Journal: Structure (London, England : 1993)

Article Title: A hotspot for disease-associated variants of human PGM1 is associated with impaired ligand binding and loop dynamics

doi: 10.1016/j.str.2018.07.005

Figure Lengend Snippet: Key Resources Table

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins Glucose-6-phosphate Dehydrogenase from Leuconostoc mesenteroides Sigma-Aldrich CA#: G8404–2KU α-D-Glucose-1,6-bisphosphate Sigma-Aldrich CA#: G6893–25MG DL-Dithiothreitol Sigma-Aldrich CA#: D9779–1G α-D-Glucose-1 -phosphate Sigma-Aldrich CA#: G7000–5G Magnesium sulfate Sigma-Aldrich CA#: M7506–500G NAD + Sigma-Aldrich CA#: N0632–5G Critical Commercial Assays Applied Biosystems Protein Thermal Shift Dye Kit ThermoFisher Scientific CA#: 4461146 Crystal Screen 1 & 2 Hampton Research CA#: HR2–110 & HR2–112 Wizard Classic Crystallization Screen 1 & 2 Emerald BioSystems Inc. CA#: 1009530 & 1009531 QuikChange II Site-Directed Mutagenesis Kit Agilent CA#: 200523 Deposited Data R503Q variant structure This paper PDB: 5VG7 R515L variant structure This paper PDB: 5VEC R515Q variant structure This paper PDB: 5VIN R515W variant structure This paper PDB: 5VBI PGM1-G6P complex structure This paper PDB: 6BJ0 Wild-type PGM1 ( Stiers et al., 2016 ) PDB: 5EPC Experimental Models: Organisms/Strains Escherichia coli: BL21DE3 New England Biosciences CA#: C2527H Recombinant DNA Plasmid: Wild-type human PGM1 ( Lee et al., 2014 ) N/A Plasmid: PGM1-R503Q missense variant This paper N/A Plasmid: PGM1-R515L missense variant This paper N/A Plasmid: PGM1-R515Q missense variant This paper N/A Plasmid: PGM1-R515W missense variant This paper N/A Software and Algorithms GROMACS molecular dynamics software ( Abraham et al., 2015 ) http://dx.doi.Org/10.1016/j.softx.2015.06.001 PyMOL ( DeLano, 2002 ) http://www.pymol.org MDAnalysis python package ( Michaud-Agrawal et al., 2011 ) https://doi.org/10.1002/jcc.21787 R ( R Core Team, 2014 ) https://cran.r-project.org/ Bio3D R-package ( Grant et al., 2006 ) https://doi.org/10.1093/bioinformatics/btl461 Other Open in a separate window Key Resources Table Crystal structures of PGM1 missense variants in an active site loop are presented Mutations cause direct effects on ligand binding and indirect effects on loop mobility The conformational ensemble of the wild-type enzyme is altered in the variants The loop is a hotspot for disease-related mutations in PGM1

Techniques: Recombinant, Crystallization Assay, Mutagenesis, Variant Assay, Plasmid Preparation, Software