7V9O

Crystal structure of the lanthipeptide zinc-metallopeptidase EryP mutant E802R from saccharopolyspora erythraea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Conformational remodeling enhances activity of lanthipeptide zinc-metallopeptidases.

Zhao, C.Sheng, W.Wang, Y.Zheng, J.Xie, X.Liang, Y.Wei, W.Bao, R.Wang, H.

(2022) Nat Chem Biol 18: 724-732

  • DOI: https://doi.org/10.1038/s41589-022-01018-2
  • Primary Citation of Related Structures:  
    7V9N, 7V9O, 7V9P, 7V9Q

  • PubMed Abstract: 

    Lanthipeptides are an important group of natural products with diverse biological functions, and their biosynthesis requires the removal of N-terminal leader peptides (LPs) by designated proteases. LanP M1 enzymes, a subgroup of M1 zinc-metallopeptidases, have been recently identified as bifunctional proteases with both endo- and aminopeptidase activities to remove LPs of class III and class IV lanthipeptides. Herein, we report the biochemical and structural characterization of EryP as the LanP M1 enzyme from the biosynthesis of class III lanthipeptide erythreapeptin. We determined X-ray crystal structures of EryP in three conformational states, the open, intermediate and closed states, and identified a unique interdomain Ca 2+ binding site as a regulatory element that modulates its domain dynamics and proteolytic activity. Inspired by this regulatory Ca 2+ binding, we developed a strategy to engineer LanP M1 enzymes for enhanced catalytic activities by strengthening interdomain associations and driving the conformational equilibrium toward their closed forms.


  • Organizational Affiliation

    Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alanine aminopeptidase884Saccharopolyspora erythraea NRRL 2338Mutation(s): 1 
Gene Names: SACE_1339A8924_1736
EC: 3.4.11.2
UniProt
Find proteins for A4F9D7 (Saccharopolyspora erythraea (strain ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338))
Explore A4F9D7 
Go to UniProtKB:  A4F9D7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4F9D7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.909α = 90
b = 143.583β = 114.76
c = 60.58γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
xia2data reduction
MLPHAREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-11
    Type: Initial release
  • Version 1.1: 2022-05-25
    Changes: Database references
  • Version 1.2: 2022-07-06
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description