Structural highlights
6abk 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.
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| Ligands: | , , |
| Related: | 6aac, 6aad, 6aan, 6aao, 6aap, 6aaq, 6aaz, 6ab0, 6ab1, 6ab2, 6ab8 |
| 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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Yanagisawa T, Kuratani M, Seki E, Hino N, Sakamoto K, Yokoyama S. Structural Basis for Genetic-Code Expansion with Bulky Lysine Derivatives by an Engineered Pyrrolysyl-tRNA Synthetase. Cell Chem Biol. 2019 Apr 5. pii: S2451-9456(19)30104-7. doi:, 10.1016/j.chembiol.2019.03.008. PMID:31031143 doi:http://dx.doi.org/10.1016/j.chembiol.2019.03.008
