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Cited by 2Bacterial biofilms and quorum sensingBacterial Genetics and BiotechnologyBiochemical and Structural Characterization

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Mutant structure of metabolic switch protein in complex with monomeric c-di-GMP reveals a potential mechanism of protein-mediated ligand dimerization

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Dubey, Badri Nath, Shyp, Viktoriya, Fucile, Geoffrey, Sondermann, Holger, Jenal, Urs, Schirmer, Tilman·2023·Scientific Reports
DOI 10.1038/s41598-023-29110-0PMC PMC9944927

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Abstract

Bacterial second messengers c-di-GMP and (p)ppGpp have broad functional repertoires ranging from growth and cell cycle control to the regulation of biofilm formation and virulence. The recent identification of SmbA, an effector protein from Caulobacter crescentus that is jointly targeted by both signaling molecules, has opened up studies on how these global bacterial networks interact. C-di-GMP and (p)ppGpp compete for the same SmbA binding site, with a dimer of c-di-GMP inducing a conformational change that involves loop 7 of the protein that leads to downstream signaling. Here, we report a crystal structure of a partial loop 7 deletion mutant, SmbA ∆loop in complex with c-di-GMP determined at 1.4 Å resolution. SmbA ∆loop binds monomeric c-di-GMP indicating that loop 7 is required for c-di-GMP dimerization. Thus the complex probably represents the first step of consecutive c-di-GMP binding to form an intercalated dimer as has been observed in wild-type SmbA. Considering the prevalence of intercalated c-di-GMP molecules observed bound to proteins, the proposed mechanism may be generally applicable to protein-mediated c-di-GMP dimerization. Notably, in the crystal, SmbA ∆loop forms a 2-fold symmetric dimer via isologous interactions with the two symmetric halves of c-di-GMP. Structural comparisons of SmbA ∆loop with wild-type SmbA in complex with dimeric c-di-GMP or ppGpp support the idea that loop 7 is critical for SmbA function by interacting with downstream partners. Our results also underscore the flexibility of c-di-GMP, to allow binding to the symmetric SmbA ∆loop dimer interface. It is envisaged that such isologous interactions of c-di-GMP could be observed in hitherto unrecognized targets.

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Metadata

Authors
Dubey, B. N., Shyp, V., Fucile, G., Sondermann, H., Jenal, U., & Schirmer, T.
Affiliations
  • University of Basel (CH)
  • Deutsches Elektronen-Synchrotron DESY (DE)
Corresponding author
Dubey, Badri Nath
ORCID
Venue
Scientific Reports
Publisher
Springer Science and Business Media LLC
Published
2023-02-21
Volume
13
Issue
1
Pages
2727-2727
ISSN
2045-2322 (ISSN-L)
DOI
10.1038/s41598-023-29110-0
PMC
PMC9944927
OpenAlex
W4321455353
Cited by
2
References
1
Citations by year
2024: 1 · 2023: 1
FWCI
0.18
Type
journal article
Language
en
Open access
Licence
Locations
  • Scientific Reports (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
  • Research Square (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • edoc (University of Basel) (acceptedVersion, other-oa)
  • DORA PSI (Paul Scherrer Institute) (submittedVersion, other-oa)
  • Desy publication database (The Deutsches Elektronen-Synchrotron) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Universität Basel
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (166652, 147090)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bacterial biofilms and quorum sensing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Structural Characterization
Keywords
c-di-GMP, Caulobacter crescentus, ppGpp, bacterial second messenger, effector proteins, protein-ligand complex, crystal structure, metabolic switch
MeSH terms
Bacterial Proteins, Cyclic GMP, Guanosine Pentaphosphate, Ligands, Dimerization

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