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| | ==Crystal Structure of BenM_DBD/catB site 1 DNA Complex== | | ==Crystal Structure of BenM_DBD/catB site 1 DNA Complex== |
| - | <StructureSection load='4ihs' size='340' side='right' caption='[[4ihs]], [[Resolution|resolution]] 3.10Å' scene=''> | + | <StructureSection load='4ihs' size='340' side='right'caption='[[4ihs]], [[Resolution|resolution]] 3.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4ihs]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Aciad Aciad]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IHS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IHS FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4ihs]] is a 8 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=4IHS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IHS FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 3.1Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3m1e|3m1e]], [[4iht|4iht]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ACIAD1435, benM, benR ([http://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=4ihs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ihs OCA], [https://pdbe.org/4ihs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ihs RCSB], [https://www.ebi.ac.uk/pdbsum/4ihs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ihs ProSAT]</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=4ihs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ihs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ihs RCSB], [http://www.ebi.ac.uk/pdbsum/4ihs PDBsum]</span></td></tr> | + | |
| | </table> | | </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. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4ihs" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Transcriptional activator 3D structures|Transcriptional activator 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aciad]] | + | [[Category: Acinetobacter baylyi ADP1]] |
| - | [[Category: Alanazi, A]] | + | [[Category: Large Structures]] |
| - | [[Category: Momany, C]] | + | [[Category: Alanazi A]] |
| - | [[Category: Neidle, E L]] | + | [[Category: Momany C]] |
| - | [[Category: Catb promoter]] | + | [[Category: Neidle EL]] |
| - | [[Category: Hth]]
| + | |
| - | [[Category: Transcription-dna complex]]
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| - | [[Category: Transcriptional regulator]]
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| - | [[Category: Whth]]
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| Structural highlights
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.
Publication Abstract from PubMed
LysR-type transcriptional regulators (LTTRs) play critical roles in metabolism and constitute the largest family of bacterial regulators. To understand protein-DNA interactions, atomic structures of the DNA-binding domain and linker-helix regions of a prototypical LTTR, BenM, were determined by X-ray crystallography. BenM structures with and without bound DNA reveal a set of highly conserved amino acids that interact directly with DNA bases. At the N-terminal end of the recognition helix (alpha3) of a winged-helix-turn-helix DNA-binding motif, several residues create hydrophobic pockets (Pro30, Pro31 and Ser33). These pockets interact with the methyl groups of two thymines in the DNA-recognition motif and its complementary strand, T-N11-A. This motif usually includes some dyad symmetry, as exemplified by a sequence that binds two subunits of a BenM tetramer (ATAC-N7-GTAT). Gln29 forms hydrogen bonds to adenine in the first position of the recognition half-site (ATAC). Another hydrophobic pocket defined by Ala28, Pro30 and Pro31 interacts with the methyl group of thymine, complementary to the base at the third position of the half-site. Arg34 interacts with the complementary base of the 3' position. Arg53, in the wing, provides AT-tract recognition in the minor groove. For DNA recognition, LTTRs use highly conserved interactions between amino acids and nucleotide bases as well as numerous less-conserved secondary interactions.
The DNA-binding domain of BenM reveals the structural basis for the recognition of a T-N11-A sequence motif by LysR-type transcriptional regulators.,Alanazi AM, Neidle EL, Momany C Acta Crystallogr D Biol Crystallogr. 2013 Oct;69(Pt 10):1995-2007. doi:, 10.1107/S0907444913017320. Epub 2013 Sep 20. PMID:24100318[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Alanazi AM, Neidle EL, Momany C. The DNA-binding domain of BenM reveals the structural basis for the recognition of a T-N11-A sequence motif by LysR-type transcriptional regulators. Acta Crystallogr D Biol Crystallogr. 2013 Oct;69(Pt 10):1995-2007. doi:, 10.1107/S0907444913017320. Epub 2013 Sep 20. PMID:24100318 doi:http://dx.doi.org/10.1107/S0907444913017320
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