5TXC

AtxE2 Isopeptidase - APO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the Lasso Peptide Isopeptidase Identifies a Topology for Processing Threaded Substrates.

Chekan, J.R.Koos, J.D.Zong, C.Maksimov, M.O.Link, A.J.Nair, S.K.

(2016) J Am Chem Soc 138: 16452-16458

  • DOI: https://doi.org/10.1021/jacs.6b10389
  • Primary Citation of Related Structures:  
    5TXC, 5TXE

  • PubMed Abstract: 

    Lasso peptides are a class of bioactive ribosomally synthesized and post-translationally modified peptides (RiPPs), with a threaded knot structure that is formed by an isopeptide bond attaching the N-terminus of the peptide to a side chain carboxylate. Some lasso peptide biosynthetic clusters harbor an enzyme that specifically hydrolyzes the isopeptide bond to yield the linear peptide. We describe here the 2.4 Å resolution structure of a lasso peptide isopeptidase revealing a topologically novel didomain architecture consisting of an open β-propeller appended to an α/β hydrolase domain. The 2.2 Å resolution cocrystal structure of an inactive variant in complex with a lasso peptide reveals deformation of the substrate, and reorganization of the enzyme active site, which exposes and orients the isopeptide bond for hydrolysis. Structure-based mutational analysis reveals how this enzyme recognizes the lasso peptide substrate by shape complementarity rather than through sequence specificity. The isopeptidase gene can be used to facilitate genome mining, as a network-based mining strategy queried with this sequence identified 87 putative lasso peptide biosynthetic clusters, 65 of which have not been previously described. Lastly, we validate this mining approach by heterologous expression of two clusters encoded within the genome of Asticcaucalis benevestitus, and demonstrate that both clusters produce lasso peptides.


  • Organizational Affiliation

    Department of Biochemistry, ‡Institute for Genomic Biology and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States and.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AtxE2
A, B
705Asticcacaulis excentricus CB 48Mutation(s): 0 
Gene Names: Astex_2444
EC: 3.4.21 (PDB Primary Data), 3.4 (UniProt)
UniProt
Find proteins for E8RUP5 (Asticcacaulis excentricus (strain ATCC 15261 / DSM 4724 / KCTC 12464 / NCIMB 9791 / VKM B-1370 / CB 48))
Explore E8RUP5 
Go to UniProtKB:  E8RUP5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE8RUP5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.492α = 90
b = 201.742β = 90
c = 109.131γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2017-01-04
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Database references, Structure summary