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2c78

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[[Image:2c78.gif|left|200px]]<br />
 
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<applet load="2c78" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2c78, resolution 1.4&Aring;" />
 
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'''EF-TU COMPLEXED WITH A GTP ANALOG AND THE ANTIBIOTIC PULVOMYCIN'''<br />
 
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==Overview==
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==EF-Tu complexed with a GTP analog and the antibiotic pulvomycin==
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Pulvomycin inhibits protein synthesis by preventing the formation of the, ternary complex between elongation factor Tu (EF-Tu) x GTP and aa-tRNA. In, this work, the crystal structure of Thermus thermophilus EF-Tu x, pulvomycin in complex with the GTP analogue guanylyl imino diphosphate, (GDPNP) at 1.4 A resolution reveals an antibiotic binding site extending, from the domain 1-3 interface to domain 2, overlapping the domain 1-2-3, junction. Pulvomycin binding interferes with the binding of the, 3'-aminoacyl group, the acceptor stem, and 5' end of tRNA. Only part of, pulvomycin overlaps the binding site of GE2270 A, a domain 2-bound, antibiotic of a structure unrelated to pulvomycin, which also hinders, aa-tRNA binding. The structure of the T. thermophilus EF-Tu x GDPNP x, GE2270 A complex ... [[http://ispc.weizmann.ac.il/pmbin/getpm?16734421 (full description)]]
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<StructureSection load='2c78' size='340' side='right'caption='[[2c78]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2c78]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C78 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C78 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]] 1.4&#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=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PUL:(1S,2S,3E,5E,7E,10S,11S,12S)-12-[(2R,4E,6E,8Z,10R,12E,14E,16Z,18S,19Z)-10,18-DIHYDROXY-12,16,19-TRIMETHYL-11,22-DIOXOOXACYCLODOCOSA-4,6,8,12,14,16,19-HEPTAEN-2-YL]-2,11-DIHYDROXY-1,10-DIMETHYL-9-OXOTRIDECA-3,5,7-TRIEN-1-YL+6-DEOXY-2,4-DI-O-METHYL-BETA-L-GALACTOPYRANOSIDE'>PUL</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=2c78 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c78 OCA], [https://pdbe.org/2c78 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c78 RCSB], [https://www.ebi.ac.uk/pdbsum/2c78 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c78 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/EFTU1_THET8 EFTU1_THET8] This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis.[HAMAP-Rule:MF_00118_B]
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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/c7/2c78_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=2c78 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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Pulvomycin inhibits protein synthesis by preventing the formation of the ternary complex between elongation factor Tu (EF-Tu) x GTP and aa-tRNA. In this work, the crystal structure of Thermus thermophilus EF-Tu x pulvomycin in complex with the GTP analogue guanylyl imino diphosphate (GDPNP) at 1.4 A resolution reveals an antibiotic binding site extending from the domain 1-3 interface to domain 2, overlapping the domain 1-2-3 junction. Pulvomycin binding interferes with the binding of the 3'-aminoacyl group, the acceptor stem, and 5' end of tRNA. Only part of pulvomycin overlaps the binding site of GE2270 A, a domain 2-bound antibiotic of a structure unrelated to pulvomycin, which also hinders aa-tRNA binding. The structure of the T. thermophilus EF-Tu x GDPNP x GE2270 A complex at 1.6 A resolution shows that GE2270 A interferes with the binding of the 3'-aminoacyl group and part of the acceptor stem of aa-tRNA but not with the 5' end. Both compounds, pulvomycin more markedly, hinder the correct positioning of domain 1 over domains 2 and 3 that characterizes the active form of EF-Tu, while they affect the domain 1 switch regions that control the EF-Tu x GDP/GTP transitions in different ways. This work reveals how two antibiotics with different structures and binding modes can employ a similar mechanism of action.
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==About this Structure==
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Structural basis of the action of pulvomycin and GE2270 A on elongation factor Tu.,Parmeggiani A, Krab IM, Okamura S, Nielsen RC, Nyborg J, Nissen P Biochemistry. 2006 Jun 6;45(22):6846-57. PMID:16734421<ref>PMID:16734421</ref>
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2C78 is a [[http://en.wikipedia.org/wiki/Single_protein Single protein]] structure of sequence from [[http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]] with MG, GNP and PUL as [[http://en.wikipedia.org/wiki/ligands ligands]]. Active as [[http://en.wikipedia.org/wiki/dGTPase dGTPase]], with EC number [[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.5.1 3.1.5.1]]. Structure known Active Site: AC1. Full crystallographic information is available from [[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2C78 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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Structural basis of the action of pulvomycin and GE2270 A on elongation factor Tu., Parmeggiani A, Krab IM, Okamura S, Nielsen RC, Nyborg J, Nissen P, Biochemistry. 2006 Jun 6;45(22):6846-57. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16734421 16734421]
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</div>
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[[Category: Single protein]]
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<div class="pdbe-citations 2c78" style="background-color:#fffaf0;"></div>
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[[Category: Thermus thermophilus]]
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[[Category: dGTPase]]
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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: Okamura, S.]]
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[[Category: Parmeggiani, A.]]
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[[Category: GNP]]
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[[Category: MG]]
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[[Category: PUL]]
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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: hydrolase]]
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[[Category: nucleotide-binding]]
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[[Category: phosphorylation]]
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[[Category: protein biosynthesis]]
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[[Category: protein synthesis]]
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[[Category: translation elongation factor]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Oct 30 17:00:21 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: Large Structures]]
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[[Category: Thermus thermophilus HB8]]
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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: Okamura S]]
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[[Category: Parmeggiani A]]

Current revision

EF-Tu complexed with a GTP analog and the antibiotic pulvomycin

PDB ID 2c78

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