5Y37 | pdb_00005y37

Crystal structure of GBS GAPDH

• PDB DOI: https://doi.org/10.2210/pdb5Y37/pdb

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


• Deposited: 2017-07-28 Released: 2018-04-18 
• Deposition Author(s): Jin, T., Zhou, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 
  0.185 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

High-resolution crystal structure of Streptococcus agalactiae glyceraldehyde-3-phosphate dehydrogenase.

Zhou, K., Fan, X., Li, Y., Zhang, C., Jin, T.

(2018) Acta Crystallogr F Struct Biol Commun 74: 236-244

• PubMed: 29633972 
• DOI: https://doi.org/10.1107/S2053230X18003801
• Primary Citation of Related Structures:  
  5Y37


• PubMed Abstract: 
  

  Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a multifunctional enzyme that plays critical roles in bacterial pathogenesis in some pathogenic bacteria. In this study, the crystal structure of group B streptococcus GAPDH was determined at 1.36 Å resolution. The structure contained an asymmetric mixed holo tetramer, with two NAD ligands bound to two protomers. Further structural analysis identified interesting phosphate ion-binding sites, which shed light on its catalytic mechanism.

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Organizational Affiliation: 

Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 149.19 kDa 
• Atom Count: 11,983 
• Modelled Residue Count: 1,350 
• Deposited Residue Count: 1,376 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A, B, C, D	344	Streptococcus agalactiae NEM316	Mutation(s): 0  Gene Names: gbs1811 EC: 1.2.1
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], G [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
SO4	F [auth A], H [auth B], I [auth C], J [auth C], K [auth C], L [auth C], M [auth C], N [auth D], O [auth D], P [auth D], Q [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free:  0.185 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.3	α = 90
b = 156.74	β = 90
c = 67.82	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-04-18 
Deposition Author(s): Jin, T., Zhou, K.

Revision History  

• Version 1.0: 2018-04-18
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description