7LKC

Crystal Structure of Keratinimicin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Potent and specific antibiotic combination therapy against Clostridioides difficile.

Chioti, V.T.McWhorter, K.L.Blue, T.C.Li, Y.Xu, F.Jeffrey, P.D.Davis, K.M.Seyedsayamdost, M.R.

(2024) Nat Chem Biol 20: 924-933

  • DOI: https://doi.org/10.1038/s41589-024-01651-z
  • Primary Citation of Related Structures:  
    7LKC, 7LTB

  • PubMed Abstract: 

    Keratinicyclins and keratinimicins are recently discovered glycopeptide antibiotics. Keratinimicins show broad-spectrum activity against Gram-positive bacteria, while keratinicyclins form a new chemotype by virtue of an unusual oxazolidinone moiety and exhibit specific antibiosis against Clostridioides difficile. Here we report the mechanism of action of keratinicyclin B (KCB). We find that steric constraints preclude KCB from binding peptidoglycan termini. Instead, KCB inhibits C. difficile growth by binding wall teichoic acids (WTAs) and interfering with cell wall remodeling. A computational model, guided by biochemical studies, provides an image of the interaction of KCB with C. difficile WTAs and shows that the same H-bonding framework used by glycopeptide antibiotics to bind peptidoglycan termini is used by KCB for interacting with WTAs. Analysis of KCB in combination with vancomycin (VAN) shows highly synergistic and specific antimicrobial activity, and that nanomolar combinations of the two drugs are sufficient for complete growth inhibition of C. difficile, while leaving common commensal strains unaffected.


  • Organizational Affiliation

    Department of Chemistry, Princeton University, Princeton, NJ, USA.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Keratinimicin A peptide moiety
A, B
7Amycolatopsis keratiniphilaMutation(s): 0 
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-rhamnopyranose-(1-2)-beta-D-glucopyranoseC [auth G],
D [auth K]
2N/A
Glycosylation Resources
GlyTouCan:  G13233ZQ
GlyCosmos:  G13233ZQ
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MAN (Subject of Investigation/LOI)
Query on MAN

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
YBJ (Subject of Investigation/LOI)
Query on YBJ

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
(2~{S},4~{S},5~{R},6~{S})-4-azanyl-5-methoxy-6-methyl-oxan-2-ol
C7 H15 N O3
ZECQVPSAXSIXIC-KQXJUZEQSA-N
FMT (Subject of Investigation/LOI)
Query on FMT

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)
Query on CL

Download Ideal Coordinates CCD File 
H [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
OMY
Query on OMY
A, B
L-PEPTIDE LINKINGC9 H10 Cl N O4TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 20.72α = 90
b = 32.251β = 90
c = 37.941γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
SHELXphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM129496
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States4R00GM129460

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-07
    Type: Initial release
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2024-07-24
    Changes: Database references