO:0030686; C:90S preribosome; HDA:SGD.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
DR GO; GO:0030688; C:preribosome, small subunit precursor; IDA:GO_Central.
DR GO; GO:0052909; F:18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity; IEA:UniProtKB-EC.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0000179; F:rRNA (adenine-N6,N6-)-dimethyltransferase activity; ISS:SGD.
DR GO; GO:0000462; P:maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IMP:SGD.
DR GO; GO:0031167; P:rRNA methylation; IBA:GO_Central.
DR GO; GO:0000154; P:rRNA modification; IMP:SGD.
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 3D-structure; Cytoplasm; Methyltransferase; Nucleus; Reference proteome;
KW Ribosome biogenesis; RNA-binding; rRNA processing; S-adenosyl-L-methionine;
KW Transferase.
FT CHAIN 1..318
FT /note="Dimethyladenosine transferase"
FT /id="PRO_0000101464"
FT BINDING 37
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01026"
FT BINDING 39
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01026"
FT BINDING 64
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01026"
FT BINDING 85
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01026"
FT BINDING 113
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01026"
FT BINDING 128
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01026"
FT HELIX 139..141
FT /evidence="ECO:0007829|PDB:6RBD"
FT STRAND 151..156
FT /evidence="ECO:0007829|PDB:6RBD"
FT HELIX 157..163
FT /evidence="ECO:0007829|PDB:6RBD"
FT STRAND 169..171
FT /evidence="ECO:0007829|PDB:6RBD"
FT HELIX 174..182
FT /evidence="ECO:0007829|PDB:6RBD"
FT STRAND 183..188
FT /evidence="ECO:0007829|PDB:6RBD"
FT STRAND 204..211
FT /evidence="ECO:0007829|PDB:6RBD"
FT HELIX 220..232
FT /evidence="ECO:0007829|PDB:6RBD"
FT STRAND 233..236
FT /evidence="ECO:0007829|PDB:6RBD"
FT HELIX 238..242
FT /evidence="ECO:0007829|PDB:6RBD"
FT STRAND 244..246
FT /evidence="ECO:0007829|PDB:6RBD"
FT HELIX 247..257
FT /evidence="ECO:0007829|PDB:6RBD"
FT TURN 258..263
FT /evidence="ECO:0007829|PDB:6RBD"
FT TURN 268..273
FT /evidence="ECO:0007829|PDB:6RBD"
FT TURN 276..278
FT /evidence="ECO:0007829|PDB:6RBD"
FT HELIX 279..287
FT /evidence="ECO:0007829|PDB:6RBD"
FT STRAND 291..293
FT /evidence="ECO:0007829|PDB:6RBD"
FT TURN 295..297
FT /evidence="ECO:0007829|PDB:6RBD"
SQ SEQUENCE 318 AA; 35951 MW; EE77C9DF574A042A CRC64;
MGKAAKKKYS GATSSKQVSA EKHLSSVFKF NTDLGQHILK NPLVAQGIVD KAQIRPSDVV
LEVGPGTGNL TVRILEQAKN VVAVEMDPRM AAELTKRVRG TPVEKKLEIM LGDFMKTELP
YFDICISNTP YQISSPLVFK LINQPRPPRV SILMFQREFA LRLLARPGDS LYCRLSANVQ
MWANVTHIMK VGKNNFRPPP QVESSVVRLE IKNPRPQVDY NEWDGLLRIV FVRKNRTISA
GFKSTTVMDI LEKNYKTFLA MNNEMVDDTK GSMHDVVKEK IDTVLKETDL GDKRAGKCDQ
NDFLRLLYAF HQVGIHFS
