5JN5

Crystal structure of the D263Y missense variant of human PGM1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

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: 10.1111/febs.14025
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphoglucomutase-1
A, B
585Homo sapiensMutation(s): 1 
Gene Names: PGM1
EC: 5.4.2.2
Find proteins for P36871 (Homo sapiens)
Go to Gene View: PGM1
Go to UniProtKB:  P36871
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A, B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.180 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 172.988α = 90.00
b = 172.988β = 90.00
c = 100.001γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2017-02-22
    Type: Database references
  • Version 1.2: 2017-03-29
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence
  • Version 1.4: 2017-11-01
    Type: Author supporting evidence