2hdn: Difference between revisions

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==Trypsin-modified Elongation Factor Tu in complex with tetracycline at 2.8 Angstrom resolution==
==Trypsin-modified Elongation Factor Tu in complex with tetracycline at 2.8 Angstrom resolution==
<StructureSection load='2hdn' size='340' side='right' caption='[[2hdn]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
<StructureSection load='2hdn' size='340' side='right'caption='[[2hdn]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2hdn]] is a 12 chain structure with 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=2HDN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HDN FirstGlance]. <br>
<table><tr><td colspan='2'>[[2hdn]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HDN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HDN FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TAC:TETRACYCLINE'>TAC</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2hcj|2hcj]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TAC:TETRACYCLINE'>TAC</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2hdn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hdn OCA], [http://pdbe.org/2hdn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hdn RCSB], [http://www.ebi.ac.uk/pdbsum/2hdn PDBsum]</span></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=2hdn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hdn OCA], [https://pdbe.org/2hdn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hdn RCSB], [https://www.ebi.ac.uk/pdbsum/2hdn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hdn ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/EFTU1_ECOLI EFTU1_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]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hd/2hdn_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hd/2hdn_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </jmolCheckbox>
</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/chain_selection.php?pdb_ID=2ata ConSurf].
</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=2hdn ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Two crystal forms of a complex between trypsin-modified elongation factor Tu-MgGDP from Escherichia coli and the antibiotic tetracycline have been solved by X-ray diffraction analysis to resolutions of 2.8 and 2.1 A, respectively. In the P2(1) form, cocrystals were grown from a solution mixture of the protein and tetracycline. Six copies of the trypsin-modified EF-Tu-MgGDP-tetracycline complex are arranged as three sets of dimers in the asymmetric unit. In the second crystal form, tetracycline was diffused into P4(3)2(1)2 crystals, resulting in a monomeric complex in the asymmetric unit. Atomic coordinates have been refined to crystallographic R factors of 18.0% for the P2(1) form and 20.0% for the P4(3)2(1)2 form. In both complexes, tetracycline makes significant interactions with the GTPase active site of EF-Tu. The phenoldiketone moiety of tetracycline interacts directly with the Mg(2+), the alpha-phosphate group of GDP and two amino acids, Thr25 and Asp80, which are conserved in the GX(4)GKS/T and DX(2)G sequence motifs found in all GTPases and many ATPases. The molecular complementarity, previously unrecognized between invariant groups present in all GTPase/ATPases and the active moiety of tetracycline, may have wide-ranging implications for all drugs containing the phenoldiketone moiety as well as for the design of new compounds targeted against a broad range of GTPases or ATPases.
Molecular complementarity between tetracycline and the GTPase active site of elongation factor Tu.,Heffron SE, Mui S, Aorora A, Abel K, Bergmann E, Jurnak F Acta Crystallogr D Biol Crystallogr. 2006 Nov;62(Pt 11):1392-400. Epub, 2006 Oct 18. PMID:17057344<ref>PMID:17057344</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2hdn" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Elongation factor|Elongation factor]]
*[[Elongation factor 3D structures|Elongation factor 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Abel, K]]
[[Category: Large Structures]]
[[Category: Aorora, A]]
[[Category: Abel K]]
[[Category: Bergmann, E]]
[[Category: Aorora A]]
[[Category: Heffron, S E]]
[[Category: Bergmann E]]
[[Category: Jurnak, F]]
[[Category: Heffron SE]]
[[Category: Mui, S]]
[[Category: Jurnak F]]
[[Category: Complex with tetracycline]]
[[Category: Mui S]]
[[Category: Gtpase center]]
[[Category: Translation]]
[[Category: Trypsin-modified ef-tu]]

Latest revision as of 12:32, 14 February 2024

Trypsin-modified Elongation Factor Tu in complex with tetracycline at 2.8 Angstrom resolutionTrypsin-modified Elongation Factor Tu in complex with tetracycline at 2.8 Angstrom resolution

Structural highlights

2hdn is a 12 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.8Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

EFTU1_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]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2hdn, resolution 2.80Å

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