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2f78

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Revision as of 07:34, 18 October 2017

BenM effector binding domain with its effector benzoate

Structural highlights

2f78 is a 2 chain structure with sequence from Acibi. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	2f6g, 2f6p, 2f7a, 2f7b, 2f7c, 2f8d, 2f97
Gene:	benM, benR (ACIBI)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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

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

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.

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^[1]

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

References

↑ Ezezika OC, Haddad S, Clark TJ, Neidle EL, Momany C. Distinct effector-binding sites enable synergistic transcriptional activation by BenM, a LysR-type regulator. J Mol Biol. 2007 Mar 30;367(3):616-29. Epub 2006 Oct 4. PMID:17291527 doi:10.1016/j.jmb.2006.09.090

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2f78"

@@ Line 1: / Line 1: @@
 ==BenM effector binding domain with its effector benzoate==
 <StructureSection load='2f78' size='340' side='right' caption='[[2f78]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
@@ Line 6: / Line 7: @@
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2f6g|2f6g]], [[2f6p|2f6p]], [[2f7a|2f7a]], [[2f7b|2f7b]], [[2f7c|2f7c]], [[2f8d|2f8d]], [[2f97|2f97]]</td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">benM, benR ([http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2f78 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f78 OCA], [http://pdbe.org/2f78 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2f78 RCSB], [http://www.ebi.ac.uk/pdbsum/2f78 PDBsum]</span></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=2f78 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f78 OCA], [http://pdbe.org/2f78 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2f78 RCSB], [http://www.ebi.ac.uk/pdbsum/2f78 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2f78 ProSAT]</span></td></tr>
 </table>
 == Function ==

2f78

From Proteopedia

Revision as of 07:34, 18 October 2017

BenM effector binding domain with its effector benzoate

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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