7LTB | pdb_00007ltb

Crystal Structure of Keratinicyclin B

• PDB DOI: https://doi.org/10.2210/pdb7LTB/pdb

• Classification: ANTIBIOTIC
• Organism(s): Amycolatopsis keratiniphila
• Mutation(s): No 


• Deposited: 2021-02-19 Released: 2022-12-07 
• Deposition Author(s): Davis, K.M., Jeffrey, P.D., Seyedsayamdost, M.R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free: 
  0.151 (Depositor), 0.152 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.147 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Starting Model: experimental

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

• PubMed: 38942968 
• DOI: https://doi.org/10.1038/s41589-024-01651-z
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry, Princeton University, Princeton, NJ, USA.
Department of Chemistry, Emory University, Atlanta, GA, USA.
Institute of Pharmaceutical Biotechnology and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
Department of Chemistry, Princeton University, Princeton, NJ, USA. [e-mail].
Department of Chemistry, Princeton University, Princeton, NJ, USA. [e-mail].
Department of Molecular Biology, Princeton University, Princeton, NJ, USA. [e-mail].

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 3.44 kDa 
• Atom Count: 277 
• Modeled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Keratinicyclin B peptide moiety	A, B	6	Amycolatopsis keratiniphila	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
3-ammonio-2,3,6-trideoxy-alpha-L-arabino-hexopyranose-(1-2)-beta-D-glucopyranose	C [auth F], D [auth J]	2		N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN (Subject of Investigation/LOI)	E [auth A], G [auth B]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
YBJ (Subject of Investigation/LOI)	F [auth A], H [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)	I [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
3FG	A, B	L-PEPTIDE LINKING	C8 H9 N O4		--
GHP	A, B	D-PEPTIDE LINKING	C8 H9 N O3		--
OMY	A, B	L-PEPTIDE LINKING	C9 H10 Cl N O4		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free:  0.151 (Depositor), 0.152 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.147 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.316	α = 90
b = 29.667	β = 90
c = 32.209	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-12-07 
Deposition Author(s): Davis, K.M., Jeffrey, P.D., Seyedsayamdost, M.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM129496
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	4R00GM129460

Revision History  

• Version 1.0: 2022-12-07
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-07-24
  Changes: Database references