6B8C | pdb_00006b8c

Crystal structure of NlpC/p60 domain of peptidoglycan hydrolase SagA

• PDB DOI: https://doi.org/10.2210/pdb6B8C/pdb

• Classification: HYDROLASE
• Organism(s): Enterococcus faecium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-10-06 Released: 2019-01-16 
• Deposition Author(s): Kim, B., Oren, D.A., Hang, H.C.
• Funding Organization(s): National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.269 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.251 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Model: experimental

Literature

Enterococcus faeciumsecreted antigen A generates muropeptides to enhance host immunity and limit bacterial pathogenesis.

Kim, B., Wang, Y.C., Hespen, C.W., Espinosa, J., Salje, J., Rangan, K.J., Oren, D.A., Kang, J.Y., Pedicord, V.A., Hang, H.C.

(2019) Elife 8

• PubMed: 30969170 
• DOI: https://doi.org/10.7554/eLife.45343
• Primary Citation Related Structures: 
  6B8C


• PubMed Abstract: 
  

  We discovered that Enterococcus faecium ( E. faecium ), a ubiquitous commensal bacterium, and its secreted peptidoglycan hydrolase (SagA) were sufficient to enhance intestinal barrier function and pathogen tolerance, but the precise biochemical mechanism was unknown. Here we show E. faecium has unique peptidoglycan composition and remodeling activity through SagA, which generates smaller muropeptides that more effectively activates nucleotide-binding oligomerization domain-containing protein 2 (NOD2) in mammalian cells. Our structural and biochemical studies show that SagA is a NlpC/p60-endopeptidase that preferentially hydrolyzes crosslinked Lys-type peptidoglycan fragments. SagA secretion and NlpC/p60-endopeptidase activity was required for enhancing probiotic bacteria activity against Clostridium difficile pathogenesis in vivo . Our results demonstrate that the peptidoglycan composition and hydrolase activity of specific microbiota species can activate host immune pathways and enhance tolerance to pathogens.

---

Organizational Affiliation: 
• Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, United States.
Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
Structural Biology Resource Center, The Rockefeller University, New York, United States.
Laboratory of Molecular Biophysics, The Rockefeller University, New York, United States.
Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, United Kingdom.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology, gel filtration

Biological Assembly 2  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 15.72 kDa 
• Atom Count: 878 
• Modeled Residue Count: 117 
• Deposited Residue Count: 150 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NLP/P60	A	150	Enterococcus faecium	Mutation(s): 0  Gene Names: FM130_01170

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.269 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.251 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.385	α = 90
b = 100.385	β = 90
c = 100.385	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-01-16 
Deposition Author(s): Kim, B., Oren, D.A., Hang, H.C.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)	United States	UL1 TR0018663

Revision History  

• Version 1.0: 2019-01-16
  Type: Initial release
  
• Version 1.1: 2019-07-31
  Changes: Data collection, Database references
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description