Summary for 3VYW
| Entry DOI | 10.2210/pdb3vyw/pdb |
| Descriptor | MNMC2, S-ADENOSYLMETHIONINE, BENZAMIDINE, ... (4 entities in total) |
| Functional Keywords | trna wobble uridine, modification enzyme, genetic code, 5-methylaminomethyl-2-thiouridine, methyltransferase, 2-codon sets, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi, transferase |
| Biological source | Aquifex aeolicus |
| Total number of polymer chains | 4 |
| Total formula weight | 146587.63 |
| Authors | Shibata, R.,Bessho, Y.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2012-10-03, release date: 2012-10-17, Last modification date: 2024-10-16) |
| Primary citation | Kitamura, A.,Nishimoto, M.,Sengoku, T.,Shibata, R.,Jager, G.,Bjork, G.R.,Grosjean, H.,Yokoyama, S.,Bessho, Y. Characterization and structure of the Aquifex aeolicus protein DUF752: a bacterial tRNA-methyltransferase (MnmC2) functioning without the usually fused oxidase domain (MnmC1). J.Biol.Chem., 287:43950-43960, 2012 Cited by PubMed Abstract: Post-transcriptional modifications of the wobble uridine (U34) of tRNAs play a critical role in reading NNA/G codons belonging to split codon boxes. In a subset of Escherichia coli tRNA, this wobble uridine is modified to 5-methylaminomethyluridine (mnm(5)U34) through sequential enzymatic reactions. Uridine 34 is first converted to 5-carboxymethylaminomethyluridine (cmnm(5)U34) by the MnmE-MnmG enzyme complex. The cmnm(5)U34 is further modified to mnm(5)U by the bifunctional MnmC protein. In the first reaction, the FAD-dependent oxidase domain (MnmC1) converts cmnm(5)U into 5-aminomethyluridine (nm(5)U34), and this reaction is immediately followed by the methylation of the free amino group into mnm(5)U34 by the S-adenosylmethionine-dependent domain (MnmC2). Aquifex aeolicus lacks a bifunctional MnmC protein fusion and instead encodes the Rossmann-fold protein DUF752, which is homologous to the methyltransferase MnmC2 domain of Escherichia coli MnmC (26% identity). Here, we determined the crystal structure of the A. aeolicus DUF752 protein at 2.5 Å resolution, which revealed that it catalyzes the S-adenosylmethionine-dependent methylation of nm(5)U in vitro, to form mnm(5)U34 in tRNA. We also showed that naturally occurring tRNA from A. aeolicus contains the 5-mnm group attached to the C5 atom of U34. Taken together, these results support the recent proposal of an alternative MnmC1-independent shortcut pathway for producing mnm(5)U34 in tRNAs. PubMed: 23091054DOI: 10.1074/jbc.M112.409300 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.49 Å) |
Structure validation
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