5mly

Closed loop conformation of PhaZ7 Y105E mutant

spinqualitylabelsall models 5mly, resolution 1.60Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5mly is a 2 chain structure with sequence from Paucimonas lemoignei. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.598Å Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function Q939Q9_PAULE Publication Abstract from PubMed An open and a closed conformation of a surface loop in PhaZ7 extracellular poly(3-hydroxybutyrate) depolymerase were identified in two high-resolution crystal structures of a PhaZ7 Y105E mutant. Molecular dynamics (MD) simulations revealed high root mean square fluctuations (RMSF) of the 281-295 loop, in particular at residue Asp289 (RMSF 7.62 A). Covalent docking between a 3-hydroxybutyric acid trimer and the catalytic residue Ser136 showed that the binding energy of the substrate is significantly more favorable in the open loop conformation compared to that in the closed loop conformation. MD simulations with the substrate covalently bound depicted 1 A RMSF higher values for the residues 281-295 in comparison to the apo (substrate-free) form. In addition, the presence of the substrate in the active site enhanced the ability of the loop to adopt a closed form. Taken together, the analysis suggests that the flexible loop 281-295 of PhaZ7 depolymerase can act as a lid domain to control substrate access to the active site of the enzyme. Proteins 2017;. (c) 2017 Wiley Periodicals, Inc. Crystal structure analysis, covalent docking, and molecular dynamics calculations reveal a conformational switch in PhaZ7 PHB depolymerase.,Kellici TF, Mavromoustakos T, Jendrossek D, Papageorgiou AC Proteins. 2017 Apr 3. doi: 10.1002/prot.25296. PMID:28370478 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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