4QX6

CRYSTAL STRUCTURE OF GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM STREPTOCOCCUS AGALACTIAE NEM316 at 2.46 ANGSTROM RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

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This is version 1.4 of the entry. See complete history


Literature

Structure of Streptococcus agalactiae glyceraldehyde-3-phosphate dehydrogenase holoenzyme reveals a novel surface.

Ayres, C.A.Schormann, N.Senkovich, O.Fry, A.Banerjee, S.Ulett, G.C.Chattopadhyay, D.

(2014) Acta Crystallogr F Struct Biol Commun 70: 1333-1339

  • DOI: https://doi.org/10.1107/S2053230X14019517
  • Primary Citation of Related Structures:  
    4QX6

  • PubMed Abstract: 

    Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a conserved cytosolic enzyme, which plays a key role in glycolysis. GAPDH catalyzes the oxidative phosphorylation of D-glyceraldehyde 3-phosphate using NAD or NADP as a cofactor. In addition, GAPDH localized on the surface of some bacteria is thought to be involved in macromolecular interactions and bacterial pathogenesis. GAPDH on the surface of group B streptococcus (GBS) enhances bacterial virulence and is a potential vaccine candidate. Here, the crystal structure of GBS GAPDH from Streptococcus agalactiae in complex with NAD is reported at 2.46 Å resolution. Although the overall structure of GBS GAPDH is very similar to those of other GAPDHs, the crystal structure reveals a significant difference in the area spanning residues 294-307, which appears to be more acidic. The amino-acid sequence of this region of GBS GAPDH is also distinct compared with other GAPDHs. This region therefore may be of interest as an immunogen for vaccine development.


  • Organizational Affiliation

    Science and Technology Honors Program, University of Alabama at Birmingham, Birmingham, AL 35294, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glyceraldehyde 3-phosphate dehydrogenase
A, B, C, D
356Streptococcus agalactiae NEM316Mutation(s): 0 
Gene Names: gapCGBS 1811
EC: 1.2.1.12
UniProt
Find proteins for Q8E3E8 (Streptococcus agalactiae serotype III (strain NEM316))
Explore Q8E3E8 
Go to UniProtKB:  Q8E3E8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8E3E8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.771α = 90
b = 107.855β = 106.57
c = 90.931γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
RAPDdata collection
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2014-12-24
    Changes: Database references
  • Version 1.2: 2015-01-28
    Changes: Advisory
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description