2GWL

Crystal structure of the Salmonella SpvB ATR Domain in complex with NADH

• PDB DOI: https://doi.org/10.2210/pdb2GWL/pdb

• Classification: TRANSFERASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-05-04 Released: 2006-08-29 
• Deposition Author(s): Stebbins, C.E., Margarit, S.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.235 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

Literature

A steric antagonism of actin polymerization by a salmonella virulence protein.

Margarit, S.M., Davidson, W., Frego, L., Stebbins, C.E.

(2006) Structure 14: 1219-1229

• PubMed: 16905096 
• DOI: https://doi.org/10.1016/j.str.2006.05.022
• Primary Citation of Related Structures:  
  2GWJ, 2GWK, 2GWL, 2GWM


• PubMed Abstract: 
  

  Salmonella spp. require the ADP-ribosyltransferase activity of the SpvB protein for intracellular growth and systemic virulence. SpvB covalently modifies actin, causing cytoskeletal disruption and apoptosis. We report here the crystal structure of the catalytic domain of SpvB, and we show by mass spectrometric analysis that SpvB modifies actin at Arg177, inhibiting its ATPase activity. We also describe two crystal structures of SpvB-modified, polymerization-deficient actin. These structures reveal that ADP-ribosylation does not lead to dramatic conformational changes in actin, suggesting a model in which this large family of toxins inhibits actin polymerization primarily through steric disruption of intrafilament contacts.

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Organizational Affiliation: 

Laboratory of Structural Microbiology, Rockefeller University, New York, New York 10021, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.28 kDa 
• Atom Count: 1,777 
• Modelled Residue Count: 200 
• Deposited Residue Count: 200 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
65 kDa virulence protein	A	200	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: mkaA EC: 2.4.2.31
UniProt
Find proteins for P21454 (Salmonella typhimurium) Explore P21454  Go to UniProtKB:  P21454

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAI	B [auth A]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.235 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.585	α = 90
b = 55.585	β = 90
c = 143.577	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-29 
Deposition Author(s): Stebbins, C.E., Margarit, S.M.

Revision History  

• Version 1.0: 2006-08-29
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2013-10-30
  Changes: Non-polymer description
• Version 1.4: 2017-10-18
  Changes: Refinement description
• Version 1.5: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary