View source for 4www


==Crystal structure of the E. coli ribosome bound to CEM-101==
<StructureSection load='4www' size='340' side='right'caption='[[4www]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4www]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4v80 4v80], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vt2 1vt2], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3or9 3or9], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ora 3ora] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3orb 3orb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WWW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WWW 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]] 3.1&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EM1:(3AS,4R,7S,9R,10R,11R,13R,15R,15AR)-1-{4-[4-(3-AMINOPHENYL)-1H-1,2,3-TRIAZOL-1-YL]BUTYL}-4-ETHYL-7-FLUORO-11-METHOXY-3A,7,9,11,13,15-HEXAMETHYL-2,6,8,14-TETRAOXOTETRADECAHYDRO-2H-OXACYCLOTETRADECINO[4,3-D][1,3]OXAZOL-10-YL+3,4,6-TRIDEOXY-3-(DIMETHYLAMINO)-BETA-D-XYLO-HEXOPYRANOSIDE'>EM1</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=4www FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4www OCA], [https://pdbe.org/4www PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4www RCSB], [https://www.ebi.ac.uk/pdbsum/4www PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4www ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RL5_ECOLI RL5_ECOLI] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Its 5S rRNA binding is significantly enhanced in the presence of L18.[HAMAP-Rule:MF_01333_B]  In the 70S ribosome in the initiation state (PubMed:12809609) was modeled to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; the protein-protein contacts between S13 and L5 in B1b change in the model with bound EF-G implicating this bridge in subunit movement (PubMed:12809609 and PubMed:18723842). In the two 3.5 A resolved ribosome structures (PubMed:16272117) the contacts between L5, S13 and S19 are different, confirming the dynamic nature of this interaction.[HAMAP-Rule:MF_01333_B]  Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333_B]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
We characterized the mechanism of action and the drug-binding site of a novel ketolide, CEM-101, which belongs to the latest generation of macrolide antibiotics. CEM-101 shows high affinity for the ribosomes of Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus aureus) bacteria. The ketolide shows high selectivity in its inhibitory action and readily interferes with synthesis of a reporter protein in the bacterial but not eukaryotic cell-free translation system. Binding of CEM-101 to its ribosomal target site was characterized biochemically and by X-ray crystallography. The X-ray structure of CEM-101 in complex with the E. coli ribosome shows that the drug binds in the major macrolide site in the upper part of the ribosomal exit tunnel. The lactone ring of the drug forms hydrophobic interactions with the walls of the tunnel, the desosamine sugar projects toward the peptidyl transferase center and interacts with the A2058/A2509 cleft, and the extended alkyl-aryl arm of the drug is oriented down the tunnel and makes contact with a base pair formed by A752 and U2609 of the 23S rRNA. The position of the CEM-101 alkyl-aryl extended arm differs from that reported for the side chain of the ketolide telithromycin complexed with either bacterial (Deinococcus radiodurans) or archaeal (Haloarcula marismortui) large ribosomal subunits but closely matches the position of the side chain of telithromycin complexed to the E. coli ribosome. Difference in the chemical structure of the side chain of CEM-101 in comparison with the side chain of telithromycin and the presence of the fluorine atom at position 2 of the lactone ring likely account for superior activity of CEM-101. The results of chemical probing suggest that the orientation of the CEM-101 extended side chain observed in the E. coli ribosome closely resembles its placement in Staphylococcus aureus ribosomes and thus likely accurately reflects interaction of CEM-101 with the ribosomes of the pathogenic bacterial targets of the drug. Chemical probing further demonstrated weak binding of CEM-101, but not of erythromycin, to the ribosome dimethylated at A2058 by the action of Erm methyltransferase.

Binding and action of CEM-101, a new fluoroketolide antibiotic that inhibits protein synthesis.,Llano-Sotelo B, Dunkle J, Klepacki D, Zhang W, Fernandes P, Cate JH, Mankin AS Antimicrob Agents Chemother. 2010 Sep 20. PMID:20855725<ref>PMID:20855725</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4www" style="background-color:#fffaf0;"></div>

==See Also==
*[[Ribosome 3D structures|Ribosome 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli K-12]]
[[Category: Large Structures]]
[[Category: Cate JHD]]
[[Category: Dunkle JA]]
[[Category: Mankin AS]]
[[Category: Zhang W]]