5vvi | pdb_00005vvi

Crystal Structure of the Ligand Binding Domain of LysR-type Transcriptional Regulator, OccR from Agrobacterium tumefaciens in the Complex with Octopine

spinqualitylabelsall models 5vvi, resolution 2.28Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5vvi is a 3 chain structure with sequence from Agrobacterium tumefaciens (strain Ach5). Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.28Å Ligands: 6DB, ACY, CL, EDO, MSE Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function OCCR_AGRT4 Positive regulatory protein for the occ operon involved in octopine catabolism and uptake. Also acts as a negative regulator of its expression. Publication Abstract from PubMed LysR-type transcriptional regulators (LTTRs) generally bind to target promoters in two conformations, depending on the availability of inducing ligands. OccR is an LTTR that regulates the octopine catabolism operon of Agrobacterium tumefaciens. OccR binds to a site located between the divergent occQ and occR promoters. Octopine triggers a conformational change that activates the occQ promoter, and does not affect autorepression. This change shortens the length of bound DNA and relaxes a high-angle DNA bend. Here we describe the crystal structure of the ligand-binding domain (LBD) of OccR apoprotein and holoprotein. Pairs of LBDs form dimers with extensive hydrogen bonding, while pairs of dimers interact via a single helix, creating a tetramer interface. Octopine causes a 70 degree rotation of each dimer with respect to the opposite dimer, precisely at the tetramer interface. We modelled the DNA binding domain (DBD), linker helix, and bound DNA onto the apoprotein and holoprotein. The two DBDs of the modelled apoprotein lie far apart and the bound DNA between them has a high angle DNA bend. In contrast, the two DBDs of the holoprotein lie closer to each other, with a low DNA bend angle. This inter-dimer pivot fully explains earlier studies of this LTTR. This article is protected by copyright. All rights reserved. Crystal Structure of the Ligand-Binding Domain of a LysR-type Transcriptional Regulator: Transcriptional Activation via a Rotary Switch.,Kim Y, Chhor G, Tsai CS, Winans JB, Jedrzejczak R, Joachimiak A, Winans SC Mol Microbiol. 2018 Aug 31. doi: 10.1111/mmi.14115. PMID:30168204 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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