2bvn

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[[Image:2bvn.gif|left|200px]]<br /><applet load="2bvn" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2bvn, resolution 2.30&Aring;" />
 
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'''E. COLI EF-TU:GDPNP IN COMPLEX WITH THE ANTIBIOTIC ENACYLOXIN IIA'''<br />
 
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==Overview==
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==E. coli EF-Tu:GDPNP in complex with the antibiotic enacyloxin IIa==
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Elongation factor (EF-) Tu.GTP is the carrier of aminoacyl-tRNA to the, programmed ribosome. Enacyloxin IIa inhibits bacterial protein synthesis, by hindering the release of EF-Tu.GDP from the ribosome. The crystal, structure of the Escherichia coli EF-Tu.guanylyl iminodiphosphate, (GDPNP).enacyloxin IIa complex at 2.3 A resolution presented here reveals, the location of the antibiotic at the interface of domains 1 and 3. The, binding site overlaps that of kirromycin, an antibiotic with a structure, that is unrelated to enacyloxin IIa but that also inhibits EF-Tu.GDP, release. As one of the major differences, the enacyloxin IIa tail borders, a hydrophobic pocket that is occupied by the longer tail of kirromycin, explaining the higher binding affinity of the latter., EF-Tu.GDPNP.enacyloxin IIa shows a disordered effector region that in the, Phe-tRNAPhe.EF-Tu (Thermus aquaticus).GDPNP.enacyloxin IIa complex, solved, at 3.1 A resolution, is stabilized by the interaction with tRNA. This work, clarifies the structural background of the action of enacyloxin IIa and, compares its properties with those of kirromycin, opening new perspectives, for structure-guided design of novel antibiotics.
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<StructureSection load='2bvn' size='340' side='right'caption='[[2bvn]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2bvn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21 Escherichia coli BL21]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BVN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BVN FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ENX:ENACYLOXIN+IIA'>ENX</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bvn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvn OCA], [https://pdbe.org/2bvn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bvn RCSB], [https://www.ebi.ac.uk/pdbsum/2bvn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bvn ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/EFTU2_ECOLI EFTU2_ECOLI] This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis.[HAMAP-Rule:MF_00118] May play an important regulatory role in cell growth and in the bacterial response to nutrient deprivation.[HAMAP-Rule:MF_00118]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bv/2bvn_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2bvn ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Elongation factor (EF-) Tu.GTP is the carrier of aminoacyl-tRNA to the programmed ribosome. Enacyloxin IIa inhibits bacterial protein synthesis by hindering the release of EF-Tu.GDP from the ribosome. The crystal structure of the Escherichia coli EF-Tu.guanylyl iminodiphosphate (GDPNP).enacyloxin IIa complex at 2.3 A resolution presented here reveals the location of the antibiotic at the interface of domains 1 and 3. The binding site overlaps that of kirromycin, an antibiotic with a structure that is unrelated to enacyloxin IIa but that also inhibits EF-Tu.GDP release. As one of the major differences, the enacyloxin IIa tail borders a hydrophobic pocket that is occupied by the longer tail of kirromycin, explaining the higher binding affinity of the latter. EF-Tu.GDPNP.enacyloxin IIa shows a disordered effector region that in the Phe-tRNAPhe.EF-Tu (Thermus aquaticus).GDPNP.enacyloxin IIa complex, solved at 3.1 A resolution, is stabilized by the interaction with tRNA. This work clarifies the structural background of the action of enacyloxin IIa and compares its properties with those of kirromycin, opening new perspectives for structure-guided design of novel antibiotics.
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==About this Structure==
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Enacyloxin IIa pinpoints a binding pocket of elongation factor Tu for development of novel antibiotics.,Parmeggiani A, Krab IM, Watanabe T, Nielsen RC, Dahlberg C, Nyborg J, Nissen P J Biol Chem. 2006 Feb 3;281(5):2893-900. Epub 2005 Oct 28. PMID:16257965<ref>PMID:16257965</ref>
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2BVN is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with MG, GNP and ENX as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Transferred_entry:_3.6.5.3 Transferred entry: 3.6.5.3], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.48 3.6.1.48] Known structural/functional Site: <scene name='pdbsite=AC1:Enx Binding Site For Chain B'>AC1</scene>. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2BVN OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Enacyloxin IIa pinpoints a binding pocket of elongation factor Tu for development of novel antibiotics., Parmeggiani A, Krab IM, Watanabe T, Nielsen RC, Dahlberg C, Nyborg J, Nissen P, J Biol Chem. 2006 Feb 3;281(5):2893-900. Epub 2005 Oct 28. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16257965 16257965]
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</div>
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[[Category: Escherichia coli]]
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<div class="pdbe-citations 2bvn" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Transferred entry: 3.6.5.3]]
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[[Category: Dahlberg, C.]]
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[[Category: Krab, I.M.]]
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[[Category: Nielsen, R.C.]]
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[[Category: Nissen, P.]]
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[[Category: Nyborg, J.]]
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[[Category: Parmeggiani, A.]]
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[[Category: Watanabe, T.]]
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[[Category: ENX]]
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[[Category: GNP]]
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[[Category: MG]]
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[[Category: antibiotic]]
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[[Category: elongation factor]]
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[[Category: gtp-binding]]
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[[Category: gtpase]]
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[[Category: phosphorylation]]
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[[Category: translation]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Dec 18 19:00:01 2007''
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==See Also==
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*[[Elongation factor 3D structures|Elongation factor 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Escherichia coli BL21]]
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[[Category: Large Structures]]
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[[Category: Dahlberg C]]
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[[Category: Krab IM]]
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[[Category: Nielsen RC]]
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[[Category: Nissen P]]
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[[Category: Nyborg J]]
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[[Category: Parmeggiani A]]
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[[Category: Watanabe T]]

Current revision

E. coli EF-Tu:GDPNP in complex with the antibiotic enacyloxin IIa

PDB ID 2bvn

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