Asp263 missense variants perturb the active site of human phosphoglucomutase 1

Stiers, Kyle M.; Graham, Abigail C.; Kain, Bailee; Beamer, Lesa J.

doi:10.1111/febs.14025

Cited by 13 publications

(21 citation statements)

References 40 publications

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“…The PGM1-2 free protein and complex structures all contain a divalent cation, complexed by the metal-binding loop in D2 and Ser135 of D1 (Figs. 2 and 3), similar to earlier published PGM1 structures [14][15][16][17] . Unlike the PGM1-2 ( Fig.…”

Section: Resultssupporting

confidence: 88%

“…That work clarified the reversible reaction mechanism of PGM1 and the rabbit PGM1 3D structure 14 . The structure of wild-type isoform 1 of human PGM1 was determined by Beamer and collaborators recently 15 , and the structures of several variants with known pathogenic mutations have also been published [15][16][17] . Both the rabbit and human PGM1 3D structures have been used to analyze the effect of additional disease-related missense mutations in human PGM1 8,15 .…”

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confidence: 99%

“…Isoform 1 encoded PGM1 is a monomeric protein and, as the other members of the α-d-phosphohexomutase superfamily, comprises four domains of roughly the same size organized in what has been described as a "heart shape" 7,15,18 . PGM1 structures of both inactive, unphosphorylated PGM1 15 and active phosphoenzyme 14,16 have been reported. Recently, Stiers and Beamer solved the structure of inactive unphosphorylated PGM1-1 in complex with G6P (PGM1-1:G6P) 17 , but until now no pair of structures of both substrate and product complexes for the same activated phospho-enzyme PGM1 variant, crucial for elucidating the detailed reaction mechanism, has been published.…”

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confidence: 99%

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Structural basis for substrate and product recognition in human phosphoglucomutase-1 (PGM1) isoform 2, a member of the α-d-phosphohexomutase superfamily

Backe

Laerdahl

Kittelsen

et al. 2020

Sci Rep

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Human phosphoglucomutase 1 (PGM1) is an evolutionary conserved enzyme that belongs to the ubiquitous and ancient α-d-phosphohexomutases, a large enzyme superfamily with members in all three domains of life. PGM1 catalyzes the bi-directional interconversion between α-d-glucose 1-phosphate (G1P) and α-d-glucose 6-phosphate (G6P), a reaction that is essential for normal carbohydrate metabolism and also important in the cytoplasmic biosynthesis of nucleotide sugars needed for glycan biosynthesis. Clinical studies have shown that mutations in the PGM1 gene may cause PGM1 deficiency, an inborn error of metabolism previously classified as a glycogen storage disease, and PGM1 deficiency was recently also shown to be a congenital disorder of glycosylation. Here we present three crystal structures of the isoform 2 variant of PGM1, both as a free enzyme and in complex with its substrate and product. The structures show the longer N-terminal of this PGM1 variant, and the ligand complex structures reveal for the first time the detailed structural basis for both G1P substrate and G6P product recognition by human PGM1. We also show that PGM1 and the paralogous gene PGM5 are the results of a gene duplication event in a common ancestor of jawed vertebrates, and, importantly, that both PGM1 isoforms are conserved and of functional significance in all vertebrates. Our finding that PGM1 encodes two equally conserved and functionally important isoforms in the human organism should be taken into account in the evaluation of disease-related missense mutations in patients in the future.

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Section: Resultssupporting

confidence: 88%

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confidence: 99%

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confidence: 99%

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Structural basis for substrate and product recognition in human phosphoglucomutase-1 (PGM1) isoform 2, a member of the α-d-phosphohexomutase superfamily

Backe

Laerdahl

Kittelsen

et al. 2020

Sci Rep

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“…The mutation of the first residue causes the loss of the conserved salt bridge with the arginine residue that reorients its side chain towards the active site, thereby interfering with the substrate binding pocket. [5] Our TPS calculations indicate additional important electrostatic roles for Arg293: 1) stabilization of the deprotonated Nδ atom of the catalytic His118 residue at the reactant state (2.48 and 3.06 Å in the steps 1 and 2 of the representative trajectory, respectively) and 2) stabilization of the HO–C4 (1.82, 1.95, and 1.80 Å in the reactant state, the TS, and the product state, respectively) and HO–C1 (3.05 Å in the product state) groups of the glucose in the second step.…”

Section: Resultsmentioning

confidence: 99%

“…Mutants that affect the enzyme folding are more common than the ones that affect the catalysis. [2b,4,5] …”

Section: Introductionmentioning

confidence: 99%

Mechanistic Insights on Human Phosphoglucomutase Revealed by Transition Path Sampling and Molecular Dynamics Calculations

Brás

Fernandes

Ramos

et al. 2018

Chemistry A European J

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Human α-phosphoglucomutase 1 (α-PGM) catalyzes the isomerization of glucose-1-phosphate into glucose-6-phosphate (G6P) through two sequential phosphoryl transfer steps with a glucose-1,6-bisphosphate (G16P) intermediate. Given that the release of G6P in the gluconeogenesis raises the glucose output levels, α-PGM represents a tempting pharmacological target for type 2 diabetes. Here, we provide the first theoretical study of the catalytic mechanism of human α-PGM. We performed transition-path sampling simulations to unveil the atomic details of the two catalytic chemical steps, which could be key for developing transition state (TS) analogue molecules with inhibitory properties. Our calculations revealed that both steps proceed through a concerted S 2-like mechanism, with a loose metaphosphate-like TS. Even though experimental data suggests that the two steps are identical, we observed noticeable differences: 1) the transition state ensemble has a well-defined TS region and a late TS for the second step, and 2) larger coordinated protein motions are required to reach the TS of the second step. We have identified key residues (Arg23, Ser117, His118, Lys389), and the Mg ion that contribute in different ways to the reaction coordinate. Accelerated molecular dynamics simulations suggest that the G16P intermediate may reorient without leaving the enzymatic binding pocket, through significant conformational rearrangements of the G16P and of specific loop regions of the human α-PGM.

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A missense variant remote from the active site impairs stability of human phosphoglucomutase 1

Stiers

Hansen

Daghlas

et al. 2020

J of Inher Metab Disea

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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.

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Asp263 missense variants perturb the active site of human phosphoglucomutase 1

Cited by 13 publications

References 40 publications

Structural basis for substrate and product recognition in human phosphoglucomutase-1 (PGM1) isoform 2, a member of the α-d-phosphohexomutase superfamily

Structural basis for substrate and product recognition in human phosphoglucomutase-1 (PGM1) isoform 2, a member of the α-d-phosphohexomutase superfamily

Mechanistic Insights on Human Phosphoglucomutase Revealed by Transition Path Sampling and Molecular Dynamics Calculations

A missense variant remote from the active site impairs stability of human phosphoglucomutase 1

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