4QX6 | pdb_00004qx6

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

• PDB DOI: https://doi.org/10.2210/pdb4QX6/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptococcus agalactiae NEM316
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-07-18 Released: 2014-10-15 
• Deposition Author(s): Ayres, C.A., Schormann, N., Banerjee, S., Chattopadhyay, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

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

• PubMed: 25286935 
• DOI: https://doi.org/10.1107/S2053230X14019517
• Primary Citation 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.

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Organizational Affiliation: 
• Science and Technology Honors Program, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
Northeastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Argonne, IL 60439, USA.
School of Medical Science and Griffith Health Institute, Griffith University, QLD 4222, Australia.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 155.64 kDa 
• Atom Count: 10,428 
• Modeled Residue Count: 1,345 
• Deposited Residue Count: 1,424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde 3-phosphate dehydrogenase	A, B, C, D	356	Streptococcus agalactiae NEM316	Mutation(s): 0  Gene Names: gapC, GBS 1811 EC: 1.2.1.12 (PDB Primary Data), 1.2.1 (UniProt)
UniProt
Find proteins for Q8E3E8 (Streptococcus agalactiae serotype III (strain NEM316)) Explore Q8E3E8  Go to UniProtKB:  Q8E3E8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], F [auth B], G [auth C], J [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
EDO	H [auth C], I [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.771	α = 90
b = 107.855	β = 106.57
c = 90.931	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
RAPD	data collection
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-15 
Deposition Author(s): Ayres, C.A., Schormann, N., Banerjee, S., Chattopadhyay, D.

Revision History  

• 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