5W75

Crystal Structure of Reconstructed Bacterial Elongation Factor Node 168

Summary for 5W75

• Entry DOI: 10.2210/pdb5w75/pdb
• Related PRD ID: PRD_900003
• Descriptor: Elongation factor Tu, beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose, GUANOSINE-5'-DIPHOSPHATE, ... (6 entities in total)
• Functional Keywords: ancestral gene reconstruction, thermostability, ef-tu, asr, translation
• Biological source: Thermotoga neapolitana (strain ATCC 49049 / DSM 4359 / NS-E)
• Cellular location: Cytoplasm : B9K884
• Total number of polymer chains: 4
• Total formula weight: 179927.88

Authors

Ortlund, E.A. (deposition date: 2017-06-19, release date: 2018-04-25, Last modification date: 2024-03-13)

Primary citation

Okafor, C.D.,Pathak, M.C.,Fagan, C.E.,Bauer, N.C.,Cole, M.F.,Gaucher, E.A.,Ortlund, E.A.
Structural and Dynamics Comparison of Thermostability in Ancient, Modern, and Consensus Elongation Factor Tus.
Structure, 26:118-129.e3, 2018

PubMed Abstract: Rationally engineering thermostability in proteins would create enzymes and receptors that function under harsh industrial applications. Several sequence-based approaches can generate thermostable variants of mesophilic proteins. To gain insight into the mechanisms by which proteins become more stable, we use structural and dynamic analyses to compare two popular approaches, ancestral sequence reconstruction (ASR) and the consensus method, used to generate thermostable variants of Elongation Factor Thermo-unstable (EF-Tu). We present crystal structures of ancestral and consensus EF-Tus, accompanied by molecular dynamics simulations aimed at probing the strategies employed to enhance thermostability. All proteins adopt crystal structures similar to extant EF-Tus, revealing no difference in average structure between the methods. Molecular dynamics reveals that ASR-generated sequences retain dynamic properties similar to extant, thermostable EF-Tu from Thermus aquaticus, while consensus EF-Tu dynamics differ from evolution-based sequences. This work highlights the advantage of ASR for engineering thermostability while preserving natural motions in multidomain proteins.

PubMed: 29276038
DOI: 10.1016/j.str.2017.11.018

Experimental method

X-RAY DIFFRACTION (2.298 Å)