View source for 4wf1


==Crystal structure of the E. coli ribosome bound to negamycin.==
<StructureSection load='4wf1' size='340' side='right'caption='[[4wf1]], [[Resolution|resolution]] 3.09&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4wf1]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Escherichia_coli_str._K-12_substr._MG1655 Escherichia coli str. K-12 substr. MG1655]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4wao 4wao], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4wap 4wap], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4waq 4waq] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4war 4war]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WF1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WF1 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]] 3.09&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NEG:NEGAMYCIN'>NEG</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=4wf1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wf1 OCA], [https://pdbe.org/4wf1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wf1 RCSB], [https://www.ebi.ac.uk/pdbsum/4wf1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wf1 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RL2_ECOLI RL2_ECOLI] One of the primary rRNA binding proteins. Located near the base of the L1 stalk, it is probably also mobile. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is highly controversial.[HAMAP-Rule:MF_01320_B]  In the E.coli 70S ribosome in the initiation state it has been modeled to make several contacts with the 16S rRNA (forming bridge B7b, PubMed:12809609); these contacts are broken in the model with bound EF-G.[HAMAP-Rule:MF_01320_B]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Negamycin is a natural product with broad-spectrum antibacterial activity and efficacy in animal models of infection. Although its precise mechanism of action has yet to be delineated, negamycin inhibits cellular protein synthesis and causes cell death. Here, we show that single point mutations within 16S rRNA that confer resistance to negamycin are in close proximity of the tetracycline binding site within helix 34 of the small subunit head domain. As expected from its direct interaction with this region of the ribosome, negamycin was shown to displace tetracycline. However, in contrast to tetracycline-class antibiotics, which serve to prevent cognate tRNA from entering the translating ribosome, single-molecule fluorescence resonance energy transfer investigations revealed that negamycin specifically stabilizes near-cognate ternary complexes within the A site during the normally transient initial selection process to promote miscoding. The crystal structure of the 70S ribosome in complex with negamycin, determined at 3.1 A resolution, sheds light on this finding by showing that negamycin occupies a site that partially overlaps that of tetracycline-class antibiotics. Collectively, these data suggest that the small subunit head domain contributes to the decoding mechanism and that small-molecule binding to this domain may either prevent or promote tRNA entry by altering the initial selection mechanism after codon recognition and before GTPase activation.

Negamycin induces translational stalling and miscoding by binding to the small subunit head domain of the Escherichia coli ribosome.,Olivier NB, Altman RB, Noeske J, Basarab GS, Code E, Ferguson AD, Gao N, Huang J, Juette MF, Livchak S, Miller MD, Prince DB, Cate JH, Buurman ET, Blanchard SC Proc Natl Acad Sci U S A. 2014 Nov 3. pii: 201414401. PMID:25368144<ref>PMID:25368144</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4wf1" style="background-color:#fffaf0;"></div>

==See Also==
*[[Ribosome 3D structures|Ribosome 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli K-12]]
[[Category: Escherichia coli str. K-12 substr. MG1655]]
[[Category: Large Structures]]
[[Category: Altman RB]]
[[Category: Basarab GS]]
[[Category: Blanchard SC]]
[[Category: Buurman ET]]
[[Category: Cate JHD]]
[[Category: Code E]]
[[Category: Ferguson AD]]
[[Category: Gao N]]
[[Category: Huang J]]
[[Category: Juette MF]]
[[Category: Livchak S]]
[[Category: Miller MD]]
[[Category: Noeske J]]
[[Category: Olivier NB]]
[[Category: Prince DB]]