7L0A | pdb_00007l0a

Crystal structure of s-formylglutathione hydrolase (FrmB) from Staphylococcus aureus, apoenzyme

• PDB DOI: https://doi.org/10.2210/pdb7L0A/pdb

• Classification: HYDROLASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2020-12-11 Released: 2020-12-23 
• Deposition Author(s): Miller, J.J., Jez, J.M., Odom John, A.R.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Structure-guided microbial targeting of antistaphylococcal prodrugs.

Miller, J.J., Shah, I.T., Hatten, J., Barekatain, Y., Mueller, E.A., Moustafa, A.M., Edwards, R.L., Dowd, C.S., Planet, P.J., Muller, F.L., Jez, J.M., Odom John, A.R.

(2021) Elife 10

• PubMed: 34279224 
• DOI: https://doi.org/10.7554/eLife.66657
• Primary Citation Related Structures: 
  7L0A, 7L0B


• PubMed Abstract: 
  

  Carboxy ester prodrugs are widely employed to increase oral absorption and potency of phosphonate antibiotics. Prodrugging can mask problematic chemical features that prevent cellular uptake and may enable tissue-specific compound delivery. However, many carboxy ester promoieties are rapidly hydrolyzed by serum esterases, limiting their therapeutic potential. While carboxy ester-based prodrug targeting is feasible, it has seen limited use in microbes as microbial esterase-specific promoieties have not been described. Here we identify the bacterial esterases, GloB and FrmB, that activate carboxy ester prodrugs in Staphylococcus aureus. Additionally, we determine the substrate specificities for FrmB and GloB and demonstrate the structural basis of these preferences. Finally, we establish the carboxy ester substrate specificities of human and mouse sera, ultimately identifying several promoieties likely to be serum esterase-resistant and microbially labile. These studies will enable structure-guided design of antistaphylococcal promoieties and expand the range of molecules to target staphylococcal pathogens.

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Organizational Affiliation: 
• Department of Pediatrics, Washington University School of Medicine, St. Louis, United States.
Department of Biology, Washington University in St. Louis, St. Louis, United States.
Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, United States.
Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Children's Hospital of Philadelphia, Philadelphia, United States.
Department of Chemistry, The George Washington University, Washington, United States.
Department of Chemistry and Biochemistry, Butler University, Indianapolis, United States.
Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 59.94 kDa 
• Atom Count: 4,610 
• Modeled Residue Count: 503 
• Deposited Residue Count: 522 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Esterase family protein	A, B	261	Staphylococcus aureus	Mutation(s): 0  Gene Names:  DD547_02660, DQV53_15175, EP54_00010, EQ90_02595, G0V24_06825, G0Z18_09875, G6Y10_06490, GO746_05055, GO803_04470, GO805_09630, GO821_02780, GO894_07900, GO942_11740, HMPREF2819_04260, HMPREF3211_01237, NCTC10654_02801, NCTC10702_04070, NCTC10988_03042, RK64_00235 EC: 3.1.2.12
UniProt
Find proteins for Q2FUY3 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FUY3  Go to UniProtKB:  Q2FUY3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth B], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.303	α = 90
b = 80.5	β = 113.84
c = 66.651	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-12-23 
Deposition Author(s): Miller, J.J., Jez, J.M., Odom John, A.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01-AI103280
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R21-AI123808
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R21-AI130584

Revision History  

• Version 1.0: 2020-12-23
  Type: Initial release
  
• Version 1.1: 2021-07-07
  Changes: Database references
• Version 1.2: 2021-08-25
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Database references, Refinement description