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2f7b

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Revision as of 10:39, 17 February 2021

CatM effector binding domain

Structural highlights

2f7b is a 1 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, 2f78, 2f7a, 2f7c, 2f8d, 2f97
Gene:	catM, catR (ACIBI)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[CATM_ACIAD] Positively regulates the expression of catA, catBCIJFD and benPK in response to cis,cis-muconate. It binds to the catB-catM intercistronic region, to a specific sequence upstream of catA and to the benPK promoter region. Can also repress pca genes.^[1] ^[2] ^[3]

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^[4]

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

References

↑ Romero-Arroyo CE, Schell MA, Gaines GL 3rd, Neidle EL. catM encodes a LysR-type transcriptional activator regulating catechol degradation in Acinetobacter calcoaceticus. J Bacteriol. 1995 Oct;177(20):5891-8. PMID:7592340
↑ Clark TJ, Momany C, Neidle EL. The benPK operon, proposed to play a role in transport, is part of a regulon for benzoate catabolism in Acinetobacter sp. strain ADP1. Microbiology. 2002 Apr;148(Pt 4):1213-23. PMID:11932465
↑ Brzostowicz PC, Reams AB, Clark TJ, Neidle EL. Transcriptional cross-regulation of the catechol and protocatechuate branches of the beta-ketoadipate pathway contributes to carbon source-dependent expression of the Acinetobacter sp. strain ADP1 pobA gene. Appl Environ Microbiol. 2003 Mar;69(3):1598-606. PMID:12620848
↑ 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 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2f7b"

@@ Line 1: / Line 1: @@
 ==CatM effector binding domain==
-<StructureSection load='2f7b' size='340' side='right' caption='[[2f7b]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='2f7b' size='340' side='right'caption='[[2f7b]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2f7b]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Acibi Acibi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F7B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F7B FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2f7b]] is a 1 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=2F7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F7B 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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2f6g|2f6g]], [[2f6p|2f6p]], [[2f78|2f78]], [[2f7a|2f7a]], [[2f7c|2f7c]], [[2f8d|2f8d]], [[2f97|2f97]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2f6g|2f6g]], [[2f6p|2f6p]], [[2f78|2f78]], [[2f7a|2f7a]], [[2f7c|2f7c]], [[2f8d|2f8d]], [[2f97|2f97]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">catM, catR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=202950 ACIBI])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">catM, catR ([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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2f7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f7b OCA], [http://pdbe.org/2f7b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2f7b RCSB], [http://www.ebi.ac.uk/pdbsum/2f7b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2f7b 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=2f7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f7b OCA], [https://pdbe.org/2f7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f7b RCSB], [https://www.ebi.ac.uk/pdbsum/2f7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f7b ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CATM_ACIAD CATM_ACIAD]] Positively regulates the expression of catA, catBCIJFD and benPK in response to cis,cis-muconate. It binds to the catB-catM intercistronic region, to a specific sequence upstream of catA and to the benPK promoter region. Can also repress pca genes.<ref>PMID:7592340</ref> <ref>PMID:11932465</ref> <ref>PMID:12620848</ref>
+[[https://www.uniprot.org/uniprot/CATM_ACIAD CATM_ACIAD]] Positively regulates the expression of catA, catBCIJFD and benPK in response to cis,cis-muconate. It binds to the catB-catM intercistronic region, to a specific sequence upstream of catA and to the benPK promoter region. Can also repress pca genes.<ref>PMID:7592340</ref> <ref>PMID:11932465</ref> <ref>PMID:12620848</ref>
 == 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/f7/2f7b_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f7/2f7b_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 30: / Line 30: @@
 </div>
 <div class="pdbe-citations 2f7b" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Transcriptional activator 3D structures|Transcriptional activator 3D structures]]
 == References ==
 <references/>
@@ Line 35: / Line 38: @@
 </StructureSection>
 [[Category: Acibi]]
+[[Category: Large Structures]]
 [[Category: Clark, T]]
 [[Category: Ezezika, O]]

2f7b

From Proteopedia

Revision as of 10:39, 17 February 2021

CatM effector binding domain

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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