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3wnc
From Proteopedia
(Difference between revisions)
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==Crystal structure of EF-Pyl in complex with GDP== | ==Crystal structure of EF-Pyl in complex with GDP== | ||
| - | <StructureSection load='3wnc' size='340' side='right' caption='[[3wnc]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='3wnc' size='340' side='right'caption='[[3wnc]], [[Resolution|resolution]] 1.90Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[3wnc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/ | + | <table><tr><td colspan='2'>[[3wnc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43340_[[methanococcus_frisius_blotevogel_et_al._1986]] Atcc 43340 [[methanococcus frisius blotevogel et al. 1986]]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WNC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3WNC FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2elf|2elf]], [[3wnb|3wnb]], [[3wnd|3wnd]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2elf|2elf]], [[3wnb|3wnb]], [[3wnd|3wnd]]</td></tr> | ||
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MM_1309 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2209 | + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MM_1309 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2209 ATCC 43340 [[Methanococcus frisius Blotevogel et al. 1986]]])</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http:// | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3wnc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wnc OCA], [http://pdbe.org/3wnc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wnc RCSB], [http://www.ebi.ac.uk/pdbsum/3wnc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wnc ProSAT]</span></td></tr> |
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | 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 A). The three domains, corresponding to domains 1, 2, and 3 of EF-Tu/SelB/aIF2gamma, 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 aIF2gamma, 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 muM, 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). | ||
| + | |||
| + | A SelB/EF-Tu/aIF2gamma-like protein from Methanosarcina mazei in the GTP-bound form binds cysteinyl-tRNA(Cys.).,Yanagisawa T, Ishii R, Hikida Y, Fukunaga R, Sengoku T, Sekine S, Yokoyama S J Struct Funct Genomics. 2015 Mar;16(1):25-41. doi: 10.1007/s10969-015-9193-6., Epub 2015 Jan 25. PMID:25618148<ref>PMID:25618148</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 3wnc" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: | + | [[Category: Large Structures]] |
[[Category: Fukunaga, R]] | [[Category: Fukunaga, R]] | ||
[[Category: Ishii, R]] | [[Category: Ishii, R]] | ||
Revision as of 06:10, 6 May 2020
Crystal structure of EF-Pyl in complex with GDP
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