5bs6: Difference between revisions
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<StructureSection load='5bs6' size='340' side='right'caption='[[5bs6]], [[Resolution|resolution]] 2.35Å' scene=''> | <StructureSection load='5bs6' size='340' side='right'caption='[[5bs6]], [[Resolution|resolution]] 2.35Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5bs6]] is a 4 chain structure with sequence from [ | <table><tr><td colspan='2'>[[5bs6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron_VPI-5482 Bacteroides thetaiotaomicron VPI-5482]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2fb1 2fb1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BS6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BS6 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=5bs6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bs6 OCA], [https://pdbe.org/5bs6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bs6 RCSB], [https://www.ebi.ac.uk/pdbsum/5bs6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bs6 ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/Q8AAV8_BACTN Q8AAV8_BACTN] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</div> | </div> | ||
<div class="pdbe-citations 5bs6" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 5bs6" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Transcriptional activator 3D structures|Transcriptional activator 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Bacteroides thetaiotaomicron VPI-5482]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Chang | [[Category: Chang C]] | ||
[[Category: Jedrzejczak | [[Category: Jedrzejczak R]] | ||
[[Category: Joachimiak | [[Category: Joachimiak A]] | ||
[[Category: Tesar C]] | |||
[[Category: Tesar | |||
Latest revision as of 09:06, 7 June 2023
Apo structure of transcriptional factor AraR from Bacteroides thetaiotaomicron VPIApo structure of transcriptional factor AraR from Bacteroides thetaiotaomicron VPI
Structural highlights
FunctionPublication Abstract from PubMedCarbohydrate metabolism plays a crucial role in the ecophysiology of human gut microbiota. Mechanisms of transcriptional regulation of sugar catabolism in commensal and prevalent human gut bacteria such as Bacteroides thetaiotaomicron remain mostly unknown. By a combination of bioinformatics and experimental approaches, we have identified an NrtR family transcription factor (BT0354 in B. thetaiotaomicron, BtAraR) as a novel regulator controlling the arabinose utilization genes. L-arabinose was confirmed to be a negative effector of BtAraR. We have solved the crystal structures of the apo and L-arabinose-bound BtAraR proteins, as well as the complex of apo-protein with a specific DNA operator. BtAraR forms a homodimer with each subunit comprised of the ligand-binding Nudix hydrolase-like domain and the DNA-binding winged-helix-turn-helix (wHTH) domain. We have identified the residues involved in binding of L-arabinose and recognition of DNA. The majority of these residues are well conserved in the AraR orthologs in Bacteroidetes. In the structure of the BtAraR-DNA complex, we found the unique interaction of arginine intercalating its guanidinum moiety into the base pair stacking of B-DNA. L-arabinose binding induces movement of wHTH domains, resulting in a conformation unsuitable for DNA binding. Our analysis facilitates reconstruction of the metabolic and regulatory networks involved in carbohydrate utilization in human gut Bacteroides. A novel transcriptional regulator of L-arabinose utilization in human gut bacteria.,Chang C, Tesar C, Li X, Kim Y, Rodionov DA, Joachimiak A Nucleic Acids Res. 2015 Oct 4. pii: gkv1005. PMID:26438537[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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