5H7K

Crystal structure of Elongation factor 2 GDP-form

Summary for 5H7K

• Entry DOI: 10.2210/pdb5h7k/pdb
• Related: 5H7J 5H7L
• Descriptor: Elongation factor 2, GUANOSINE-5'-DIPHOSPHATE (3 entities in total)
• Functional Keywords: elongation factor, protein biosynthesis, gtp-binding, translation
• Biological source: Pyrococcus horikoshii OT3
• Cellular location: Cytoplasm : O59521
• Total number of polymer chains: 1
• Total formula weight: 45262.13

Authors

Tanzawa, T.,Kato, K.,Uchiumi, T.,Yao, M. (deposition date: 2016-11-18, release date: 2018-02-21, Last modification date: 2024-03-20)

Primary citation

Tanzawa, T.,Kato, K.,Girodat, D.,Ose, T.,Kumakura, Y.,Wieden, H.J.,Uchiumi, T.,Tanaka, I.,Yao, M.
The C-terminal helix of ribosomal P stalk recognizes a hydrophobic groove of elongation factor 2 in a novel fashion
Nucleic Acids Res., 46:3232-3244, 2018

PubMed Abstract: Archaea and eukaryotes have ribosomal P stalks composed of anchor protein P0 and aP1 homodimers (archaea) or P1•P2 heterodimers (eukaryotes). These P stalks recruit translational GTPases to the GTPase-associated center in ribosomes to provide energy during translation. The C-terminus of the P stalk is known to selectively recognize GTPases. Here we investigated the interaction between the P stalk and elongation factor 2 by determining the structures of Pyrococcus horikoshii EF-2 (PhoEF-2) in the Apo-form, GDP-form, GMPPCP-form (GTP-form), and GMPPCP-form bound with 11 C-terminal residues of P1 (P1C11). Helical structured P1C11 binds to a hydrophobic groove between domain G and subdomain G' of PhoEF-2, where is completely different from that of aEF-1α in terms of both position and sequence, implying that such interaction characteristic may be requested by how GTPases perform their functions on the ribosome. Combining PhoEF-2 P1-binding assays with a structural comparison of current PhoEF-2 structures and molecular dynamics model of a P1C11-bound GDP form, the conformational changes of the P1C11-binding groove in each form suggest that in response to the translation process, the groove has three states: closed, open, and release for recruiting and releasing GTPases.

PubMed: 29471537
DOI: 10.1093/nar/gky115

Experimental method

X-RAY DIFFRACTION (1.599 Å)