Structure of the human glycogen‐associated protein phosphatase 1 regulatory subunit hGM: Homology modeling revealed an (α/β)₈‐barrel‐like fold in the multidomain protein

Abstract

Protein phosphatase 1 (PP1) is widely distributed among tissues and species and acts as a regulator of many important cellular processes. By targeting the catalytic part of PP1 (PP1C) toward particular loci and substrates, regulatory subunits constitute key elements conferring specificity to the holoenzyme. Here, we report the identification of an (alpha/beta)8-barrel-like structure within the N-ter stretch of the human PP1 regulatory subunit hGM, which is part of the family of diverse proteins associated with glycogen metabolism. Protein homology modeling gave rise to a three-dimensional (3D) model for the 381 N-ter residue stretch of hGM, based on sequence similarity with Streptomyces olivochromogenes xylose isomerase, identified by using FASTA. The alignment was subsequently extended by using hydrophobic cluster analysis. The homology-derived model includes the putative glycogen binding area located within the 142-230 domain of hGM as well as a structural characterization of the PP1C interacting domain (segment 51-67). Refinement of the latter by molecular dynamics afforded a topology that is in agreement with previous X-ray studies (Egloff et al., 1997). Finite difference Poisson-Boltzmann calculations performed on the interacting domains of PP1C and hGM confirm the complementarity of the local electrostatic potentials of the two partners. This work highlights the presence of a conserved fold among distant species (mammalian, Caenorhabditis elegans, yeast) and, thus, emphasizes the involvement of PP1 in crucial basic cellular functions.

Solution structure of family 21 carbohydrate-binding module from Rhizopus oryzae glucoamylase

“…A better model will help to define a detailed molecular mechanism by which PP1G regulates glycogen synthesis and carbohydrate metabolism. However, a molecular model of PP1G built by Souchet et al [60] (based on homology modeling of the ∼ 300-residue protein fragment) deviates substantially from our RoCBM21 structure in the theoretical CBM21 region. Whether the CBM21 in PP1G compromises the overall similarity to the ∼ 300-residue protein fragment (maintaining a modular structure, as in RoCBM21) or compromises the modular homology {forming a part of the (α/β) 8 -barrel, as Souchet et al [60] proposed} is an interesting question worthy of further investigation.…”

The evolution of putative starch‐binding domains

“…Two template SBDs were used for defining the lengths of the SBD‐like sequences in studied proteins: (i) the SBD from Aspergillus niger [31] as the CBM20 representative; and (ii) the SBD from Rhizopus oryzae [32] as the CBM21 representative. Some information was extracted also from the sequence‐structural studies published previously [10–13,22–28,33–35]. In order to catch all possible examples of SBD‐like sequences, especially from the unfinished genome sequencing projects, BLAST [36] tools were used.…”

“…Beside the eventuality that the two CBM families could constitute a common CBM clan, that study [13] delivered some putative SBDs from GH13 amylopullulanases forming the intermediate group. The interest in the novel, perhaps putative SBDs has been evoked by several fundamental findings, mainly that the SBD and/or SBD‐like sequences are present in various regulatory proteins, such as: (i) regulatory subunit of protein phosphatase 1 [22–24]; (ii) laforin [25]; (iii) genethonin‐1 [26]; (iv) β‐subunit of AMP‐activated protein kinase (AMPK) [27]; and (v) starch excess 4 (SEX4) protein [28]. These observations have often concerned the binding and degradation of glycogen that is an analogue of starch in mammals [29].…”