4B2O

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

Summary for 4B2O

• Entry DOI: 10.2210/pdb4b2o/pdb
• Descriptor: YMDB PHOSPHODIESTERASE, PHOSPHATE ION, FE (II) ION, ... (4 entities in total)
• Functional Keywords: hydrolase, phosphodiesterase, biofilm, sporulation, metalloprotein
• Biological source: BACILLUS SUBTILIS SUBSP. SUBTILIS
• Total number of polymer chains: 4
• Total formula weight: 127911.52

Authors

Newman, J.A.,Diethmaier, C.,Kovacs, A.T.,Rodrigues, C.,Kuipers, O.P.,Stulke, J.,Lewis, R.J. (deposition date: 2012-07-17, release date: 2013-07-24, Last modification date: 2023-12-20)

Primary citation

Diethmaier, C.,Newman, J.A.,Kovacs, A.T.,Kaever, V.,Herzberg, C.,Rodrigues, C.,Boonstra, M.,Kuipers, O.P.,Lewis, R.J.,Stulke, J.
The Ymdb Phosphodiesterase is a Global Regulator of Late Adaptive Responses in Bacillus Subtilis.
J.Bacteriol., 196:265-, 2014

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.

PubMed: 24163345
DOI: 10.1128/JB.00826-13

Experimental method

X-RAY DIFFRACTION (1.64 Å)