6SNP

Crystal structures of human PGM1 isoform 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

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

Backe, P.H.Laerdahl, J.K.Kittelsen, L.S.Dalhus, B.Morkrid, L.Bjoras, M.

(2020) Sci Rep 10: 5656-5656

  • DOI: https://doi.org/10.1038/s41598-020-62548-0
  • Primary Citation of Related Structures:  
    6SNP

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    Department of Microbiology, Oslo University Hospital, Oslo, Norway. paul.hoff.backe@rr-research.no.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoglucomutase-1583Homo sapiensMutation(s): 0 
Gene Names: PGM1
EC: 5.4.2.2
UniProt & NIH Common Fund Data Resources
Find proteins for P36871 (Homo sapiens)
Explore P36871 
Go to UniProtKB:  P36871
PHAROS:  P36871
GTEx:  ENSG00000079739 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36871
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.339α = 90
b = 53.382β = 100.15
c = 76.066γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MrBUMPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Council of NorwayNorway2015095

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-08
    Type: Initial release