4aca: Difference between revisions
No edit summary |
No edit summary |
||
| (4 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
==CRYSTAL STRUCTURE OF TRANSLATION ELONGATION FACTOR SELB FROM METHANOCOCCUS MARIPALUDIS, APO FORM== | |||
<StructureSection load='4aca' size='340' side='right'caption='[[4aca]], [[Resolution|resolution]] 3.15Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4aca]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanococcus_maripaludis Methanococcus maripaludis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1wb2 1wb2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ACA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ACA FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.15Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=CMH:S-(METHYLMERCURY)-L-CYSTEINE'>CMH</scene>, <scene name='pdbligand=DXC:(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC+ACID'>DXC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4aca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4aca OCA], [https://pdbe.org/4aca PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4aca RCSB], [https://www.ebi.ac.uk/pdbsum/4aca PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4aca ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q8J307_METMI Q8J307_METMI] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
Selenocysteine tRNA-specific elongation factor SelB is a structural chimaera of elongation and initiation factors.,Leibundgut M, Frick C, Thanbichler M, Bock A, Ban N EMBO J. 2005 Jan 12;24(1):11-22. Epub 2004 Dec 23. PMID:15616587<ref>PMID:15616587</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4aca" style="background-color:#fffaf0;"></div> | |||
== | ==See Also== | ||
[[ | *[[Elongation factor 3D structures|Elongation factor 3D structures]] | ||
*[[SelB|SelB]] | |||
== | == References == | ||
< | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Methanococcus maripaludis]] | [[Category: Methanococcus maripaludis]] | ||
[[Category: Ban | [[Category: Ban N]] | ||
[[Category: Boeck | [[Category: Boeck A]] | ||
[[Category: Frick | [[Category: Frick C]] | ||
[[Category: Leibundgut | [[Category: Leibundgut M]] | ||
[[Category: Thanbichler | [[Category: Thanbichler M]] | ||
Latest revision as of 14:24, 20 December 2023
CRYSTAL STRUCTURE OF TRANSLATION ELONGATION FACTOR SELB FROM METHANOCOCCUS MARIPALUDIS, APO FORMCRYSTAL STRUCTURE OF TRANSLATION ELONGATION FACTOR SELB FROM METHANOCOCCUS MARIPALUDIS, APO FORM
Structural highlights
FunctionPublication Abstract from PubMedIn 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. Selenocysteine tRNA-specific elongation factor SelB is a structural chimaera of elongation and initiation factors.,Leibundgut M, Frick C, Thanbichler M, Bock A, Ban N EMBO J. 2005 Jan 12;24(1):11-22. Epub 2004 Dec 23. PMID:15616587[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
| ||||||||||||||||||