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| | <StructureSection load='4aca' size='340' side='right'caption='[[4aca]], [[Resolution|resolution]] 3.15Å' scene=''> | | <StructureSection load='4aca' size='340' side='right'caption='[[4aca]], [[Resolution|resolution]] 3.15Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4aca]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43000 Atcc 43000]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ACA FirstGlance]. <br> | + | <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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</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> | + | </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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CMH:S-(METHYLMERCURY)-L-CYSTEINE'>CMH</scene></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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1wb2|1wb2]], [[1wb3|1wb3]], [[4ac9|4ac9]], [[4acb|4acb]]</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> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4aca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4aca OCA], [http://pdbe.org/4aca PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4aca RCSB], [http://www.ebi.ac.uk/pdbsum/4aca PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4aca ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q8J307_METMI Q8J307_METMI] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[Elongation factor|Elongation factor]] | + | *[[Elongation factor 3D structures|Elongation factor 3D structures]] |
| | *[[SelB|SelB]] | | *[[SelB|SelB]] |
| | == References == | | == References == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 43000]] | + | [[Category: Large Structures]] |
| - | [[Category: Ban, N]] | + | [[Category: Methanococcus maripaludis]] |
| - | [[Category: Boeck, A]] | + | [[Category: Ban N]] |
| - | [[Category: Frick, C]] | + | [[Category: Boeck A]] |
| - | [[Category: Leibundgut, M]] | + | [[Category: Frick C]] |
| - | [[Category: Thanbichler, M]] | + | [[Category: Leibundgut M]] |
| - | [[Category: Ef-sec]]
| + | [[Category: Thanbichler M]] |
| - | [[Category: Secis element]]
| + | |
| - | [[Category: Selenocysteine]]
| + | |
| - | [[Category: Translation]]
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| Structural highlights
Function
Q8J307_METMI
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ 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. 2005 Jan 12;24(1):11-22. Epub 2004 Dec 23. PMID:15616587
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