5IZM

The crystal structure of human eEFSec in complex with GDPNP

Summary for 5IZM

• Entry DOI: 10.2210/pdb5izm/pdb
• Related: 5IZK 5IZL
• Descriptor: Selenocysteine-specific elongation factor, MANGANESE (II) ION, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (3 entities in total)
• Functional Keywords: elongation factor, selenocysteine, selenocysteine trna, translation, gtpase, gdpnp, gtp
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 2
• Total formula weight: 137876.63

Authors

Dobosz-Bartoszek, M.,Otwinowski, Z.,Simonovic, M. (deposition date: 2016-03-25, release date: 2016-10-12, Last modification date: 2024-11-20)

Primary citation

Dobosz-Bartoszek, M.,Pinkerton, M.H.,Otwinowski, Z.,Chakravarthy, S.,Soll, D.,Copeland, P.R.,Simonovic, M.
Crystal structures of the human elongation factor eEFSec suggest a non-canonical mechanism for selenocysteine incorporation.
Nat Commun, 7:12941-12941, 2016

PubMed Abstract: Selenocysteine is the only proteinogenic amino acid encoded by a recoded in-frame UGA codon that does not operate as the canonical opal stop codon. A specialized translation elongation factor, eEFSec in eukaryotes and SelB in prokaryotes, promotes selenocysteine incorporation into selenoproteins by a still poorly understood mechanism. Our structural and biochemical results reveal that four domains of human eEFSec fold into a chalice-like structure that has similar binding affinities for GDP, GTP and other guanine nucleotides. Surprisingly, unlike in eEF1A and EF-Tu, the guanine nucleotide exchange does not cause a major conformational change in domain 1 of eEFSec, but instead induces a swing of domain 4. We propose that eEFSec employs a non-canonical mechanism involving the distinct C-terminal domain 4 for the release of the selenocysteinyl-tRNA during decoding on the ribosome.

PubMed: 27708257
DOI: 10.1038/ncomms12941

Experimental method

X-RAY DIFFRACTION (3.4 Å)