3WNC

Crystal structure of EF-Pyl in complex with GDP

Summary for 3WNC

• Entry DOI: 10.2210/pdb3wnc/pdb
• Related: 2ELF 3WNB 3WND
• Descriptor: Protein translation elongation factor 1A, GUANOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi, trna, elongation factor, pyrrolysine, translation
• Biological source: Methanosarcina mazei
• Total number of polymer chains: 1
• Total formula weight: 41242.14

Authors

Yanagisawa, T.,Ishii, R.,Fukunaga, R.,Sengoku, T.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2013-12-08, release date: 2014-12-10, Last modification date: 2024-10-16)

Primary citation

Yanagisawa, T.,Ishii, R.,Hikida, Y.,Fukunaga, R.,Sengoku, T.,Sekine, S.,Yokoyama, S.
A SelB/EF-Tu/aIF2 gamma-like protein from Methanosarcina mazei in the GTP-bound form binds cysteinyl-tRNA(Cys.).
J. Struct. Funct. Genomics, 16:25-41, 2015

PubMed Abstract: The putative translation elongation factor Mbar_A0971 from the methanogenic archaeon Methanosarcina barkeri was proposed to be the pyrrolysine-specific paralogue of EF-Tu ("EF-Pyl"). In the present study, the crystal structures of its homologue from Methanosarcina mazei (MM1309) were determined in the GMPPNP-bound, GDP-bound, and apo forms, by the single-wavelength anomalous dispersion phasing method. The three MM1309 structures are quite similar (r.m.s.d. < 0.1 Å). The three domains, corresponding to domains 1, 2, and 3 of EF-Tu/SelB/aIF2γ, are packed against one another to form a closed architecture. The MM1309 structures resemble those of bacterial/archaeal SelB, bacterial EF-Tu in the GTP-bound form, and archaeal initiation factor aIF2γ, in this order. The GMPPNP and GDP molecules are visible in their co-crystal structures. Isothermal titration calorimetry measurements of MM1309·GTP·Mg(2+), MM1309·GDP·Mg(2+), and MM1309·GMPPNP·Mg(2+) provided dissociation constants of 0.43, 26.2, and 222.2 μM, respectively. Therefore, the affinities of MM1309 for GTP and GDP are similar to those of SelB rather than those of EF-Tu. Furthermore, the switch I and II regions of MM1309 are involved in domain-domain interactions, rather than nucleotide binding. The putative binding pocket for the aminoacyl moiety on MM1309 is too small to accommodate the pyrrolysyl moiety, based on a comparison of the present MM1309 structures with that of the EF-Tu·GMPPNP·aminoacyl-tRNA ternary complex. A hydrolysis protection assay revealed that MM1309 binds cysteinyl (Cys)-tRNA(Cys) and protects the aminoacyl bond from non-enzymatic hydrolysis. Therefore, we propose that MM1309 functions as either a guardian protein that protects the Cys moiety from oxidation or an alternative translation factor for Cys-tRNA(Cys).

PubMed: 25618148
DOI: 10.1007/s10969-015-9193-6

Experimental method

X-RAY DIFFRACTION (1.9 Å)