6UO6

Crystal Structure of the R422Q missense variant of human PGM1

Summary for 6UO6

• Entry DOI: 10.2210/pdb6uo6/pdb
• Related: 5epc
• Descriptor: Phosphoglucomutase-1, MAGNESIUM ION, SULFATE ION, ... (4 entities in total)
• Functional Keywords: isomerase, enzyme, missense variant
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 2
• Total formula weight: 129142.44

Authors

Beamer, L.J.,Stiers, K.M. (deposition date: 2019-10-14, release date: 2020-03-04, Last modification date: 2023-10-11)

Primary citation

Stiers, K.M.,Hansen, R.P.,Daghlas, B.A.,Mason, K.N.,Zhu, J.S.,Jakeman, D.L.,Beamer, L.J.
A missense variant remote from the active site impairs stability of human phosphoglucomutase 1.
J. Inherit. Metab. Dis., 43:861-870, 2020

PubMed Abstract: Missense variants of human phosphoglucomutase 1 (PGM1) cause the inherited metabolic disease known as PGM1 deficiency. This condition is categorised as both a glycogen storage disease and a congenital disorder of glycosylation. Approximately 20 missense variants of PGM1 are linked to PGM1 deficiency, and biochemical studies have suggested that they fall into two general categories: those affecting the active site and catalytic efficiency, and those that appear to impair protein folding and/or stability. In this study, we characterise a novel variant of Arg422, a residue distal from the active site of PGM1 and the site of a previously identified disease-related variant (Arg422Trp). In prior studies, the R422W variant was found to produce insoluble protein in a recombinant expression system, precluding further in vitro characterisation. Here we investigate an alternative variant of this residue, Arg422Gln, which is amenable to experimental characterisation presumably due to its more conservative physicochemical substitution. Biochemical, crystallographic, and computational studies of R422Q establish that this variant causes only minor changes in catalytic efficiency and 3D structure, but is nonetheless dramatically reduced in stability. Unexpectedly, binding of a substrate analog is found to further destabilise the protein, in contrast to its stabilising effect on wild-type PGM1 and several other missense variants. This work establishes Arg422 as a lynchpin residue for the stability of PGM1 and supports the impairment of protein stability as a pathomechanism for variants that cause PGM1 deficiency. SYNOPSIS: Biochemical and structural studies of a missense variant far from the active site of human PGM1 identify a residue with a key role in enzyme stability.

PubMed: 32057119
DOI: 10.1002/jimd.12222

Experimental method

X-RAY DIFFRACTION (2.15 Å)