Substrate binding modifies the hinge bending characteristics of human 3‐phosphoglycerate kinase: A molecular dynamics study

Abstract

3-Phosphogycerate kinase (PGK) is a two domain enzyme, with a binding site of the 1,3-bisphosphoglycerate on the N-domain and of the ADP on the C-domain. To transfer a phosphate group the enzyme has to undergo a hinge bending motion from open to closed conformation to bring the substrates to close proximity. Molecular dynamics simulation was used to elucidate the effect of ligand binding onto the domain motions of this enzyme. The simulation results of the apo form indicate a hinge bending motion in the ns timescale while the time period of the hinge bending motion of the complex form is clearly over the 20 ns simulation time. The apo form exhibits several hinge points that contribute to the hinge bending motion while upon binding the ligands, the hinge bending becomes strictly restrained with one dominant hinge point in the vicinity of the substrates. At the same time, ligand binding results in an enhanced correlation of internal domain motions.

A new variant of phosphoglycerate kinase deficiency (p.I371K) with multiple tissue involvement: Molecular and functional characterization

“…During the catalytic cycle the enzyme undergoes a hinge bending type of motion [11] which brings the two binding sites into close proximity, thus allowing a direct phosphotransfer between substrates. Four hinge points contribute to the interdomain motions, even though the bending becomes restrained to a single hinge dominant point upon ligand binding [11][12][13]. Interestingly, mammalian PGKs exhibit non-Michaelis-Menten kinetics, being activated at high substrate concentration [14].…”

A Spring-loaded Release Mechanism Regulates Domain Movement and Catalysis in Phosphoglycerate Kinase

“…In the closed conformation of PGK, the two domains reorient by 33°, compared with the open form, about central hinge regions to bring the substrates together. Much effort has been put into elucidating the mechanism of this hinge bending and the role that substrate binding plays in inducing the conformational changes needed for catalysis to occur (15)(16)(17)(18)(19).…”

Protein Stability, Folding and Misfolding in Human PGK1 Deficiency

“…The N-domain binds 1,3-BPG or 3-PG, while the C-domain binds the nucleotides. The domains are separated by a deep cleft and linked by two alpha-helices (α-helix 7 and α-helix 14) [59,60]. Contacts between the two domains are formed through hydrophobic interactions and hydrogen bonds [61,62].…”

“…The enzyme can adopt different conformational states and transition between these states can be triggered by ligand binding. Four hinge points contribute to the interdomain motions, even though, upon binding of both ligands the bending becomes restrained to a single hinge dominant point [59]. Binding of the two substrates is independent of each other and the two binding sites in the absence of ligands (open form) are rather far from each other for phosphoryl transfer.…”

“… # variants characterized; a according to [59]; * solvent accessible; b catalytic efficiency toward 3-PG or Mg-ATP: ○○○ < 1%; ○○ < 10%; ○ < 25%; - comparable to WT; c heat stability (T m ): ○○○ nearly 10 °C lowered; ○○ nearly 3–7 °C lowered; ○ nearly 2 °C lowered; - comparable to WT; d A: anemia (+/-: compensated hemolytic anemia with occasional hemolytic crises); M: muscular disorders (+/-: sporadic manifestations); N: neurological disorders; N.A. : not available.…”