6VOT | pdb_00006vot

Crystal structure of Pseudomonas aerugonisa PBP3 complexed to gamma-lactam YU253434

• PDB DOI: https://doi.org/10.2210/pdb6VOT/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-01-31 Released: 2020-05-13 
• Deposition Author(s): van den Akker, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.236 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

A gamma-Lactam Siderophore Antibiotic Effective against Multidrug-Resistant Gram-Negative Bacilli.

Goldberg, J.A., Nguyen, H., Kumar, V., Spencer, E.J., Hoyer, D., Marshall, E.K., Cmolik, A., O'Shea, M., Marshall, S.H., Hujer, A.M., Hujer, K.M., Rudin, S.D., Domitrovic, T.N., Bethel, C.R., Papp-Wallace, K.M., Logan, L.K., Perez, F., Jacobs, M.R., van Duin, D., Kreiswirth, B.M., Bonomo, R.A., Plummer, M.S., van den Akker, F.

(2020) J Med Chem 63: 5990-6002

• PubMed: 32420736 
• DOI: https://doi.org/10.1021/acs.jmedchem.0c00255
• Primary Citation Related Structures: 
  6VOT


• PubMed Abstract: 
  

  Treatment of multidrug-resistant Gram-negative bacterial pathogens represents a critical clinical need. Here, we report a novel γ-lactam pyrazolidinone that targets penicillin-binding proteins (PBPs) and incorporates a siderophore moiety to facilitate uptake into the periplasm. The MIC values of γ-lactam YU253434, 1 , are reported along with the finding that 1 is resistant to hydrolysis by all four classes of β-lactamases. The druglike characteristics and mouse PK data are described along with the X-ray crystal structure of 1 binding to its target PBP3.

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Organizational Affiliation: 
• Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States.
Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States.
Yale Center for Molecular Discovery, West Haven, Connecticut 06516, United States.
Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States.
Department of Pediatrics, Rush University Medical Center, Rush Medical College, Chicago, Illinois 60612, United States.
Cook County Health and Hospital Systems, Chicago, Illinois 60612, United States.
Geriatric Research, Education and Clinical Center, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States.
Department of Pathology, University Hospitals Cleveland Medical Center, Division of Clinical Microbiology, Cleveland, Ohio 44106, United States.
University of North Carolina School of Medicine, Chapel Hill, North Carolina 27514, United States.
Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07601, United States.
Departments of Pharmacology, Molecular Biology & Microbiology, and Proteomics & Bioinformatics, Case Western Reserve University, Cleveland, Ohio 44106, United States.
CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio 44106, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 59.02 kDa 
• Atom Count: 3,951 
• Modeled Residue Count: 499 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan D,D-transpeptidase FtsI	A	538	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names:  pbpB, ftsI, ftsI_2, ALP65_00912, CAZ10_21230, CGU42_01090, DZ934_06595, DZ962_00565, E4V10_06485, ECC04_026610, ERJ99_003095, FCG96_14995, FLI88_02250, IPC1481_11065, IPC1482_17070, IPC165_24935, IPC170_23205, IPC669_10550, RW109_RW109_05757 EC: 3.4.16.4
UniProt
Find proteins for G3XD46 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore G3XD46  Go to UniProtKB:  G3XD46

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R7G (Subject of Investigation/LOI)	B [auth A]	1-[(2S)-2-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(2-carboxypropan-2-yl)oxy]imino}acetyl]amino}-3-oxopropyl]-4-{[2-(5,6 -dihydroxy-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)ethyl]carbamoyl}-2,5-dihydro-1H-pyrazole-3-carboxylic acid C27 H28 N8 O12 S AUDGPVZSFLGMAE-ZJIUGIBFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.236 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.107	α = 90
b = 83.813	β = 90
c = 89.74	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-05-13 
Deposition Author(s): van den Akker, F.

Revision History  

• Version 1.0: 2020-05-13
  Type: Initial release
  
• Version 1.1: 2020-07-01
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary