6A4S

Crystal structure of peptidase E with ordered active site loop from Salmonella enterica

• PDB DOI: https://doi.org/10.2210/pdb6A4S/pdb

• Classification: HYDROLASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-06-20 Released: 2018-10-31 
• Deposition Author(s): Yadav, P., Chandravanshi, K., Goyal, V.D., Singh, R., Kumar, A., Gokhale, S.M., Makde, R.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.211 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 

Literature

Structure of Asp-bound peptidase E from Salmonella enterica: Active site at dimer interface illuminates Asp recognition.

Yadav, P., Goyal, V.D., Gaur, N.K., Kumar, A., Gokhale, S.M., Makde, R.D.

(2018) FEBS Lett 592: 3346-3354

• PubMed: 30194851 
• DOI: https://doi.org/10.1002/1873-3468.13247
• Primary Citation of Related Structures:  
  6A4R, 6A4S


• PubMed Abstract: 
  

  Peptidase-E, a nonclassical serine peptidase, is specific for dipeptides with an N-terminal aspartate. This stringent substrate specificity remains largely unexplained. We report an aspartate-bound structure of peptidase-E at 1.83 Å resolution. In contrast to previous reports, the enzyme forms a dimer, and the active site is located at the dimer interface, well shielded from the solvent. Our findings further suggest that the stringent aspartate specificity of the enzyme is due to electrostatics and molecular complementarity in the active site. The new structural information presented herein may provide insights into the role of functionally important residues in peptidase-E.

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Organizational Affiliation: 

High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 57.19 kDa 
• Atom Count: 3,837 
• Modelled Residue Count: 465 
• Deposited Residue Count: 530 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase E	A, B	265	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: pepE, STM4190 EC: 3.4.13.21
UniProt
Find proteins for P36936 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P36936  Go to UniProtKB:  P36936

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.211 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.452	α = 90
b = 42.933	β = 106.39
c = 89.149	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
PHASER	phasing
Aimless	data scaling
XDS	data reduction
MAR345dtb	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-31 
Deposition Author(s): Yadav, P., Chandravanshi, K., Goyal, V.D., Singh, R., Kumar, A., Gokhale, S.M., Makde, R.D.

Revision History  

• Version 1.0: 2018-10-31
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description