4B2O

Crystal structure of Bacillus subtilis YmdB, a global regulator of late adaptive responses.

• PDB DOI: https://doi.org/10.2210/pdb4B2O/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-07-17 Released: 2013-07-24 
• Deposition Author(s): Newman, J.A., Diethmaier, C., Kovacs, A.T., Rodrigues, C., Kuipers, O.P., Stulke, J., Lewis, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.185 
• R-Value Work: 0.159 
• R-Value Observed: 0.160 

Starting Model: experimental

Literature

The Ymdb Phosphodiesterase is a Global Regulator of Late Adaptive Responses in Bacillus Subtilis.

Diethmaier, C., Newman, J.A., Kovacs, A.T., Kaever, V., Herzberg, C., Rodrigues, C., Boonstra, M., Kuipers, O.P., Lewis, R.J., Stulke, J.

(2014) J Bacteriol 196: 265

• PubMed: 24163345 
• DOI: https://doi.org/10.1128/JB.00826-13
• Primary Citation of Related Structures:  
  4B2O


• PubMed Abstract: 
  

  Bacillus subtilis mutants lacking ymdB are unable to form biofilms, exhibit a strong overexpression of the flagellin gene hag, and are deficient in SlrR, a SinR antagonist. Here, we report the functional and structural characterization of YmdB, and we find that YmdB is a phosphodiesterase with activity against 2',3'- and 3',5'-cyclic nucleotide monophosphates. The structure of YmdB reveals that the enzyme adopts a conserved phosphodiesterase fold with a binuclear metal center. Mutagenesis of a catalytically crucial residue demonstrates that the enzymatic activity of YmdB is essential for biofilm formation. The deletion of ymdB affects the expression of more than 800 genes; the levels of the σ(D)-dependent motility regulon and several sporulation genes are increased, and the levels of the SinR-repressed biofilm genes are decreased, confirming the role of YmdB in regulating late adaptive responses of B. subtilis.

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Organizational Affiliation: 

Department of General Microbiology, Georg August University Göttingen, Göttingen, Germany.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 127.91 kDa 
• Atom Count: 9,784 
• Modelled Residue Count: 1,056 
• Deposited Residue Count: 1,144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YMDB PHOSPHODIESTERASE	A, B, C, D	286	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  EC: 3.1.4.16
UniProt
Find proteins for O31775 (Bacillus subtilis (strain 168)) Explore O31775  Go to UniProtKB:  O31775

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A], H [auth B], K [auth C], N [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
FE2	F [auth A], G [auth A], I [auth B], J [auth B], L [auth C], M [auth C], O [auth D], P [auth D]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.185 
• R-Value Work: 0.159 
• R-Value Observed: 0.160 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.855	α = 90
b = 105.997	β = 108.3
c = 77.92	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-24 
Deposition Author(s): Newman, J.A., Diethmaier, C., Kovacs, A.T., Rodrigues, C., Kuipers, O.P., Stulke, J., Lewis, R.J.

Revision History  

• Version 1.0: 2013-07-24
  Type: Initial release
  
• Version 1.1: 2014-01-29
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description