6F32

Crystal structure of a dual function amine oxidase/cyclase in complex with substrate analogues


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Insights into a dual function amide oxidase/macrocyclase from lankacidin biosynthesis.

Dorival, J.Risser, F.Jacob, C.Collin, S.Drager, G.Paris, C.Chagot, B.Kirschning, A.Gruez, A.Weissman, K.J.

(2018) Nat Commun 9: 3998-3998

  • DOI: https://doi.org/10.1038/s41467-018-06323-w
  • Primary Citation of Related Structures:  
    6F32, 6F7L, 6F7V, 6FJH

  • PubMed Abstract: 

    Acquisition of new catalytic activity is a relatively rare evolutionary event. A striking example appears in the pathway to the antibiotic lankacidin, as a monoamine oxidase (MAO) family member, LkcE, catalyzes both an unusual amide oxidation, and a subsequent intramolecular Mannich reaction to form the polyketide macrocycle. We report evidence here for the molecular basis for this dual activity. The reaction sequence involves several essential active site residues and a conformational change likely comprising an interdomain hinge movement. These features, which have not previously been described in the MAO family, both depend on a unique dimerization mode relative to all structurally characterized members. Taken together, these data add weight to the idea that designing new multifunctional enzymes may require changes in both architecture and catalytic machinery. Encouragingly, however, our data also show LkcE to bind alternative substrates, supporting its potential utility as a general cyclization catalyst in synthetic biology.


  • Organizational Affiliation

    UMR 7365, Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, Campus Biologie Santé, 9 Avenue de la Forêt de Haye, BP 20199, 54505, Vandœuvre-lès-Nancy Cedex, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Amine oxidase LkcE
A, B
442Streptomyces rocheiMutation(s): 0 
Gene Names: lkcE
UniProt
Find proteins for Q83X90 (Streptomyces rochei)
Explore Q83X90 
Go to UniProtKB:  Q83X90
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ83X90
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
CJ8 (Subject of Investigation/LOI)
Query on CJ8

Download Ideal Coordinates CCD File 
E [auth A](2~{R},3~{R})-2,3-bis(oxidanyl)-~{N},~{N}'-dipropyl-butanediamide
C10 H20 N2 O4
GCNAACQQQUCOMO-HTQZYQBOSA-N
CJE (Subject of Investigation/LOI)
Query on CJE

Download Ideal Coordinates CCD File 
P [auth B]ethyl (2~{R})-2-methyl-3-oxidanylidene-butanoate
C7 H12 O3
FNENWZWNOPCZGK-RXMQYKEDSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A]
Q [auth B]
R [auth B]
S [auth B]
T [auth B]
H [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B],
K [auth B],
L [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
M [auth B],
N [auth B],
O [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.504α = 90
b = 125.504β = 90
c = 156.686γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFrancePKS-PPIs / AAP JCJC SVS3 8 2011

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-10-10
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations