DIM1_HUMAN
ID DIM1_HUMAN Reviewed; 313 AA.
AC Q9UNQ2; O76025; Q9BU77; Q9UES1;
DT 13-DEC-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 197.
DE RecName: Full=Probable dimethyladenosine transferase;
DE EC=2.1.1.183 {ECO:0000269|PubMed:25851604};
DE AltName: Full=DIM1 dimethyladenosine transferase 1 homolog;
DE AltName: Full=DIM1 dimethyladenosine transferase 1-like;
DE AltName: Full=Probable 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase;
DE AltName: Full=Probable 18S rRNA dimethylase;
DE AltName: Full=Probable S-adenosylmethionine-6-N',N'-adenosyl(rRNA) dimethyltransferase;
GN Name=DIMT1; Synonyms=DIMT1L; ORFNames=HUSSY-05;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC TISSUE=Aorta;
RA Wei Y.J., Ding J.F., Liu Y.Q., Xu Y.Y., Hui R.T., Sheng H., Zhao X.W.,
RA Jiang Y.X., Liu D.Q., Zhao Y., Cao H.Q., Meng X.M., Liu S.;
RL Submitted (OCT-1998) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Lung, and Placenta;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 157-313.
RC TISSUE=Brain;
RX PubMed=11124703;
RX DOI=10.1002/1097-0061(200101)18:1<69::aid-yea647>3.0.co;2-h;
RA Stanchi F., Bertocco E., Toppo S., Dioguardi R., Simionati B., Cannata N.,
RA Zimbello R., Lanfranchi G., Valle G.;
RT "Characterization of 16 novel human genes showing high similarity to yeast
RT sequences.";
RL Yeast 18:69-80(2001).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 158-313.
RA Barrow I.K.-P., Boguski M.S., Touchman J.W., Spencer F.;
RT "Full-insert sequence of mapped XREF EST.";
RL Submitted (AUG-1998) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=12429849; DOI=10.1091/mbc.e02-05-0271;
RA Scherl A., Coute Y., Deon C., Calle A., Kindbeiter K., Sanchez J.-C.,
RA Greco A., Hochstrasser D.F., Diaz J.-J.;
RT "Functional proteomic analysis of human nucleolus.";
RL Mol. Biol. Cell 13:4100-4109(2002).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T.,
RA Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, AND SUBCELLULAR LOCATION.
RX PubMed=25851604; DOI=10.1091/mbc.e15-02-0073;
RA Zorbas C., Nicolas E., Wacheul L., Huvelle E., Heurgue-Hamard V.,
RA Lafontaine D.L.;
RT "The human 18S rRNA base methyltransferases DIMT1L and WBSCR22-TRMT112 but
RT not rRNA modification are required for ribosome biogenesis.";
RL Mol. Biol. Cell 26:2080-2095(2015).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 31-313 IN COMPLEX WITH
RP S-ADENOSYL-L-METHIONINE.
RG Structural genomics consortium (SGC);
RT "Crystal structure of human dimethyladenosine transferase with SAM.";
RL Submitted (MAY-2005) to the PDB data bank.
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 (PubMed:25851604). Involved in the pre-rRNA processing steps leading to
CC small-subunit rRNA production independently of its RNA-modifying
CC catalytic activity (PubMed:25851604). {ECO:0000269|PubMed:25851604}.
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:0000269|PubMed:25851604};
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleoplasm
CC {ECO:0000269|PubMed:25851604}. Nucleus, nucleolus
CC {ECO:0000269|PubMed:12429849, ECO:0000269|PubMed:25851604}.
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC72947.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Sequence of unknown origin in the N-terminal part.; Evidence={ECO:0000305};
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DR EMBL; AF102147; AAC97955.1; -; mRNA.
DR EMBL; BC002841; AAH02841.1; -; mRNA.
DR EMBL; BC010874; AAH10874.1; -; mRNA.
DR EMBL; AJ009761; CAA08815.1; -; mRNA.
DR EMBL; AF091078; AAC72947.1; ALT_SEQ; mRNA.
DR CCDS; CCDS3981.1; -.
DR RefSeq; NP_001335005.1; NM_001348076.1.
DR RefSeq; NP_055288.1; NM_014473.3.
DR PDB; 1ZQ9; X-ray; 1.90 A; A/B=31-313.
DR PDB; 6W6C; X-ray; 2.38 A; A/B=1-313.
DR PDB; 6W6F; X-ray; 3.20 A; A/B=1-313.
DR PDB; 7MQA; EM; 2.70 A; NL=1-313.
DR PDBsum; 1ZQ9; -.
DR PDBsum; 6W6C; -.
DR PDBsum; 6W6F; -.
DR PDBsum; 7MQA; -.
DR AlphaFoldDB; Q9UNQ2; -.
DR SMR; Q9UNQ2; -.
DR BioGRID; 118116; 154.
DR IntAct; Q9UNQ2; 31.
DR MINT; Q9UNQ2; -.
DR STRING; 9606.ENSP00000199320; -.
DR GlyGen; Q9UNQ2; 3 sites, 1 O-linked glycan (3 sites).
DR iPTMnet; Q9UNQ2; -.
DR PhosphoSitePlus; Q9UNQ2; -.
DR BioMuta; DIMT1; -.
DR DMDM; 27151492; -.
DR SWISS-2DPAGE; Q9UNQ2; -.
DR EPD; Q9UNQ2; -.
DR jPOST; Q9UNQ2; -.
DR MassIVE; Q9UNQ2; -.
DR MaxQB; Q9UNQ2; -.
DR PaxDb; Q9UNQ2; -.
DR PeptideAtlas; Q9UNQ2; -.
DR PRIDE; Q9UNQ2; -.
DR ProteomicsDB; 85325; -.
DR Antibodypedia; 23684; 168 antibodies from 25 providers.
DR DNASU; 27292; -.
DR Ensembl; ENST00000199320.9; ENSP00000199320.4; ENSG00000086189.11.
DR GeneID; 27292; -.
DR KEGG; hsa:27292; -.
DR MANE-Select; ENST00000199320.9; ENSP00000199320.4; NM_014473.4; NP_055288.1.
DR UCSC; uc003jta.4; human.
DR CTD; 27292; -.
DR DisGeNET; 27292; -.
DR GeneCards; DIMT1; -.
DR HGNC; HGNC:30217; DIMT1.
DR HPA; ENSG00000086189; Low tissue specificity.
DR MIM; 612499; gene.
DR neXtProt; NX_Q9UNQ2; -.
DR OpenTargets; ENSG00000086189; -.
DR PharmGKB; PA162383599; -.
DR VEuPathDB; HostDB:ENSG00000086189; -.
DR eggNOG; KOG0820; Eukaryota.
DR GeneTree; ENSGT00950000183142; -.
DR InParanoid; Q9UNQ2; -.
DR OMA; KEEEPYF; -.
DR OrthoDB; 963506at2759; -.
DR PhylomeDB; Q9UNQ2; -.
DR TreeFam; TF354255; -.
DR PathwayCommons; Q9UNQ2; -.
DR Reactome; R-HSA-6790901; rRNA modification in the nucleus and cytosol.
DR SignaLink; Q9UNQ2; -.
DR BioGRID-ORCS; 27292; 621 hits in 1086 CRISPR screens.
DR ChiTaRS; DIMT1; human.
DR EvolutionaryTrace; Q9UNQ2; -.
DR GenomeRNAi; 27292; -.
DR Pharos; Q9UNQ2; Tbio.
DR PRO; PR:Q9UNQ2; -.
DR Proteomes; UP000005640; Chromosome 5.
DR RNAct; Q9UNQ2; protein.
DR Bgee; ENSG00000086189; Expressed in medial globus pallidus and 204 other tissues.
DR ExpressionAtlas; Q9UNQ2; baseline and differential.
DR Genevisible; Q9UNQ2; HS.
DR GO; GO:0005829; C:cytosol; IDA:HPA.
DR GO; GO:0005730; C:nucleolus; IDA:UniProtKB.
DR GO; GO:0005654; C:nucleoplasm; IDA:HPA.
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; HDA:UniProtKB.
DR GO; GO:0000179; F:rRNA (adenine-N6,N6-)-dimethyltransferase activity; IMP:UniProtKB.
DR GO; GO:2000234; P:positive regulation of rRNA processing; IMP:UniProtKB.
DR GO; GO:0031167; P:rRNA methylation; IMP:UniProtKB.
