5dzq | pdb_00005dzq

C3larvin toxin, an ADP-ribosyltransferase from Paenibacillus larvae, Orthorhombic Form

spinqualitylabelsall models 5dzq, resolution 1.89Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5dzq is a 2 chain structure with sequence from Paenibacillus larvae subsp. larvae BRL-230010. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.892Å Ligands: GOL, MG Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function W2E3J5_9BACL Publication Abstract from PubMed C3larvin toxin is a new member of the C3 class of the mono-ADP-ribosyltransferase toxin family. The C3 toxins are known to covalently modify small G-proteins, e.g. RhoA, impairing their function, and serving as virulence factors for an offending pathogen. A full-length X-ray structure of C3larvin (2.3 A) revealed that the characteristic mixed alpha/beta fold consists of a central beta-core flanked by two helical regions. Topologically, the protein can be separated into N and C lobes, each formed by a beta-sheet and an alpha-motif, and connected by exposed loops involved in the recognition, binding, and catalysis of the toxin/enzyme, i.e. the ADP-ribosylation turn-turn and phosphate-nicotinamide PN loops. Herein, we provide two new C3larvin X-ray structures and present a systematic study of the toxin dynamics by first analyzing the experimental variability of the X-ray data-set followed by contrasting those results with theoretical predictions based on Elastic Network Models (GNM and ANM). We identify residues that participate in the stability of the N-lobe, putative hinges at loop residues, and energy-favored deformation vectors compatible with conformational changes of the key loops and 3D-subdomains (N/C-lobes), among the X-ray structures. We analyze a larger ensemble of known C3bot1 conformations and conclude that the characteristic 'crab-claw' movement may be driven by the main intrinsic modes of motion. Finally, via computational simulations, we identify harmonic and anharmonic fluctuations that might define the C3larvin 'native state.' Implications for docking protocols are derived. Structural variability of C3larvin toxin. Intrinsic dynamics of the alpha/beta fold of the C3-like group of mono-ADP-ribosyltransferase toxins.,Lugo MR, Ravulapalli R, Dutta D, Rod Merrill A J Biomol Struct Dyn. 2016 Dec;34(12):2537-2560. Epub 2016 Apr 21. PMID:26610041 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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