View source for 5dm7


==Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A==
<StructureSection load='5dm7' size='340' side='right'caption='[[5dm7]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5dm7]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DM7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DM7 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&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HGR:HYGROMYCIN+A'>HGR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=5dm7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dm7 OCA], [https://pdbe.org/5dm7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dm7 RCSB], [https://www.ebi.ac.uk/pdbsum/5dm7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dm7 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RL29_DEIRA RL29_DEIRA] Binds the 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00374]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Hygromycin A (HygA) binds to the large ribosomal subunit and inhibits its peptidyl transferase (PT) activity. The presented structural and biochemical data indicate that HygA does not interfere with the initial binding of aminoacyl-tRNA to the A site, but prevents its subsequent adjustment such that it fails to act as a substrate in the PT reaction. Structurally we demonstrate that HygA binds within the peptidyl transferase center (PTC) and induces a unique conformation. Specifically in its ribosomal binding site HygA would overlap and clash with aminoacyl-A76 ribose moiety and, therefore, its primary mode of action involves sterically restricting access of the incoming aminoacyl-tRNA to the PTC.

Crystallographic characterization of the ribosomal binding site and molecular mechanism of action of Hygromycin A.,Kaminishi T, Schedlbauer A, Fabbretti A, Brandi L, Ochoa-Lizarralde B, He CG, Milon P, Connell SR, Gualerzi CO, Fucini P Nucleic Acids Res. 2015 Nov 16;43(20):10015-25. doi: 10.1093/nar/gkv975. Epub, 2015 Oct 12. PMID:26464437<ref>PMID:26464437</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5dm7" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Deinococcus radiodurans]]
[[Category: Large Structures]]
[[Category: Connell SR]]
[[Category: Fucini P]]
[[Category: Kaminishi T]]
[[Category: Ochoa-Lizarralde B]]
[[Category: Schedlbauer A]]