6DGM

Streptococcus pyogenes phosphoglycerol transferase GacH in complex with sn-glycerol-1-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Discovery of glycerol phosphate modification on streptococcal rhamnose polysaccharides.

Edgar, R.J.van Hensbergen, V.P.Ruda, A.Turner, A.G.Deng, P.Le Breton, Y.El-Sayed, N.M.Belew, A.T.McIver, K.S.McEwan, A.G.Morris, A.J.Lambeau, G.Walker, M.J.Rush, J.S.Korotkov, K.V.Widmalm, G.van Sorge, N.M.Korotkova, N.

(2019) Nat Chem Biol 15: 463-471

  • DOI: https://doi.org/10.1038/s41589-019-0251-4
  • Primary Citation of Related Structures:  
    5U9Z, 6DGM

  • PubMed Abstract: 

    Cell wall glycopolymers on the surface of Gram-positive bacteria are fundamental to bacterial physiology and infection biology. Here we identify gacH, a gene in the Streptococcus pyogenes group A carbohydrate (GAC) biosynthetic cluster, in two independent transposon library screens for its ability to confer resistance to zinc and susceptibility to the bactericidal enzyme human group IIA-secreted phospholipase A 2 . Subsequent structural and phylogenetic analysis of the GacH extracellular domain revealed that GacH represents an alternative class of glycerol phosphate transferase. We detected the presence of glycerol phosphate in the GAC, as well as the serotype c carbohydrate from Streptococcus mutans, which depended on the presence of the respective gacH homologs. Finally, nuclear magnetic resonance analysis of GAC confirmed that glycerol phosphate is attached to approximately 25% of the GAC N-acetylglucosamine side-chains at the C6 hydroxyl group. This previously unrecognized structural modification impacts host-pathogen interaction and has implications for vaccine design.


  • Organizational Affiliation

    Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoglycerol transferase GacH
A, B
383Streptococcus pyogenes MGAS5005Mutation(s): 0 
Gene Names: SPy_0793
UniProt
Find proteins for Q48UA4 (Streptococcus pyogenes serotype M28 (strain MGAS6180))
Explore Q48UA4 
Go to UniProtKB:  Q48UA4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ48UA4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1GP (Subject of Investigation/LOI)
Query on 1GP

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
SN-GLYCEROL-1-PHOSPHATE
C3 H9 O6 P
AWUCVROLDVIAJX-VKHMYHEASA-N
MN (Subject of Investigation/LOI)
Query on MN

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.65α = 90
b = 82.97β = 90
c = 130.36γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1R21AI113253
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30GM110787

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2019-04-03
    Changes: Data collection, Database references
  • Version 1.2: 2019-04-17
    Changes: Data collection, Database references
  • Version 1.3: 2019-05-01
    Changes: Data collection, Database references
  • Version 1.4: 2019-05-08
    Changes: Data collection, Database references
  • Version 1.5: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.6: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description