2bvn

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[[Image:2bvn.gif|left|200px]]
 
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{{Structure
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==E. coli EF-Tu:GDPNP in complex with the antibiotic enacyloxin IIa==
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|PDB= 2bvn |SIZE=350|CAPTION= <scene name='initialview01'>2bvn</scene>, resolution 2.30&Aring;
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<StructureSection load='2bvn' size='340' side='right'caption='[[2bvn]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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|SITE= <scene name='pdbsite=AC1:Enx+Binding+Site+For+Chain+B'>AC1</scene>
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== Structural highlights ==
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|LIGAND= <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>
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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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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein-synthesizing_GTPase Protein-synthesizing GTPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.5.3 3.6.5.3] </span>
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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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|GENE=
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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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|DOMAIN=
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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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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2bvn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bvn OCA], [http://www.ebi.ac.uk/pdbsum/2bvn PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2bvn RCSB]</span>
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== Function ==
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}}
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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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'''E. COLI EF-TU:GDPNP IN COMPLEX WITH THE ANTIBIOTIC ENACYLOXIN IIA'''
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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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==Overview==
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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 ==
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.
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 [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.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://www.ncbi.nlm.nih.gov/pubmed/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: Protein-synthesizing GTPase]]
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[[Category: Single protein]]
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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: 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://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:12:26 2008''
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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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