9DK3 | pdb_00009dk3

Lexapeptide dehydratase complex LxmKY, hydrolysed ATP bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.257 (Depositor), 0.256 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.212 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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 of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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:  (by identity cutoff)  |  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
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
I [auth A],
K [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A],
N [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
M [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY
Query on ACY

Download Ideal Coordinates CCD File 
G [auth A],
J [auth A]
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
L [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.257 (Depositor), 0.256 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.212 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.175α = 90
b = 91.583β = 90
c = 151.372γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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