4b2o: Difference between revisions
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==Crystal structure of Bacillus subtilis YmdB, a global regulator of late adaptive responses.== | |||
<StructureSection load='4b2o' size='340' side='right'caption='[[4b2o]], [[Resolution|resolution]] 1.64Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4b2o]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4B2O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4B2O FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.64Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4b2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4b2o OCA], [https://pdbe.org/4b2o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4b2o RCSB], [https://www.ebi.ac.uk/pdbsum/4b2o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4b2o ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/YMDB_BACSU YMDB_BACSU] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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 sigma(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. | |||
The YmdB Phosphodiesterase Is a Global Regulator of Late Adaptive Responses in Bacillus subtilis.,Diethmaier C, Newman JA, Kovacs AT, Kaever V, Herzberg C, Rodrigues C, Boonstra M, Kuipers OP, Lewis RJ, Stulke J J Bacteriol. 2014 Jan;196(2):265-75. doi: 10.1128/JB.00826-13. Epub 2013 Oct 25. PMID:24163345<ref>PMID:24163345</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4b2o" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Bacillus subtilis subsp. subtilis str. 168]] | |||
[[Category: Large Structures]] | |||
[[Category: Diethmaier C]] | |||
[[Category: Kovacs AT]] | |||
[[Category: Kuipers OP]] | |||
[[Category: Lewis RJ]] | |||
[[Category: Newman JA]] | |||
[[Category: Rodrigues C]] | |||
[[Category: Stulke J]] | |||
Latest revision as of 11:41, 20 December 2023
Crystal structure of Bacillus subtilis YmdB, a global regulator of late adaptive responses.
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