Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 29.25 kDa 
• Atom Count: 1840 
• Modelled Residue Count: 197 
• Deposited Residue Count: 252 
• Unique protein chains: 1

2XGR

extracellular endonuclease

• PDB DOI: 10.2210/pdb2XGR/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus pyogenes serotype M1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-06-07 Released: 2011-07-20 
• Deposition Author(s): Korczynska, J.E., Turkenburg, J.P., Taylor, E.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.204 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 

Literature

The Structural Characterization of a Prophage-Encoded Extracellular DNase from Streptococcus Pyogenes.

Korczynska, J.E., Turkenburg, J.P., Taylor, E.J.

(2012) Nucleic Acids Res 40: 928

• PubMed: 21948797 
• DOI: 10.1093/nar/gkr789
• Primary Citation of Related Structures:  
  2XGR, 2XH3


• PubMed Abstract: 
  

The pathogenic bacterium Group A Streptococcus pyogenes produces several extracellular DNases that have been shown to facilitate invasive infection by evading the human host immune system. DNases degrade the chromatin in neutrophil extracellular traps, enabling the bacterium to evade neutrophil capture. Spd1 is a type I, nonspecific ββα/metal-dependent nuclease from Streptococcus pyogenes, which is encoded by the SF370.1 prophage and is likely to be expressed as a result of prophage induction. We present here the X-ray structure of this DNase in the wild-type and Asn145Ala mutant form. Through structural and sequence alignments as well as mutagenesis studies, we have identified the key residues His121, Asn145 and Glu164, which are crucial for Spd1 nucleolytic activity and shown the active site constellation. Our wild-type structure alludes to the possibility of a catalytically blocked dimeric form of the protein. We have investigated the multimeric nature of Spd1 using size-exclusion chromatography with multi-angle light scattering (SEC-MALLS) in the presence and absence of the divalent metal ion Mg(2+), which suggests that Spd1 exists in a monomeric form in solution.

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Organizational Affiliation: 

Department of Chemistry, Structural Biology Laboratory, The University of York, YO10 5YW, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SPD1 NUCLEASE	A	252	Streptococcus pyogenes serotype M1	Mutation(s): 0  Gene Names: mf2, SPy_0712 EC: 3.1.21.1
UniProt
Find proteins for Q9A0M1 (Streptococcus pyogenes serotype M1) Explore Q9A0M1  Go to UniProtKB:  Q9A0M1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.204 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.42	α = 90
b = 76.42	β = 90
c = 80.434	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-06-07 
• Released Date: 2011-07-20 
Deposition Author(s): Korczynska, J.E., Turkenburg, J.P., Taylor, E.J.

Revision History  

• Version 1.0: 2011-07-20
  Type: Initial release
  
• Version 1.1: 2011-10-19
  Changes: Database references
• Version 1.2: 2012-01-25
  Changes: Other