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; Methyltransferase; Nucleus; Reference proteome; RNA-binding;
KW rRNA processing; S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..313
FT /note="Probable dimethyladenosine transferase"
FT /id="PRO_0000101465"
FT REGION 1..21
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 37
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01026,
FT ECO:0000269|Ref.9"
FT BINDING 39
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01026,
FT ECO:0000269|Ref.9"
FT BINDING 64
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01026,
FT ECO:0000269|Ref.9"
FT BINDING 85
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01026,
FT ECO:0000269|Ref.9"
FT BINDING 113
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01026,
FT ECO:0000269|Ref.9"
FT BINDING 128
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01026,
FT ECO:0000269|Ref.9"
FT CONFLICT 157..158
FT /note="RE -> EN (in Ref. 3; CAA08815)"
FT /evidence="ECO:0000305"
FT CONFLICT 265..275
FT /note="IIPEDFSIADK -> VSAAVYPVKQI (in Ref. 2; AAH02841)"
FT /evidence="ECO:0000305"
FT CONFLICT 276..313
FT /note="Missing (in Ref. 2; AAH02841)"
FT /evidence="ECO:0000305"
FT HELIX 42..51
FT /evidence="ECO:0007829|PDB:1ZQ9"
FT STRAND 59..63
FT /evidence="ECO:0007829|PDB:1ZQ9"
FT HELIX 71..77
FT /evidence="ECO:0007829|PDB:1ZQ9"
FT STRAND 78..86
FT /evidence="ECO:0007829|PDB:1ZQ9"
FT HELIX 88..98
FT /evidence="ECO:0007829|PDB:1ZQ9"
FT HELIX 104..106
FT /evidence="ECO:0007829|PDB:1ZQ9"
FT STRAND 107..112
FT /evidence="ECO:0007829|PDB:1ZQ9"
FT TURN 114..116
FT /evidence="ECO:0007829|PDB:1ZQ9"
FT STRAND 123..128
FT /evidence="ECO:0007829|PDB:1ZQ9"
FT HELIX 131..133
FT /evidence="ECO:0007829|PDB:1ZQ9"
FT HELIX 134..143
FT /evidence="ECO:0007829|PDB:1ZQ9"
FT STRAND 149..156
FT /evidence="ECO:0007829|PDB:1ZQ9"
FT HELIX 157..164
FT /evidence="ECO:0007829|PDB:1ZQ9"
FT HELIX 174..182
FT /evidence="ECO:0007829|PDB:1ZQ9"
FT STRAND 183..191
FT /evidence="ECO:0007829|PDB:1ZQ9"
FT HELIX 193..195
FT /evidence="ECO:0007829|PDB:1ZQ9"
FT STRAND 196..198
FT /evidence="ECO:0007829|PDB:1ZQ9"
FT STRAND 204..211
FT /evidence="ECO:0007829|PDB:1ZQ9"
FT HELIX 220..231
FT /evidence="ECO:0007829|PDB:1ZQ9"
FT TURN 232..235
FT /evidence="ECO:0007829|PDB:1ZQ9"
FT HELIX 238..241
FT /evidence="ECO:0007829|PDB:1ZQ9"
FT HELIX 245..262
FT /evidence="ECO:0007829|PDB:1ZQ9"
FT HELIX 272..282
FT /evidence="ECO:0007829|PDB:1ZQ9"
FT HELIX 290..292
FT /evidence="ECO:0007829|PDB:1ZQ9"
FT HELIX 295..306
FT /evidence="ECO:0007829|PDB:1ZQ9"
FT TURN 307..309
FT /evidence="ECO:0007829|PDB:1ZQ9"
SQ SEQUENCE 313 AA; 35236 MW; 306B9D4A4F9494A6 CRC64;
MPKVKSGAIG RRRGRQEQRR ELKSAGGLMF NTGIGQHILK NPLIINSIID KAALRPTDVV
LEVGPGTGNM TVKLLEKAKK VVACELDPRL VAELHKRVQG TPVASKLQVL VGDVLKTDLP
FFDTCVANLP YQISSPFVFK LLLHRPFFRC AILMFQREFA LRLVAKPGDK LYCRLSINTQ
LLARVDHLMK VGKNNFRPPP KVESSVVRIE PKNPPPPINF QEWDGLVRIT FVRKNKTLSA
AFKSSAVQQL LEKNYRIHCS VHNIIIPEDF SIADKIQQIL TSTGFSDKRA RSMDIDDFIR
LLHGFNAEGI HFS
