Crystal structure of the D263Y missense variant of human PGM1

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

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This is version 2.0 of the entry. See complete history


Asp263 missense variants perturb the active site of human phosphoglucomutase 1.

Stiers, K.M.Graham, A.C.Kain, B.N.Beamer, L.J.

(2017) FEBS J 284: 937-947

  • DOI: https://doi.org/10.1111/febs.14025
  • Primary Citation of Related Structures:  
    5JN5, 5TR2

  • PubMed Abstract: 

    The enzyme phosphoglucomutase 1 (PGM1) plays a central role in glucose homeostasis. Clinical studies have identified mutations in human PGM1 as the cause of PGM1 deficiency, an inherited metabolic disease. One residue, Asp263, has two known variants associated with disease: D263G and D263Y. Biochemical studies have shown that these mutants are soluble and well folded, but have significant catalytic impairment. To better understand this catalytic defect, we determined crystal structures of these two missense variants, both of which reveal a similar and indirect structural change due to the loss of a conserved salt bridge between Asp263 and Arg293. The arginine reorients into the active site, making interactions with residues responsible for substrate binding. Biochemical studies also show that the catalytic phosphoserine of the missense variants is more stable to hydrolysis relative to wild-type enzyme. The structural perturbation resulting from mutation of this single amino acid reveals the molecular mechanism underlying PGM1 deficiency in these missense variants. Structural data are available in the PDB under the accession numbers 5JN5 and 5TR2.

  • Organizational Affiliation

    Biochemistry Department, University of Missouri, Columbia, MO, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
585Homo sapiensMutation(s): 1 
Gene Names: PGM1
UniProt & NIH Common Fund Data Resources
Find proteins for P36871 (Homo sapiens)
Explore P36871 
Go to UniProtKB:  P36871
GTEx:  ENSG00000079739 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36871
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on SEP
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.988α = 90
b = 172.988β = 90
c = 100.001γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB-0918389

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2017-02-22
    Changes: Database references
  • Version 1.2: 2017-03-29
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.4: 2017-11-01
    Changes: Author supporting evidence
  • Version 2.0: 2019-11-27
    Changes: Atomic model, Author supporting evidence