9DK1 | pdb_00009dk1

Lexapeptide dehydratase complex LxmKY apo


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.265 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.215 (DCC) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9DK1

This is version 1.1 of the entry. See complete history

Literature

A Stable Dehydratase Complex Catalyzes the Formation of Dehydrated Amino Acids in a Class V Lanthipeptide.

Randall, G.T.Grant-Mackie, E.S.Chunkath, S.Williams, E.T.Middleditch, M.J.Tao, M.Harris, P.W.R.Brimble, M.A.Bashiri, G.

(2024) ACS Chem Biol 19: 2548-2556

  • DOI: https://doi.org/10.1021/acschembio.4c00637
  • Primary Citation Related Structures: 
    9DK1, 9DK2, 9DK3

  • PubMed Abstract: 

    Lanthipeptides are ribosomally synthesized and post-translationally modified peptides that bear the characteristic lanthionine (Lan) or methyllanthionine (MeLan) thioether linkages. (Me)Lan moieties bestow lanthipeptides with robust stability and diverse antimicrobial, anticancer, and antiallodynic activities. Installation of (Me)Lan requires dehydration of serine and threonine residues to 2,3-dehydroalanine (Dha) and ( Z )-2,3-dehydrobutyrine (Dhb), respectively. LxmK and LxmY enzymes comprise the biosynthetic machinery of a newly discovered class V lanthipeptide, lexapeptide, and are proposed to catalyze the dehydration of serine and threonine residues in the precursor peptide. We demonstrate that LxmK and LxmY form a stable dehydratase complex to dehydrate precursor peptides. In addition, we present crystal structures of the LxmKY heterodimer, revealing structural and mechanistic features that enable iterative phosphorylation and elimination by the LxmKY complex. These findings provide molecular insights into class V lanthionine synthetases and lay the foundation for their applications as enzymatic tools in the biosynthesis of exquisitely modified peptides.


  • Organizational Affiliation
    • School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.

Macromolecule Content 

  • Total Structure Weight: 82.83 kDa 
  • Atom Count: 4,899 
  • Modeled Residue Count: 651 
  • Deposited Residue Count: 781 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Kinase403Streptomyces rocheiMutation(s): 0 
Gene Names: lxmK
UniProt
Find proteins for A0AAX3ZKT3 (Streptomyces rochei)
Explore A0AAX3ZKT3 
Go to UniProtKB:  A0AAX3ZKT3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAX3ZKT3
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Lyase378Streptomyces rocheiMutation(s): 0 
Gene Names: lxmY
UniProt
Find proteins for A0A0K1TP21 (Streptomyces rochei)
Explore A0A0K1TP21 
Go to UniProtKB:  A0A0K1TP21
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0K1TP21
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.265 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.215 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.704α = 90
b = 90.28β = 90
c = 148.953γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Marsden FundNew Zealand--
Other privateAuckland Medical Research Foundation

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release
  • Version 1.1: 2025-01-01
    Changes: Database references