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2xgd

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Crystal structure of a designed homodimeric variant T-A(L)A(L) of the tetracycline repressor

Structural highlights

2xgd is a 1 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 2.25Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TETR4_ECOLX TetR is the repressor of the tetracycline resistance element; its N-terminal region forms a helix-turn-helix structure and binds DNA. Binding of tetracycline to TetR reduces the repressor affinity for the tetracycline resistance gene (tetA) promoter operator sites.TETR2_ECOLX TetR is the repressor of the tetracycline resistance element; its N-terminal region forms a helix-turn-helix structure and binds DNA. Binding of tetracycline to TetR reduces the repressor affinity for the tetracycline resistance gene (tetA) promoter operator sites.

Evolutionary Conservation

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

Publication Abstract from PubMed

The specificity and selectivity of protein-protein interactions are of central importance for many biological processes, including signal transduction and transcription control. We used the in-house side-chain packing program MUMBO to computationally design a chain-specific heterodimeric variant of the bacterial transcription regulator tetracycline repressor (TetR), called T-A(A)B. Our goal was to engineer two different TetR chain variants, A and B, that no longer interact as AA or BB homodimers but selectively recombine to form heterodimers. Although 56 residues from each chain contribute to a dimer interface as large as 2200 A(2) in wild-type TetR, the substitution of only three residues in one chain and two residues in a second chain sufficed for generating specificity in a T-A(A)B heterodimer variant. The design was corroborated in vivo by a cell-based transcription assay, and in vitro by CD spectroscopy and X-ray crystallography. Crystal structure analyses showed that while selectivity in the B chain is achieved entirely through van der Waals repulsion, the best selectivity in the A chain is obtained for the variant with the lowest number of atoms in the interface, thus possibly leading to underpacking of the dimer interface. This results in a marked decrease in thermal stability and a drastic reduction in the solubility of the T-A(A)A(A) homodimer in comparison to the designed T-A(A)B heterodimer variant.

Computational Design of a Chain-Specific Tetracycline Repressor Heterodimer.,Stiebritz MT, Wengrzik S, Klein DL, Richter JP, Srebrzynski A, Weiler S, Muller YA J Mol Biol. 2010 Sep 10. PMID:20816982^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Stiebritz MT, Wengrzik S, Klein DL, Richter JP, Srebrzynski A, Weiler S, Muller YA. Computational Design of a Chain-Specific Tetracycline Repressor Heterodimer. J Mol Biol. 2010 Sep 10. PMID:20816982 doi:10.1016/j.jmb.2010.07.055

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2xgd"

@@ Line 1: / Line 1: @@
-==CRYSTAL STRUCTURE OF A DESIGNED HOMODIMERIC VARIANT T-A(L)A(L) OF THE TETRACYCLINE REPRESSOR==
+==Crystal structure of a designed homodimeric variant T-A(L)A(L) of the tetracycline repressor==
-<StructureSection load='2xgd' size='340' side='right' caption='[[2xgd]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
+<StructureSection load='2xgd' size='340' side='right'caption='[[2xgd]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2xgd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XGD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XGD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2xgd]] is a 1 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=2XGD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XGD FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 2.25&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1a6i|1a6i]], [[2x6o|2x6o]], [[1qpi|1qpi]], [[1bjz|1bjz]], [[2x9d|2x9d]], [[2vke|2vke]], [[1du7|1du7]], [[2trt|2trt]], [[2vkv|2vkv]], [[2xb5|2xb5]], [[1ork|1ork]], [[1bj0|1bj0]], [[1bjy|1bjy]], [[2tct|2tct]], [[2xgc|2xgc]], [[2xge|2xge]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=2xgd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xgd OCA], [http://pdbe.org/2xgd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2xgd RCSB], [http://www.ebi.ac.uk/pdbsum/2xgd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2xgd ProSAT]</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=2xgd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xgd OCA], [https://pdbe.org/2xgd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xgd RCSB], [https://www.ebi.ac.uk/pdbsum/2xgd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xgd ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TETR2_ECOLX TETR2_ECOLX]] TetR is the repressor of the tetracycline resistance element; its N-terminal region forms a helix-turn-helix structure and binds DNA. Binding of tetracycline to TetR reduces the repressor affinity for the tetracycline resistance gene (tetA) promoter operator sites.
+[https://www.uniprot.org/uniprot/TETR4_ECOLX TETR4_ECOLX] TetR is the repressor of the tetracycline resistance element; its N-terminal region forms a helix-turn-helix structure and binds DNA. Binding of tetracycline to TetR reduces the repressor affinity for the tetracycline resistance gene (tetA) promoter operator sites.[https://www.uniprot.org/uniprot/TETR2_ECOLX TETR2_ECOLX] TetR is the repressor of the tetracycline resistance element; its N-terminal region forms a helix-turn-helix structure and binds DNA. Binding of tetracycline to TetR reduces the repressor affinity for the tetracycline resistance gene (tetA) promoter operator sites.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xg/2xgd_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xg/2xgd_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 31: / Line 31: @@
 ==See Also==
-*[[Tetracycline repressor protein|Tetracycline repressor protein]]
+*[[Tetracycline repressor protein 3D structures|Tetracycline repressor protein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Muller, Y A]]
+[[Category: Large Structures]]
-[[Category: Richter, J P]]
+[[Category: Muller YA]]
-[[Category: Stiebritz, M T]]
+[[Category: Richter JP]]
-[[Category: Wengrzik, S]]
+[[Category: Stiebritz MT]]
-[[Category: Antibiotic resistance]]
+[[Category: Wengrzik S]]
-[[Category: Chimera]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]

2xgd

From Proteopedia

Current revision

Crystal structure of a designed homodimeric variant T-A(L)A(L) of the tetracycline repressor

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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