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4u0y

From Proteopedia

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Crystal structure of the DNA-binding domains of YvoA in complex with palindromic operator DNA

Structural highlights

4u0y is a 6 chain structure with sequence from Bacillus subtilis subsp. subtilis str. 168. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.91Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NAGR_BACSU Main transcriptional repressor of genes involved in N-acetylglucosamine (GlcNAc) transport and utilization (PubMed:21602348, PubMed:20047956, PubMed:24673833). Represses the expression of the nagAB and nagP operons by binding directly within their upstream regions (PubMed:21602348, PubMed:24673833). Binds to the DNA consensus sequence 5'-ATTGGTATAGACAACT-3' (PubMed:21602348). Also acts as a weak repressor of mapB expression (PubMed:16207374).^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

The uptake and metabolism of N-acetylglucosamine (GlcNAc) in Bacillus subtilis is controlled by NagR (formerly named YvoA), a member of the widely-occurring GntR/HutC family of transcription regulators. Upon binding to specific DNA operator sites (dre-sites) NagR blocks the transcription of genes for GlcNAc utilization and interaction of NagR with effectors abrogates gene repression. Here we report crystal structures of NagR in complex with operator DNA and in complex with the putative effector molecules glucosamine-6-phosphate (GlcN-6-P) and N-acetylglucosamine-6-phosphate (GlcNAc-6-P). A comparison of the distinct conformational states suggests that effectors are able to displace the NagR-DNA-binding domains (NagR-DBDs) by almost 70 A upon binding. In addition, a high-resolution crystal structure of isolated NagR-DBDs in complex with palindromic double-stranded DNA (dsDNA) discloses both the determinants for highly sequence-specific operator dre-site recognition and for the unspecific binding of NagR to dsDNA. Extensive biochemical binding studies investigating the affinities of full-length NagR and isolated NagR-DBDs for either random DNA, dre-site-derived palindromic or naturally occurring non-palindromic dre-site sequences suggest that proper NagR function relies on an effector-induced fine-tuning of the DNA-binding affinities of NagR and not on a complete abrogation of its DNA binding.

Structural insight into operator dre-sites recognition and effector binding in the GntR/HutC transcription regulator NagR.,Fillenberg SB, Grau FC, Seidel G, Muller YA Nucleic Acids Res. 2015 Jan 6. pii: gku1374. PMID:25564531^[5]

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

References

↑ You C, Lu H, Sekowska A, Fang G, Wang Y, Gilles AM, Danchin A. The two authentic methionine aminopeptidase genes are differentially expressed in Bacillus subtilis. BMC Microbiol. 2005 Oct 5;5:57. PMID:16207374 doi:10.1186/1471-2180-5-57
↑ Resch M, Schiltz E, Titgemeyer F, Muller YA. Insight into the induction mechanism of the GntR/HutC bacterial transcription regulator YvoA. Nucleic Acids Res. 2010 Apr;38(7):2485-97. Epub 2010 Jan 4. PMID:20047956 doi:10.1093/nar/gkp1191
↑ Bertram R, Rigali S, Wood N, Lulko AT, Kuipers OP, Titgemeyer F. Regulon of the N-acetylglucosamine utilization regulator NagR in Bacillus subtilis. J Bacteriol. 2011 Jul;193(14):3525-36. PMID:21602348 doi:10.1128/JB.00264-11
↑ Gaugué I, Oberto J, Plumbridge J. Regulation of amino sugar utilization in Bacillus subtilis by the GntR family regulators, NagR and GamR. Mol Microbiol. 2014 Apr;92(1):100-15. PMID:24673833 doi:10.1111/mmi.12544
↑ Fillenberg SB, Grau FC, Seidel G, Muller YA. Structural insight into operator dre-sites recognition and effector binding in the GntR/HutC transcription regulator NagR. Nucleic Acids Res. 2015 Jan 6. pii: gku1374. PMID:25564531 doi:http://dx.doi.org/10.1093/nar/gku1374

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4u0y"

Categories: Bacillus subtilis subsp. subtilis str. 168 | Large Structures | Fillenberg SB | Muller YA

@@ Line 1: / Line 1: @@
 ==Crystal structure of the DNA-binding domains of YvoA in complex with palindromic operator DNA==
-<StructureSection load='4u0y' size='340' side='right' caption='[[4u0y]], [[Resolution|resolution]] 1.91&Aring;' scene=''>
+<StructureSection load='4u0y' size='340' side='right'caption='[[4u0y]], [[Resolution|resolution]] 1.91&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4u0y]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U0Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4U0Y FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4u0y]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U0Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4U0Y 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></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]] 1.91&#8491;</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=4u0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u0y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4u0y RCSB], [http://www.ebi.ac.uk/pdbsum/4u0y PDBsum]</span></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></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=4u0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u0y OCA], [https://pdbe.org/4u0y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4u0y RCSB], [https://www.ebi.ac.uk/pdbsum/4u0y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4u0y ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/YVOA_BACSU YVOA_BACSU]] Acts as a weak repressor of yflG expression.
+[https://www.uniprot.org/uniprot/NAGR_BACSU NAGR_BACSU] Main transcriptional repressor of genes involved in N-acetylglucosamine (GlcNAc) transport and utilization (PubMed:21602348, PubMed:20047956, PubMed:24673833). Represses the expression of the nagAB and nagP operons by binding directly within their upstream regions (PubMed:21602348, PubMed:24673833). Binds to the DNA consensus sequence 5'-ATTGGTATAGACAACT-3' (PubMed:21602348). Also acts as a weak repressor of mapB expression (PubMed:16207374).<ref>PMID:16207374</ref> <ref>PMID:20047956</ref> <ref>PMID:21602348</ref> <ref>PMID:24673833</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 16: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4u0y" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Fillenberg, S B]]
+[[Category: Bacillus subtilis subsp. subtilis str. 168]]
-[[Category: Muller, Y A]]
+[[Category: Large Structures]]
-[[Category: Bacterial transcription regulation]]
+[[Category: Fillenberg SB]]
-[[Category: Dna-binding]]
+[[Category: Muller YA]]
-[[Category: Gntr/hutc family]]
-[[Category: N-acetylglucosamine utilization]]
-[[Category: Operator-binding]]
-[[Category: Repressor]]
-[[Category: Transcription]]
-[[Category: Transcription factor]]
-[[Category: Winged helix-turn-helix motif]]

4u0y

From Proteopedia

Current revision

Crystal structure of the DNA-binding domains of YvoA in complex with palindromic operator DNA

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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