5A3C | pdb_00005a3c

Crystal structure of the ADP-ribosylating sirtuin (SirTM) from Streptococcus pyogenes in complex with NAD

• PDB DOI: https://doi.org/10.2210/pdb5A3C/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus pyogenes str. Manfredo
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-05-28 Released: 2015-07-29 
• Deposition Author(s): Rack, J.G.M., Morra, R., Barkauskaite, E., Kraehenbuehl, R., Ariza, A., Qu, Y., Ortmayer, M., Leidecker, O., Cameron, D.R., Matic, I., Peleg, A.Y., Leys, D., Traven, A., Ahel, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 
  0.233 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.176 (Depositor) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

Identification of a Class of Protein Adp-Ribosylating Sirtuins in Microbial Pathogens.

Rack, J.G., Morra, R., Barkauskaite, E., Kraehenbuehl, R., Ariza, A., Qu, Y., Ortmayer, M., Leidecker, O., Cameron, D.R., Matic, I., Peleg, A.Y., Leys, D., Traven, A., Ahel, I.

(2015) Mol Cell 59: 309

• PubMed: 26166706 
• DOI: https://doi.org/10.1016/j.molcel.2015.06.013
• Primary Citation Related Structures: 
  5A35, 5A3A, 5A3B, 5A3C


• PubMed Abstract: 
  

  Sirtuins are an ancient family of NAD(+)-dependent deacylases connected with the regulation of fundamental cellular processes including metabolic homeostasis and genome integrity. We show the existence of a hitherto unrecognized class of sirtuins, found predominantly in microbial pathogens. In contrast to earlier described classes, these sirtuins exhibit robust protein ADP-ribosylation activity. In our model organisms, Staphylococcus aureus and Streptococcus pyogenes, the activity is dependent on prior lipoylation of the target protein and can be reversed by a sirtuin-associated macrodomain protein. Together, our data describe a sirtuin-dependent reversible protein ADP-ribosylation system and establish a crosstalk between lipoylation and mono-ADP-ribosylation. We propose that these posttranslational modifications modulate microbial virulence by regulating the response to host-derived reactive oxygen species.

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Organizational Affiliation: 
• Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
Cancer Research UK Manchester Institute, Wilmslow Road, Manchester M20 4BX, UK.
Department of Microbiology, Monash University, Malvern East, VIC 3145, Australia.
Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9b, Cologne 50931, Germany.
Department of Infectious Diseases, The Alfred Hospital and Monash University, Malvern East, VIC 3145, Australia.
Department of Microbiology, Monash University, Malvern East, VIC 3145, Australia; Department of Infectious Diseases, The Alfred Hospital and Monash University, Malvern East, VIC 3145, Australia.
Department of Biochemistry and Molecular Biology, Monash University, Malvern East, VIC 3145, Australia.
Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 36.23 kDa 
• Atom Count: 2,617 
• Modeled Residue Count: 286 
• Deposited Residue Count: 303 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SIR2 FAMILY PROTEIN	A	303	Streptococcus pyogenes str. Manfredo	Mutation(s): 0  EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
UniProt
Find proteins for P0DN71 (Streptococcus pyogenes serotype M5 (strain Manfredo)) Explore P0DN71  Go to UniProtKB:  P0DN71

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	F [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
GLY	B [auth A], C [auth A], D [auth A]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free:  0.233 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.176 (Depositor) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.88	α = 99.55
b = 41.48	β = 93.61
c = 51.26	γ = 92.98

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-29 
Deposition Author(s): Rack, J.G.M., Morra, R., Barkauskaite, E., Kraehenbuehl, R., Ariza, A., Qu, Y., Ortmayer, M., Leidecker, O., Cameron, D.R., Matic, I., Peleg, A.Y., Leys, D., Traven, A., Ahel, I.

Revision History  

• Version 1.0: 2015-07-29
  Type: Initial release
  
• Version 1.1: 2015-10-07
  Changes: Atomic model, Derived calculations
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other