Structures of Streptococcus agalactiae GBS GAPDH in different enzymatic states

Experimental Data Snapshot

  • Resolution: 2.62 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Crystal Structures of Group B Streptococcus Glyceraldehyde-3-Phosphate Dehydrogenase: Apo-Form, Binary and Ternary Complexes.

Schormann, N.Ayres, C.A.Fry, A.Green, T.J.Banerjee, S.Ulett, G.C.Chattopadhyay, D.

(2016) PLoS One 11: e0165917-e0165917

  • DOI: https://doi.org/10.1371/journal.pone.0165917
  • Primary Citation of Related Structures:  
    5JY6, 5JYA, 5JYE, 5JYF

  • PubMed Abstract: 

    Glyceraldehyde 3-phosphate dehydrogenase or GAPDH is an evolutionarily conserved glycolytic enzyme. It catalyzes the two step oxidative phosphorylation of D-glyceraldehyde 3-phosphate into 1,3-bisphosphoglycerate using inorganic phosphate and NAD+ as cofactor. GAPDH of Group B Streptococcus is a major virulence factor and a potential vaccine candidate. Moreover, since GAPDH activity is essential for bacterial growth it may serve as a possible drug target. Crystal structures of Group B Streptococcus GAPDH in the apo-form, two different binary complexes and the ternary complex are described here. The two binary complexes contained NAD+ bound to 2 (mixed-holo) or 4 (holo) subunits of the tetrameric protein. The structure of the mixed-holo complex reveals the effects of NAD+ binding on the conformation of the protein. In the ternary complex, the phosphate group of the substrate was bound to the new Pi site in all four subunits. Comparison with the structure of human GAPDH showed several differences near the adenosyl binding pocket in Group B Streptococcus GAPDH. The structures also reveal at least three surface-exposed areas that differ in amino acid sequence compared to the corresponding areas of human GAPDH.

  • Organizational Affiliation

    Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States of America.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenase
A, B, C, D
356Streptococcus agalactiaeMutation(s): 0 
Gene Names: gapgapAEN72_09590ERS039640_00200ERS046921_00390RDF_1710
EC: 1.2.1
Find proteins for Q9ALW2 (Streptococcus agalactiae)
Explore Q9ALW2 
Go to UniProtKB:  Q9ALW2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ALW2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.62 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.215α = 90
b = 112.634β = 90
c = 147.633γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references
  • Version 1.2: 2024-04-03
    Changes: Refinement description