6ab8 | pdb_00006ab8

Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with ZLys

spinqualitylabelsall models 6ab8, resolution 1.75Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6ab8 is a 1 chain structure with sequence from Methanosarcina mazei jcm 9314. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: 9VC, ATP, K, MG Related: 6aac, 6aad, 6aan, 6aao, 6aap, 6aaq, 6aaz, 6ab0, 6ab1, 6ab2 Gene: pylS, DU43_20175, DU67_18120 (Methanosarcina mazei JCM 9314) Activity: Pyrrolysine--tRNA(Pyl) ligase, with EC number 6.1.1.26 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [A0A0F8JXW8_METMZ] Catalyzes the attachment of pyrrolysine to tRNA(Pyl). Pyrrolysine is a lysine derivative encoded by the termination codon UAG.[HAMAP-Rule:MF_01573] Publication Abstract from PubMed Pyrrolysyl-tRNA synthetase (PylRS) and tRNA(Pyl) have been extensively used for genetic-code expansion. A Methanosarcina mazei PylRS mutant bearing the Y306A and Y384F mutations (PylRS(Y306A/Y384F)) encodes various bulky non-natural lysine derivatives by UAG. In this study, we examined how PylRS(Y306A/Y384F) recognizes many amino acids. Among 17 non-natural lysine derivatives, N(varepsilon)-(benzyloxycarbonyl)lysine (ZLys) and 10 ortho/meta/para-substituted ZLys derivatives were efficiently ligated to tRNA(Pyl) and were incorporated into proteins by PylRS(Y306A/Y384F). We determined crystal structures of 14 non-natural lysine derivatives bound to the PylRS(Y306A/Y384F) catalytic fragment. The meta- and para-substituted ZLys derivatives are snugly accommodated in the productive mode. In contrast, ZLys and the unsubstituted or ortho-substituted ZLys derivatives exhibited an alternative binding mode in addition to the productive mode. PylRS(Y306A/Y384F) displayed a high aminoacylation rate for ZLys, indicating that the double-binding mode minimally affects aminoacylation. These precise substrate recognition mechanisms by PylRS(Y306A/Y384F) may facilitate the structure-based design of novel non-natural amino acids. Structural Basis for Genetic-Code Expansion with Bulky Lysine Derivatives by an Engineered Pyrrolysyl-tRNA Synthetase.,Yanagisawa T, Kuratani M, Seki E, Hino N, Sakamoto K, Yokoyama S Cell Chem Biol. 2019 Apr 5. pii: S2451-9456(19)30104-7. doi:, 10.1016/j.chembiol.2019.03.008. PMID:31031143 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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