2o7o

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[[Image:2o7o.gif|left|200px]]<br /><applet load="2o7o" size="350" color="white" frame="true" align="right" spinBox="true"
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[[Image:2o7o.gif|left|200px]]
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caption="2o7o, resolution 1.89&Aring;" />
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'''Crystal structure analysis of TetR(D) complex with doxycycline'''<br />
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{{Structure
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|PDB= 2o7o |SIZE=350|CAPTION= <scene name='initialview01'>2o7o</scene>, resolution 1.89&Aring;
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|SITE=
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|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene> and <scene name='pdbligand=DXT:(4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE'>DXT</scene>
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|ACTIVITY=
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|GENE=
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}}
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'''Crystal structure analysis of TetR(D) complex with doxycycline'''
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==Overview==
==Overview==
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==About this Structure==
==About this Structure==
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2O7O 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 <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=CL:'>CL</scene> and <scene name='pdbligand=DXT:'>DXT</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O7O OCA].
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2O7O 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=2O7O OCA].
==Reference==
==Reference==
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Protonation patterns in tetracycline:tet repressor recognition: simulations and experiments., Aleksandrov A, Proft J, Hinrichs W, Simonson T, Chembiochem. 2007 Apr 16;8(6):675-85. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17361981 17361981]
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Protonation patterns in tetracycline:tet repressor recognition: simulations and experiments., Aleksandrov A, Proft J, Hinrichs W, Simonson T, Chembiochem. 2007 Apr 16;8(6):675-85. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17361981 17361981]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Single protein]]
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[[Category: metal coordination]]
[[Category: metal coordination]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:15:22 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:56:08 2008''

Revision as of 15:56, 20 March 2008

Image:2o7o.gif


PDB ID 2o7o

Drag the structure with the mouse to rotate
, resolution 1.89Å
Ligands: , , and
Coordinates: save as pdb, mmCIF, xml



Crystal structure analysis of TetR(D) complex with doxycycline


Overview

Resistance to the antibiotic tetracycline (Tc) is regulated by its binding as a Tc:Mg2+ complex to the Tet Repressor protein (TetR). Tc:TetR recognition is a complex problem, with the protein and ligand each having several possible conformations and protonation states, which are difficult to elucidate by experiment alone. We used a combination of free-energy simulations and crystallographic analysis to investigate the electrostatic interactions between protein and ligand and the possible role of induced fit in Tc binding. Tc in solution was described quantum mechanically, while Tc:TetR interactions were described by a recent, high-quality molecular-mechanics model. The orientations of the amide and imidazole groups were determined experimentally by a careful analysis of Debye-Waller factors in alternate crystallographic models. The agreement with experiment for these orientations suggested that the simulations and their more detailed, thermodynamic predictions were reliable. We found that the ligand prefers an extended, zwitterionic state both in solution and in complexation with the protein. Tc is thus preorganized for binding, while the protein combines lock-and-key behavior for regions close to the ligand's amide, enolate, and ammonium groups, with an induced fit for regions close to the Mg2+ ion. These insights and the modeling techniques employed should be of interest for engineering improved TetR ligands and improved TetR proteins for gene regulation, as well as for drug design.

About this Structure

2O7O is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.

Reference

Protonation patterns in tetracycline:tet repressor recognition: simulations and experiments., Aleksandrov A, Proft J, Hinrichs W, Simonson T, Chembiochem. 2007 Apr 16;8(6):675-85. PMID:17361981

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