4u0y | pdb_00004u0y

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

spinqualitylabelsall models 4u0y, resolution 1.91Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D 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: CL 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). 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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