PXD033346

PXD033346 is an original dataset announced via ProteomeXchange.

Title	Structural basis for the c-di-AMP - dependent regulation of the stringent response by DarB
Description	The bacterial second messenger c-di-AMP controls various cellular processes including potassium and osmolyte homeostasis. The c-di-AMP receptor protein DarB of Bacillus subtilis binds to the Rel protein and triggers the Rel-dependent stringent response. Here we report crystal structures of DarB in the ligand-free state and of DarB complexes with c-di-AMP, 3´3´-cGAMP and AMP. DarB consists of two CBS domains and forms a homo-dimer with a parallel, head-to-head assembly of the monomers. The DarB dimer binds two cyclic di-nucleotide molecules or two AMP molecules. Only one adenine of bound c-di-AMP is specifically recognized by DarB, while the second one protrudes out of the donut-shaped protein. This enables DarB to bind also 3´3´-cGAMP, as only the adenine fits to the active site, but not the guanine. In absence of c-di-AMP DarB binds to Rel and stimulates (p)ppGpp synthesis, whereas the presence of c-di-AMP abolishes the interaction. The DarB crystal structures reveal no conformational changes upon c-di-AMP binding, hence, the regulatory function of DarB on Rel must be controlled directly by the bound c-di-AMP. A structural model of the DarB-Rel complex was erived from in silico docking, validated with a mass spectrometric analysis of the chemically cross-linked DarB-Rel complex and mutagenesis studies. Based on the predicted complex structure a mechanism of stringent response regulation by c-di-AMP is suggested.
HostingRepository	PRIDE
AnnounceDate	2022-08-12
AnnouncementXML	Submission_2022-08-12_00:33:22.084.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Aleksandar Chernev
SpeciesList	scientific name: Bacillus subtilis subsp. subtilis; NCBI TaxID: 135461;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-04-21 06:48:49	ID requested
⏵ 1	2022-08-12 00:33:22	announced

Heidemann JL, Neumann P, Kr, ü, ger L, Wicke D, Vinhoven L, Linden A, Dickmanns A, St, ü, lke J, Urlaub H, Ficner R, Structural basis for c-di-AMP-dependent regulation of the bacterial stringent response by receptor protein DarB. J Biol Chem, 298(7):102144(2022) [pubmed]

submitter keyword: CX-MS, BS3, DarB

Henning Urlaub
contact affiliation	Bioanalytical Mass Spectrometry Group, Max-Planck-Institute for Multidisciplinary Sciences, Goettingen Bioanalytics, Institute for Clinical Chemistry, Goettingen
contact email	henning.urlaub@mpinat.mpg.de
lab head
Aleksandar Chernev
contact affiliation	MPIbpc
contact email	aleksandar.chernev@mpibpc.mpg.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD033346
     1. Label: PRIDE project
     2. Name: Structural basis for the c-di-AMP - dependent regulation of the stringent response by DarB