Protein:TRDMT1 |
Protein Summary |
 Gene summary |
| Gene name: TRDMT1 | ASpdb.0 ID: 1787 | Gene | Gene symbol | TRDMT1 | Gene ID | 1787 |
| Gene name | tRNA aspartic acid methyltransferase 1 |
| Synonyms | DMNT2|DNMT2|MHSAIIP|PUMET|RNMT1 |
| Cytomap | 10p13 |
| Type of gene | protein-coding |
| Description | tRNA (cytosine(38)-C(5))-methyltransferaseDNA (cytosine-5)-methyltransferase-like protein 2DNA MTase homolog HsaIIPDNA cytosine-5 methyltransferase 2DNA methyltransferase-2tRNA (cytosine-5-)-methyltransferase |
| Modification date | 20240403 |
| UniProtAcc | O14717 |
| Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Gene | TRDMT1 | GO:0005737 | cytoplasm | 16424344 |
| Gene | TRDMT1 | GO:0008175 | tRNA methyltransferase activity | 16424344 |
| Gene | TRDMT1 | GO:0030488 | tRNA methylation | 16424344 |
AS Summary |
| Information of the canonical protein with experimentally identified structure from PDB (2023). |
| UniProt Acc | File name | PDB ID | Method | Resolution | Chain | Start | End |
| O14717-1 | O14717-1_1g55_A.pdb | 1G55 | X-ray | 1.8 | A | 2 | 391 |
| ASpdb's canonical and alternatively spliced isoform information. |
| accession_id | gene_name | canonical_id | alternative_id | canonical_length | alternative_length | canonical_start | canonical_end | type | originalSEQ | variationSEQ | alternative_start | alternative_end |
| O14717 | TRDMT1 | O14717-1 | O14717-2 | 391 | 367 | 84 | 107 | Deletion | none | none | 83 | 83 |
| O14717 | TRDMT1 | O14717-1 | O14717-3 | 391 | 345 | 84 | 129 | Deletion | none | none | 83 | 83 |
| O14717 | TRDMT1 | O14717-1 | O14717-4 | 391 | 63 | 59 | 63 | Substitution | GITLE | DWPAG | 59 | 63 |
| O14717 | TRDMT1 | O14717-1 | O14717-4 | 391 | 63 | 64 | 391 | Deletion | none | none | 63 | 63 |
| O14717 | TRDMT1 | O14717-1 | O14717-5 | 391 | 71 | 59 | 71 | Substitution | GITLEEFDRLSFD | ITKITKVYSFGKC | 59 | 71 |
| O14717 | TRDMT1 | O14717-1 | O14717-5 | 391 | 71 | 72 | 391 | Deletion | none | none | 71 | 71 |
| O14717 | TRDMT1 | O14717-1 | O14717-6 | 391 | 107 | 59 | 107 | Substitution | GITLEEFDRLSFDMILMSPPCQPFTRIGRQGDMTDSRTNSFLHILDILP | RPLDTNNRKLWLSVPRVYIISNLSWHSKFKATIFSYCKASVRAITLSSP | 59 | 107 |
| O14717 | TRDMT1 | O14717-1 | O14717-6 | 391 | 107 | 108 | 391 | Deletion | none | none | 107 | 107 |
| Multiple sequence alignment of our canonical and alternatively spliced TRDMT1 |
| Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of TRDMT1 |
| UniProt-id | ENSG | ENST | ENSP |
| O14717-1 | ENSG00000107614.22 | ENST00000377799.8 | ENSP00000367030.3 |
| O14717-4 | ENSG00000107614.22 | ENST00000495022.5 | ENSP00000417594.1 |
| UniProt-id | NM ID | NP ID |
| O14717-1 | NM_004412.6 | NP_004403.1 |
| Amino acid sequences of our canonical and alternatively spliced TRDMT1 |
| accession_id | Protein sequence |
| O14717-1 | MEPLRVLELYSGVGGMHHALRESCIPAQVVAAIDVNTVANEVYKYNFPHTQLLAKTIEGITLEEFDRLSFDMILMSPPCQPFTRIGRQGD MTDSRTNSFLHILDILPRLQKLPKYILLENVKGFEVSSTRDLLIQTIENCGFQYQEFLLSPTSLGIPNSRLRYFLIAKLQSEPLPFQAPG QVLMEFPKIESVHPQKYAMDVENKIQEKNVEPNISFDGSIQCSGKDAILFKLETAEEIHRKNQQDSDLSVKMLKDFLEDDTDVNQYLLPP KSLLRYALLLDIVQPTCRRSVCFTKGYGSYIEGTGSVLQTAEDVQVENIYKSLTNLSQEEQITKLLILKLRYFTPKEIANLLGFPPEFGF |
