5TXE

AtxE2 Isopeptidase - S527A Variant with Astexin3-dC4 Bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.157 

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:  
    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 ...

    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

    Departments of Chemical and Biological Engineering, ⊥Molecular Biology, and #Chemistry Princeton University , Princeton, New Jersey 08544, United States.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AtxE2A,
C [auth B]
705Asticcacaulis excentricus CB 48Mutation(s): 1 
Gene Names: Astex_2444atxE2
EC: 3.4
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
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Astexin3-dC4B [auth C],
D
24Asticcacaulis excentricus CB 48Mutation(s): 0 
Gene Names: Astex_2447AtxA3
UniProt
Find proteins for E8RUP8 (Asticcacaulis excentricus (strain ATCC 15261 / DSM 4724 / KCTC 12464 / NCIMB 9791 / VKM B-1370 / CB 48))
Explore E8RUP8 
Go to UniProtKB:  E8RUP8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE8RUP8
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.157 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.253α = 90
b = 202.854β = 90
c = 110.399γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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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