3b0u | pdb_00003b0u

tRNA-dihydrouridine synthase from Thermus thermophilus in complex with tRNA fragment

spinqualitylabelsall models 3b0u, resolution 1.95Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3b0u is a 4 chain structure with sequence from Thermus thermophilus HB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.948Å Ligands: FMN, H2U Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function DUSAL_THET8 Catalyzes the synthesis of 5,6-dihydrouridine (D), a modified base found in the D-loop of most tRNAs, via the reduction of the C5-C6 double bond in target uridines. Specifically modifies U20 and U20a in tRNAs.[HAMAP-Rule:MF_02041] Publication Abstract from PubMed 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. Molecular basis of dihydrouridine formation on tRNA.,Yu F, Tanaka Y, Yamashita K, Suzuki T, Nakamura A, Hirano N, Suzuki T, Yao M, Tanaka I Proc Natl Acad Sci U S A. 2011 Dec 6;108(49):19593-8. Epub 2011 Nov 28. PMID:22123979 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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