5TXE

AtxE2 Isopeptidase - S527A Variant with Astexin3-dC4 Bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1021/jacs.6b10389
  • Primary Citation of Related Structures:  

  • 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 carboxylat ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AtxE2
A, B
705Asticcacaulis excentricus (strain ATCC 15261 / DSM 4724 / VKM B-1370 / CB 48)Mutation(s): 1 
Find proteins for E8RUP5 (Asticcacaulis excentricus (strain ATCC 15261 / DSM 4724 / VKM B-1370 / CB 48))
Go to UniProtKB:  E8RUP5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Astexin3-dC4
C, D
24Asticcacaulis excentricus (strain ATCC 15261 / DSM 4724 / VKM B-1370 / CB 48)Mutation(s): 0 
Find proteins for E8RUP8 (Asticcacaulis excentricus (strain ATCC 15261 / DSM 4724 / VKM B-1370 / CB 48))
Go to UniProtKB:  E8RUP8
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.154 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 151.253α = 90.00
b = 202.854β = 90.00
c = 110.399γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2017-01-04
    Type: Database references