4ACB

CRYSTAL STRUCTURE OF TRANSLATION ELONGATION FACTOR SELB FROM METHANOCOCCUS MARIPALUDIS IN COMPLEX WITH THE GTP ANALOGUE GPPNHP

Replaces:  1WB3

Summary for 4ACB

• Entry DOI: 10.2210/pdb4acb/pdb
• Related: 1WB2 1WB3 4AC9 4ACA
• Descriptor: TRANSLATION ELONGATION FACTOR SELB, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER, MAGNESIUM ION, ... (8 entities in total)
• Functional Keywords: selenocysteine, translation, secis element, ef-sec, sec-trna(sec)
• Biological source: METHANOCOCCUS MARIPALUDIS
• Total number of polymer chains: 4
• Total formula weight: 221287.63

Authors

Leibundgut, M.,Frick, C.,Thanbichler, M.,Boeck, A.,Ban, N. (deposition date: 2011-12-14, release date: 2012-11-07, Last modification date: 2024-10-23)

Primary citation

Leibundgut, M.,Frick, C.,Thanbichler, M.,Bock, A.,Ban, N.
Selenocysteine tRNA-Specific Elongation Factor Selb is a Structural Chimaera of Elongation and Initiation Factors.
Embo J., 24:11-, 2005

PubMed Abstract: In all three kingdoms of life, SelB is a specialized translation elongation factor responsible for the cotranslational incorporation of selenocysteine into proteins by recoding of a UGA stop codon in the presence of a downstream mRNA hairpin loop. Here, we present the X-ray structures of SelB from the archaeon Methanococcus maripaludis in the apo-, GDP- and GppNHp-bound form and use mutational analysis to investigate the role of individual amino acids in its aminoacyl-binding pocket. All three SelB structures reveal an EF-Tu:GTP-like domain arrangement. Upon binding of the GTP analogue GppNHp, a conformational change of the Switch 2 region in the GTPase domain leads to the exposure of SelB residues involved in clamping the 5' phosphate of the tRNA. A conserved extended loop in domain III of SelB may be responsible for specific interactions with tRNA(Sec) and act as a ruler for measuring the extra long acceptor arm. Domain IV of SelB adopts a beta barrel fold and is flexibly tethered to domain III. The overall domain arrangement of SelB resembles a 'chalice' observed so far only for initiation factor IF2/eIF5B. In our model of SelB bound to the ribosome, domain IV points towards the 3' mRNA entrance cleft ready to interact with the downstream secondary structure element.

PubMed: 15616587
DOI: 10.1038/SJ.EMBOJ.7600505

Experimental method

X-RAY DIFFRACTION (3.34 Å)