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TitleThe discovery and structural basis of two distinct state-dependent inhibitors of BamA.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 8718, Year 2024
Publish dateOct 8, 2024
AuthorsDawei Sun / Kelly M Storek / Dimitry Tegunov / Ying Yang / Christopher P Arthur / Matthew Johnson / John G Quinn / Weijing Liu / Guanghui Han / Hany S Girgis / Mary Kate Alexander / Austin K Murchison / Stephanie Shriver / Christine Tam / Hiroshi Ijiri / Hiroko Inaba / Tatsuya Sano / Hayato Yanagida / Junichi Nishikawa / Christopher E Heise / Wayne J Fairbrother / Man-Wah Tan / Nicholas Skelton / Wendy Sandoval / Benjamin D Sellers / Claudio Ciferri / Peter A Smith / Patrick C Reid / Christian N Cunningham / Steven T Rutherford / Jian Payandeh /
PubMed AbstractBamA is the central component of the essential β-barrel assembly machine (BAM), a conserved multi-subunit complex that dynamically inserts and folds β-barrel proteins into the outer membrane of ...BamA is the central component of the essential β-barrel assembly machine (BAM), a conserved multi-subunit complex that dynamically inserts and folds β-barrel proteins into the outer membrane of Gram-negative bacteria. Despite recent advances in our mechanistic and structural understanding of BamA, there are few potent and selective tool molecules that can bind to and modulate BamA activity. Here, we explored in vitro selection methods and different BamA/BAM protein formulations to discover peptide macrocycles that kill Escherichia coli by targeting extreme conformational states of BamA. Our studies show that Peptide Targeting BamA-1 (PTB1) targets an extracellular divalent cation-dependent binding site and locks BamA into a closed lateral gate conformation. By contrast, PTB2 targets a luminal binding site and traps BamA into an open lateral gate conformation. Our results will inform future antibiotic discovery efforts targeting BamA and provide a template to prospectively discover modulators of other dynamic integral membrane proteins.
External linksNat Commun / PubMed:39379361 / PubMed Central
MethodsEM (single particle)
Resolution2.6 - 4.0 Å
Structure data

45764

9cnw

EMDB-45764, PDB-9cnw:
CryoEM structure of the APO-BAM complex in DDM detergent
Method: EM (single particle) / Resolution: 2.6 Å

45765

9cnx

EMDB-45765, PDB-9cnx:
CryoEM structure of BAM in complex with the PTB1 closed-state inhibitor (in DDM detergent)
Method: EM (single particle) / Resolution: 3.55 Å

45766

9cny

EMDB-45766, PDB-9cny:
CryoEM structure of the APO-BAM complex in SMA nanodisc
Method: EM (single particle) / Resolution: 4.0 Å

45767

9cnz

EMDB-45767, PDB-9cnz:
Structure of BAM complexed with PTB2 ligand in detergent
Method: EM (single particle) / Resolution: 3.1 Å

45768

9co0

EMDB-45768, PDB-9co0:
CryoEM structure of BAM in complex with the PTB2 open-state inhibitor (in SMA nanodisc)
Method: EM (single particle) / Resolution: 3.3 Å

Chemicals

ChemComp-ZN:
Unknown entry

Source
  • escherichia coli (E. coli)
  • synthetic construct (others)
KeywordsMEMBRANE PROTEIN / protein structure / circular peptide

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