2f6p

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:39, 17 February 2021) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2f6p.jpg|left|200px]]
 
-
<!--
+
==BenM effector binding domain- SeMet derivative==
-
The line below this paragraph, containing "STRUCTURE_2f6p", creates the "Structure Box" on the page.
+
<StructureSection load='2f6p' size='340' side='right'caption='[[2f6p]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[2f6p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acibi Acibi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F6P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F6P FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
-->
+
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-
{{STRUCTURE_2f6p| PDB=2f6p | SCENE= }}
+
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2f6g|2f6g]], [[2f78|2f78]], [[2f7a|2f7a]], [[2f7b|2f7b]], [[2f7c|2f7c]], [[2f8d|2f8d]], [[2f97|2f97]]</div></td></tr>
 +
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">benM, benR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=202950 ACIBI])</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=2f6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f6p OCA], [https://pdbe.org/2f6p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f6p RCSB], [https://www.ebi.ac.uk/pdbsum/2f6p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f6p ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[[https://www.uniprot.org/uniprot/BENM_ACIAD BENM_ACIAD]] Positive regulator of the ben and cat genes for benzoate degradation. BenM is necessary for ben gene expression but not for expression of the cat genes, which can be regulated by CatM. Binds to the inducers cis,cis-muconate and benzoate.
 +
== 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/f6/2f6p_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</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/main_output.php?pdb_ID=2f6p ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
BenM, a bacterial transcriptional regulator, responds synergistically to two effectors, benzoate and cis,cis-muconate. CatM, a paralog with overlapping function, responds only to muconate. Structures of their effector-binding domains revealed two effector-binding sites in BenM. BenM and CatM are the first LysR-type regulators to be structurally characterized while bound with physiologically relevant exogenous inducers. The effector complexes were obtained by soaking crystals with stabilizing solutions containing high effector concentrations and minimal amounts of competing ions. This strategy, including data collection with fragments of fractured crystals, may be generally applicable to related proteins. In BenM and CatM, the binding of muconate to an interdomain pocket was facilitated by helix dipoles that provide charge stabilization. In BenM, benzoate also bound in an adjacent hydrophobic region where it alters the effect of muconate bound in the primary site. A charge relay system within the BenM protein appears to underlie synergistic transcriptional activation. According to this model, Glu162 is a pivotal residue that forms salt-bridges with different arginine residues depending on the occupancy of the secondary effector-binding site. Glu162 interacts with Arg160 in the absence of benzoate and with Arg146 when benzoate is bound. This latter interaction enhances the negative charge of muconate bound to the adjacent primary effector-binding site. The redistribution of the electrostatic potential draws two domains of the protein more closely towards muconate, with the movement mediated by the dipole moments of four alpha helices. Therefore, with both effectors, BenM achieves a unique conformation capable of high level transcriptional activation.
-
'''BenM effector binding domain- SeMet derivative'''
+
Distinct effector-binding sites enable synergistic transcriptional activation by BenM, a LysR-type regulator.,Ezezika OC, Haddad S, Clark TJ, Neidle EL, Momany C J Mol Biol. 2007 Mar 30;367(3):616-29. Epub 2006 Oct 4. PMID:17291527<ref>PMID:17291527</ref>
-
 
+
-
 
+
-
==Overview==
+
-
BenM, a bacterial transcriptional regulator, responds synergistically to two effectors, benzoate and cis,cis-muconate. CatM, a paralog with overlapping function, responds only to muconate. Structures of their effector-binding domains revealed two effector-binding sites in BenM. BenM and CatM are the first LysR-type regulators to be structurally characterized while bound with physiologically relevant exogenous inducers. The effector complexes were obtained by soaking crystals with stabilizing solutions containing high effector concentrations and minimal amounts of competing ions. This strategy, including data collection with fragments of fractured crystals, may be generally applicable to related proteins. In BenM and CatM, the binding of muconate to an interdomain pocket was facilitated by helix dipoles that provide charge stabilization. In BenM, benzoate also bound in an adjacent hydrophobic region where it alters the effect of muconate bound in the primary site. A charge relay system within the BenM protein appears to underlie synergistic transcriptional activation. According to this model, Glu162 is a pivotal residue that forms salt-bridges with different arginine residues depending on the occupancy of the secondary effector-binding site. Glu162 interacts with Arg160 in the absence of benzoate and with Arg146 when benzoate is bound. This latter interaction enhances the negative charge of muconate bound to the adjacent primary effector-binding site. The redistribution of the electrostatic potential draws two domains of the protein more closely towards muconate, with the movement mediated by the dipole moments of four alpha helices. Therefore, with both effectors, BenM achieves a unique conformation capable of high level transcriptional activation.
+
-
==About this Structure==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
2F6P is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Acinetobacter_baylyi Acinetobacter baylyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F6P OCA].
+
</div>
 +
<div class="pdbe-citations 2f6p" style="background-color:#fffaf0;"></div>
-
==Reference==
+
==See Also==
-
Distinct effector-binding sites enable synergistic transcriptional activation by BenM, a LysR-type regulator., Ezezika OC, Haddad S, Clark TJ, Neidle EL, Momany C, J Mol Biol. 2007 Mar 30;367(3):616-29. Epub 2006 Oct 4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17291527 17291527]
+
*[[Transcriptional activator 3D structures|Transcriptional activator 3D structures]]
-
[[Category: Acinetobacter baylyi]]
+
== References ==
-
[[Category: Single protein]]
+
<references/>
-
[[Category: Clark, T.]]
+
__TOC__
-
[[Category: Ezezika, O.]]
+
</StructureSection>
-
[[Category: Haddad, S.]]
+
[[Category: Acibi]]
-
[[Category: Momany, C.]]
+
[[Category: Large Structures]]
-
[[Category: Neidle, E.]]
+
[[Category: Clark, T]]
 +
[[Category: Ezezika, O]]
 +
[[Category: Haddad, S]]
 +
[[Category: Momany, C]]
 +
[[Category: Neidle, E]]
[[Category: Effector binding domain]]
[[Category: Effector binding domain]]
 +
[[Category: Gene regulation]]
[[Category: Inducer binding domain]]
[[Category: Inducer binding domain]]
[[Category: Lttr]]
[[Category: Lttr]]
[[Category: Lysr-type transcriptional regulator]]
[[Category: Lysr-type transcriptional regulator]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 03:31:46 2008''
 

Current revision

BenM effector binding domain- SeMet derivative

PDB ID 2f6p

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2f6p"
Personal tools