3B0V
tRNA-dihydrouridine synthase from Thermus thermophilus in complex with tRNA
Summary for 3B0V
| Entry DOI | 10.2210/pdb3b0v/pdb |
| Related | 3B0P 3B0U |
| Descriptor | tRNA, tRNA-dihydrouridine synthase, FLAVIN MONONUCLEOTIDE (3 entities in total) |
| Functional Keywords | tim barrel, oxidoreductase-rna complex, oxidoreductase/rna |
| Biological source | Thermus thermophilus More |
| Total number of polymer chains | 4 |
| Total formula weight | 132725.90 |
| Authors | Yu, F.,Tanaka, Y.,Yamashita, K.,Nakamura, A.,Yao, M.,Tanaka, I. (deposition date: 2011-06-14, release date: 2011-12-14, Last modification date: 2024-10-23) |
| Primary citation | Yu, F.,Tanaka, Y.,Yamashita, K.,Suzuki, T.,Nakamura, A.,Hirano, N.,Suzuki, T.,Yao, M.,Tanaka, I. Molecular basis of dihydrouridine formation on tRNA Proc.Natl.Acad.Sci.USA, 108:19593-19598, 2011 Cited by PubMed Abstract: Dihydrouridine (D) is a highly conserved modified base found in tRNAs from all domains of life. Dihydrouridine synthase (Dus) catalyzes the D formation of tRNA through reduction of uracil base with flavin mononucleotide (FMN) as a cofactor. Here, we report the crystal structures of Thermus thermophilus Dus (TthDus), which is responsible for D formation at positions 20 and 20a, in complex with tRNA and with a short fragment of tRNA (D-loop). Dus interacts extensively with the D-arm and recognizes the elbow region composed of the kissing loop interaction between T- and D-loops in tRNA, pulling U20 into the catalytic center for reduction. Although distortion of the D-loop structure was observed upon binding of Dus to tRNA, the canonical D-loop/T-loop interaction was maintained. These results were consistent with the observation that Dus preferentially recognizes modified rather than unmodified tRNAs, indicating that Dus introduces D20 by monitoring the complete L-shaped structure of tRNAs. In the active site, U20 is stacked on the isoalloxazine ring of FMN, and C5 of the U20 uracil ring is covalently cross linked to the thiol group of Cys93, implying a catalytic mechanism of D20 formation. In addition, the involvement of a cofactor molecule in uracil ring recognition was proposed. Based on a series of mutation analyses, we propose a molecular basis of tRNA recognition and D formation catalyzed by Dus. PubMed: 22123979DOI: 10.1073/pnas.1112352108 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (3.51 Å) |
Structure validation
Download full validation report
