5zvh | pdb_00005zvh

The crystal structure of NSun6 from Pyrococcus horikoshii with SFG

spinqualitylabelsall models 5zvh, resolution 2.50Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5zvh is a 2 chain structure with sequence from Pyrococcus horikoshii OT3. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.5Å Ligands: SFG Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function NSUN6_PYRHO S-adenosyl-L-methionine-dependent methyltransferase that specifically methylates the C5 position of cytosine 72 in several tRNAs. This modification appears to slightly promote the thermal stability of P.horikoshii tRNAs, but does not affect their amino acid accepting activity. Four elements in the acceptor stems of tRNAs are essential for substrate recognition by this enzyme: the target site C72, the 3'-CCA terminus, U73 or G73, and the second base pair C2:G71. Publication Abstract from PubMed Human NOL1/NOP2/Sun RNA methyltransferase family member 6 (hNSun6) generates 5-methylcytosine (m5C) at C72 of four specific tRNAs, and its homologs are present only in higher eukaryotes and hyperthermophilic archaea. Archaeal NSun6 homologs possess conserved catalytic residues, but have distinct differences in their RNA recognition motifs from eukaryotic NSun6s. Until now, the biochemical properties and functions of archaeal NSun6 homologs were unknown. In archaeon Pyrococcus horikoshii OT3, the gene encoding the NSun6 homolog is PH1991. We demonstrated that the PH1991 protein could catalyze m5C72 formation on some specific PhtRNAs in vitro and was thus named as PhNSun6. Remarkably, PhNSun6 has a much wider range of tRNA substrates than hNSun6, which was attributed to its tRNA substrate specificity. The mechanism was further elucidated using biochemical and crystallographic experiments. Structurally, the binding pocket for nucleotide 73 in PhNSun6 is specific to accommodate U73 or G73-containing PhtRNAs. Furthermore, PhNSun6 lacks the eukaryotic NSun6-specific Lys-rich loop, resulting in the non-recognition of D-stem region by PhNSun6. Functionally, the m5C72 modification could slightly promote the thermal stability of PhtRNAs, but did not affect the amino acid accepting activity of PhtRNAs. Archaeal NSUN6 catalyzes m5C72 modification on a wide-range of specific tRNAs.,Li J, Li H, Long T, Dong H, Wang ED, Liu RJ Nucleic Acids Res. 2019 Feb 28;47(4):2041-2055. doi: 10.1093/nar/gky1236. PMID:30541086 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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