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2h9b

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Current revision

Crystal structure of the effector binding domain of a BenM variant (BenM R156H/T157S)

Structural highlights

2h9b is a 2 chain structure with sequence from Acinetobacter baylyi ADP1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	,
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 and CatM control transcription of a complex regulon for aromatic compound degradation. These Acinetobacter baylyi paralogues belong to the largest family of prokaryotic transcriptional regulators, the LysR-type proteins. Whereas BenM activates transcription synergistically in response to two effectors, benzoate and cis,cis-muconate, CatM responds only to cis,cis-muconate. Here, site-directed mutagenesis was used to determine the physiological significance of an unexpected benzoate-binding pocket in BenM discovered during structural studies. Residues in BenM were changed to match those of CatM in this hydrophobic pocket. Two BenM residues, R160 and Y293, were found to mediate the response to benzoate. Additionally, alteration of these residues caused benzoate to inhibit activation by cis,cis-muconate, positioned in a separate primary effector-binding site of BenM. The location of the primary site, in an interdomain cleft, is conserved in diverse LysR-type regulators. To improve understanding of this important family, additional regulatory mutants were analysed. The atomic-level structures were characterized of the effector-binding domains of variants that do not require inducers for activation, CatM(R156H) and BenM(R156H,T157S). These structures clearly resemble those of the wild-type proteins in their activated muconate-bound complexes. Amino acid replacements that enable activation without effectors reside at protein interfaces that may impact transcription through effects on oligomerization.

Inducer responses of BenM, a LysR-type transcriptional regulator from Acinetobacter baylyi ADP1.,Craven SH, Ezezika OC, Haddad S, Hall RA, Momany C, Neidle EL Mol Microbiol. 2009 May;72(4):881-94. Epub 2009 Apr 8. PMID:19400783^[1]

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

References

↑ Craven SH, Ezezika OC, Haddad S, Hall RA, Momany C, Neidle EL. Inducer responses of BenM, a LysR-type transcriptional regulator from Acinetobacter baylyi ADP1. Mol Microbiol. 2009 May;72(4):881-94. Epub 2009 Apr 8. PMID:19400783 doi:10.1111/j.1365-2958.2009.06686.x

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/2h9b"

@@ Line 3: / Line 3: @@
 <StructureSection load='2h9b' size='340' side='right'caption='[[2h9b]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2h9b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aciad Aciad]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2H9B FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2h9b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baylyi_ADP1 Acinetobacter baylyi ADP1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2H9B FirstGlance]. <br>
-</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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2f6p|2f6p]], [[2f7a|2f7a]], [[2f78|2f78]], [[2f97|2f97]], [[2f8d|2f8d]], [[2h98|2h98]], [[2h99|2h99]], [[2h9q|2h9q]]</div></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='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=62977 ACIAD])</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=2h9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9b OCA], [https://pdbe.org/2h9b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2h9b RCSB], [https://www.ebi.ac.uk/pdbsum/2h9b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2h9b 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.
+[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]]
@@ Line 37: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Aciad]]
+[[Category: Acinetobacter baylyi ADP1]]
 [[Category: Large Structures]]
-[[Category: Craven, S H]]
+[[Category: Craven SH]]
-[[Category: Ezezika, O C]]
+[[Category: Ezezika OC]]
-[[Category: Momany, C]]
+[[Category: Momany C]]
-[[Category: Neidle, E L]]
+[[Category: Neidle EL]]
-[[Category: Benm]]
-[[Category: Lttr]]
-[[Category: Lysr-type transcriptional regulator]]
-[[Category: Transcription]]
-[[Category: Transcriptional activator]]

2h9b

From Proteopedia

Current revision

Crystal structure of the effector binding domain of a BenM variant (BenM R156H/T157S)

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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