6ITE

Crystal structure of group A Streptococcal surface dehydrogenase (SDH)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural determination of group A Streptococcal surface dehydrogenase and characterization of its interaction with urokinase-type plasminogen activator receptor.

Li, R.Liang, C.Jiang, L.Yuan, C.Huang, M.

(2019) Biochem Biophys Res Commun 510: 539-544

  • DOI: https://doi.org/10.1016/j.bbrc.2019.01.102
  • Primary Citation of Related Structures:  
    6ITE

  • PubMed Abstract: 

    Streptococcus pyogenes (group A Streptococcus, GAS) has caused a wide variety of human diseases. Its multifunctional surface dehydrogenase (SDH) is crucial for GAS life cycle. Furthermore, GAS infection into human pharyngeal cells has been previously shown to be mediated by the interaction between SDH and host urokinase-type plasminogen activator receptor (uPAR). However, the structural information of SDH remains to be elucidated and there are few detailed studies to characterize its interaction with uPAR. In-depth research on these issues will provide potential targets and strategies for combating GAS. Here, we prepared recombinant SDH tetramer in Escherichia coli BL21 (DE3) cells. After purification and crystallization, we determined its crystal structure at 1.74 Å. The unique characteristics might be potentially explored as drug targets or vaccine immunogen. We subsequently performed gel filtration chromatography, native-polyacrylamide gel electrophoresis (PAGE) and in vitro pull-down analyses. The results showed that their interaction was too weak to form stable complexes and the role of uPAR involved in GAS infection needs further demonstration. Altogether the current work provides the first view of SDH and deepens the knowledge of GAS infection.


  • Organizational Affiliation

    Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China. Electronic address: lirui860620@sina.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenaseA [auth P],
B [auth Q],
C [auth R],
D [auth O]
342Streptococcus pyogenesMutation(s): 0 
Gene Names: gapgapAplr
EC: 1.2.1.12
UniProt
Find proteins for P0C0G6 (Streptococcus pyogenes)
Explore P0C0G6 
Go to UniProtKB:  P0C0G6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0G6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
E [auth P],
G [auth Q],
J [auth R],
L [auth O]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth P]
H [auth Q]
I [auth Q]
K [auth R]
M [auth O]
F [auth P],
H [auth Q],
I [auth Q],
K [auth R],
M [auth O],
N [auth O]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.427α = 90
b = 82.781β = 102.05
c = 148.921γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
HKL-2000data scaling
Cootmodel building
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
China--

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description