Biological Assembly 1  

 3D View: Structure

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 44.12 kDa 
• Atom Count: 3546 
• Modelled Residue Count: 381 
• Deposited Residue Count: 390 
• Unique protein chains: 1

1SUL

Crystal Structure of the apo-YsxC

• DOI: 10.2210/pdb1SUL/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-03-26 Released: 2004-05-25 
• Deposition Author(s): Ruzheinikov, S.N., Das, K.S., Sedelnikova, S.E., Baker, P.J., Artymiuk, P.J., Garcia-Lara, J., Foster, S.J., Rice, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.251 
• R-Value Work: 0.173 
• R-Value Observed: 0.177 

Literature

Analysis of the Open and Closed Conformations of the GTP-binding Protein YsxC from Bacillus subtilis.

Ruzheinikov, S.N., Das, S.K., Sedelnikova, S.E., Baker, P.J., Artymiuk, P.J., Garcia-Lara, J., Foster, S.J., Rice, D.W.

(2004) J Mol Biol 339: 265-278

• PubMed: 15136032 
• DOI: 10.1016/j.jmb.2004.03.043
• Primary Citation of Related Structures:  
  1SUL, 1SVI, 1SVW


• PubMed Abstract: 
  

Genetic analysis has suggested that the product of the Bacillus subtilis ysxC gene is essential for survival of the microorganism and hence may represent a target for the development of a novel anti-infective agent. B.subtilis YsxC is a member of the translation factor related class of GTPases and its crystal structure has been determined in an apo form and in complex with GDP and GMPPNP/Mg2+. Analysis of these structures has allowed us to examine the conformational changes that occur during the process of nucleotide binding and GTP hydrolysis. These structural changes particularly affect parts of the switch I and switch II region of YsxC, which become ordered and disordered, respectively in the "closed" or "on" GTP-bound state and disordered and ordered, respectively, in the "open" or "off" GDP-bound conformation. Finally, the binding of the magnesium cation results in subtle shifts of residues in the G3 region, at the start of switch II, which serve to optimize the interaction with a key aspartic acid residue. The structural flexibility observed in YsxC is likely to contribute to the role of the protein, possibly allowing transduction of an essential intracellular signal, which may be mediated via interactions with a conserved patch of surface-exposed, basic residues that lies adjacent to the GTP-binding site.

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Related Citations: 

• Expression, purification, crystallization and preliminary crystallographic analysis of a putative GTP-binding protein, YsxC, from Bacillus subtilis .
  Das, S.K., Sedelnikova, S.E., Baker, P.J., Ruzheinikov, S.N., Foster, S.J., Rice, D.W.
  () To be published --: --

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Organizational Affiliation: 

Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding protein YsxC	A, B	195	Bacillus subtilis	Mutation(s): 0  Gene Names: ysxC, engB, BSU28190
UniProt
Find proteins for P38424 (Bacillus subtilis (strain 168)) Explore P38424  Go to UniProtKB:  P38424

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.251 
• R-Value Work: 0.173 
• R-Value Observed: 0.177 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.67	α = 90
b = 36.52	β = 122.16
c = 83.253	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling
MLPHARE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-03-26 
• Released Date: 2004-05-25 
Deposition Author(s): Ruzheinikov, S.N., Das, K.S., Sedelnikova, S.E., Baker, P.J., Artymiuk, P.J., Garcia-Lara, J., Foster, S.J., Rice, D.W.

Revision History  

• Version 1.0: 2004-05-25
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description