| O14717-2 | MEPLRVLELYSGVGGMHHALRESCIPAQVVAAIDVNTVANEVYKYNFPHTQLLAKTIEGITLEEFDRLSFDMILMSPPCQPFTRLQKLPK YILLENVKGFEVSSTRDLLIQTIENCGFQYQEFLLSPTSLGIPNSRLRYFLIAKLQSEPLPFQAPGQVLMEFPKIESVHPQKYAMDVENK IQEKNVEPNISFDGSIQCSGKDAILFKLETAEEIHRKNQQDSDLSVKMLKDFLEDDTDVNQYLLPPKSLLRYALLLDIVQPTCRRSVCFT KGYGSYIEGTGSVLQTAEDVQVENIYKSLTNLSQEEQITKLLILKLRYFTPKEIANLLGFPPEFGFPEKITVKQRYRLLGNSLNVHVVAK |
| O14717-3 | MEPLRVLELYSGVGGMHHALRESCIPAQVVAAIDVNTVANEVYKYNFPHTQLLAKTIEGITLEEFDRLSFDMILMSPPCQPFTRDLLIQT IENCGFQYQEFLLSPTSLGIPNSRLRYFLIAKLQSEPLPFQAPGQVLMEFPKIESVHPQKYAMDVENKIQEKNVEPNISFDGSIQCSGKD AILFKLETAEEIHRKNQQDSDLSVKMLKDFLEDDTDVNQYLLPPKSLLRYALLLDIVQPTCRRSVCFTKGYGSYIEGTGSVLQTAEDVQV |
| O14717-4 | |
| O14717-5 | |
| O14717-6 | MEPLRVLELYSGVGGMHHALRESCIPAQVVAAIDVNTVANEVYKYNFPHTQLLAKTIERPLDTNNRKLWLSVPRVYIISNLSWHSKFKAT |
Protein Functional Features |
| Main function of this protein. (from UniProt) |
| TRDMT1 (go to UniProt):O14717 |
| Retention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at * Minus value of BPloci means that the break pointn is located before the CDS. |
| - Retained protein feature among the 13 regional features. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| O14717 | Domain | 4 | 391 | Note=SAM-dependent MTase C5-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01016 | Type=Deletion;Start=84;End=107 |
| O14717 | Domain | 4 | 391 | Note=SAM-dependent MTase C5-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01016 | Type=Deletion;Start=84;End=129 |
| O14717 | Domain | 4 | 391 | Note=SAM-dependent MTase C5-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01016 | Type=Substitution;Start=59;End=63 |
| O14717 | Domain | 4 | 391 | Note=SAM-dependent MTase C5-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01016 | Type=Deletion;Start=64;End=391 |
| O14717 | Domain | 4 | 391 | Note=SAM-dependent MTase C5-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01016 | Type=Substitution;Start=59;End=71 |
| O14717 | Domain | 4 | 391 | Note=SAM-dependent MTase C5-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01016 | Type=Deletion;Start=72;End=391 |
| O14717 | Domain | 4 | 391 | Note=SAM-dependent MTase C5-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01016 | Type=Substitution;Start=59;End=107 |
| O14717 | Domain | 4 | 391 | Note=SAM-dependent MTase C5-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01016 | Type=Deletion;Start=108;End=391 |
Gene Isoform Structures and Expression Levels for TRDMT1 |
| Gene structures of our canonical and alternative spliced genes of TRDMT1 * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Expression levels of gene isoforms across GTEx. |
 |
| Expression levels of gene isoforms across TCGA. |
 |
Protein Structures |
| PDB and CIF files of the predicted protein structures * Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format. |
| 3D view using mol* of O14717-1 |
| 3D view using mol* of O14717-2 |
| 3D view using mol* of O14717-3 |
| 3D view using mol* of O14717-4 |
| 3D view using mol* of O14717-5 |
| 3D view using mol* of O14717-6 |
pLDDT Score Distribution |
| pLDDT score distribution of the predicted protein structures from AlphaFold2 * AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. |
| pLDDT distribution across the protein length of O14717-1 |
 |
| pLDDT distribution across the protein length of O14717-2 |
 |
| pLDDT distribution across the protein length of O14717-3 |
 |
| pLDDT distribution across the protein length of O14717-4 |
 |
| pLDDT distribution across the protein length of O14717-5 |
 |
| pLDDT distribution across the protein length of O14717-6 |
 |
Ramachandran Plot of Protein Structures |
| Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide. |
| Ramachandran plot of O14717-1 |
 |
| Ramachandran plot of O14717-3 |
 |
| Ramachandran plot of O14717-5 |
 |
| Ramachandran plot of O14717-6 |
 |
Potential Active Site Information |
| The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite. |
| UniProt-id | Site score | Size | D score | Volume | Exposure | Enclosure | Contact | Phobic | Philic | Balance | Don/Acc | Residues |
| O14717-1 | 1.069 | 188 | 0.982 | 480.886 | 0.392 | 0.8 | 1.098 | 0.45 | 1.343 | 0.335 | 0.609 | 8,9,10,11,12,13,14,15,16,33,34,35,36,39,55,56,57,5 8,76,77,78,79,80,95,98,119,120,121,160,162,294,295 ,371,372,374,375,376,377 |
| O14717-2 | 1.126 | 147 | 1.178 | 255.535 | 0.398 | 0.8 | 1.017 | 1.815 | 0.741 | 2.45 | 0.841 | 7,9,10,57,65,73,75,77,79,80,81,82,83,84,85,88,89,9 2,94,100,105,109,112,113,115,116,118 |
| O14717-3 | 1.053 | 397 | 1.079 | 833.833 | 0.41 | 0.755 | 0.99 | 1.1 | 0.962 | 1.144 | 0.764 | 4,8,9,10,11,12,13,14,15,16,34,35,36,39,56,57,58,70 ,71,72,73,74,75,76,77,78,79,80,81,82,83,84,87,91,9 6,114,116,117,118,119,120,121,122,123,325,326,328, 329,330,331,332,336,339,340,343,344 |
| O14717-4 | 0.562 | 17 | 0.494 | 35.672 | 0.485 | 0.625 | 1.017 | 0.405 | 0.825 | 0.491 | 1.031 | 33,53,55,56,57,59,60,61
|
| O14717-5 | 0.59 | 35 | 0.512 | 66.199 | 0.696 | 0.532 | 0.783 | 0.162 | 1.116 | 0.145 | 0.283 | 17,21,27,28,29,30,46,47,48,49,50,51,69
|
| O14717-6 | 0.961 | 44 | 1.012 | 98.098 | 0.397 | 0.779 | 1.078 | 4.283 | 0.242 | 17.734 | 0.434 | 4,6,16,19,20,23,25,27,76,78,83,87
|
Protein Structure and Feature Comparision |
| Protein Structure Comparision Using Template Modeling Scores (TM-score). |
 |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green) |
| 3D view using mol* of O14717-1_O14717-1_1g55_A.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of O14717-1_1g55_A_O14717-2.pdb |
| 3D view using mol* of O14717-1_1g55_A_O14717-3.pdb |
| 3D view using mol* of O14717-1_1g55_A_O14717-4.pdb |
| 3D view using mol* of O14717-1_1g55_A_O14717-5.pdb |
| 3D view using mol* of O14717-1_1g55_A_O14717-6.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of O14717-1_O14717-2.pdb |
| 3D view using mol* of O14717-1_O14717-3.pdb |
| 3D view using mol* of O14717-1_O14717-4.pdb |
| 3D view using mol* of O14717-1_O14717-5.pdb |
| 3D view using mol* of O14717-1_O14717-6.pdb |
| Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/O14717-1_vs_O14717-2.png |
 < |
| ./stats/secondary_structure/figure/O14717-1_vs_O14717-3.png |
 < |
| ./stats/secondary_structure/figure/O14717-1_vs_O14717-4.png |
 < |
| ./stats/secondary_structure/figure/O14717-1_vs_O14717-5.png |
 < |
| ./stats/secondary_structure/figure/O14717-1_vs_O14717-6.png |
 < |
| Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/O14717-1_vs_O14717-2.png |
 < |
| ./stats/relative_asa/O14717-1_vs_O14717-3.png |
 < |
| ./stats/relative_asa/O14717-1_vs_O14717-4.png |
 < |
| ./stats/relative_asa/O14717-1_vs_O14717-5.png |
 < |
| ./stats/relative_asa/O14717-1_vs_O14717-6.png |
 < |
Protein-Protein Interaction |
| Interactors from UniProt. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| Interactors from STRING. |
| Gene name | Interactors |
Related Drugs to TRDMT1 |
| Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
| O14717 | TRDMT1 | DB01752 | S-adenosyl-L-homocysteine | experimental | |
| O14717 | TRDMT1 | DB09462 | Glycerin | approved, investigational | |
| O14717 | TRDMT1 | DB00738 | Pentamidine | approved, investigational | other |
Related Diseases to TRDMT1 |
| Previous studies relating to the alternative splicing of TRDMT1 and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
| TRDMT1 | 11551826 | Five novel alternatively spliced transcripts of DNA (cytosine-5) methyltransferase 2 in human peripheral blood leukocytes. | Alternative splicing of RNA molecules transcribed from DNA (cytosine-5) methyltransferases has been proposed as a mechanism by which methylation is able to effect diverse biological processes in higher eukaryotes. This study has investigated transcriptional versatility of DNA (cytosine-5) methyltransferase 2, which may methylate cytosine residues within 5'-CCTGG-3' pentanucleotides in regions of the human genome devoid of 5'-CG-3' methylation. Five novel splice variants of DNA (cytosine-5) methyltransferase 2 were identified in the peripheral blood leukocytes of healthy subjects following cloning and sequencing of RT-PCR products amplified using gene specific oligodeoxyribonucleotide primers. The generation of some of these splice variants may be influenced by the formation of secondary structures within pre-mRNA due to the repetition of sequences flanking alternatively spliced exons in a reverse and complementary orientation on the same strand. These findings enable novel approaches to investigate the role of RNA secondary structures in alternative splicing. The DNA (cytosine-5) methyltransferase 2 splice variants are generated in all the major cell types of peripheral blood, as well as in neoplastic lymphoid cells indicating that they are unlikely to generate proteins involved in control of the cell cycle or cellular differentiation. Interestingly, the gene products generated by some splice variants completely or partially lack highly conserved amino acid motifs shown to be important for the catalysis of cytosine methylation. The possibility cannot be excluded, therefore, that alternative splicing of DNA (cytosine-5) methyltransferase 2 pre-mRNA may generate protein isoforms which have different methylating capabilities or which are involved in biological processes other than the catalysis of cytosine methylation. | D008228 | Lymphoma, Non-Hodgkin |
Clinically important variants in TRDMT1 |
| (ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
Copyright 2024-PresentThe University of Texas Health Science Center at Houston (UTHealth Houston) Web File Viewing | Emergency Information |