7JSD

Hydroxylase homolog of BesD with Fe(II), alpha-ketoglutarate, and lysine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Reaction pathway engineering converts a radical hydroxylase into a halogenase.

Neugebauer, M.E.Kissman, E.N.Marchand, J.A.Pelton, J.G.Sambold, N.A.Millar, D.C.Chang, M.C.Y.

(2022) Nat Chem Biol 18: 171-179

  • DOI: https://doi.org/10.1038/s41589-021-00944-x
  • Primary Citation of Related Structures:  
    7JSD

  • PubMed Abstract: 

    Fe II /α-ketoglutarate (Fe II /αKG)-dependent enzymes offer a promising biocatalytic platform for halogenation chemistry owing to their ability to functionalize unactivated C-H bonds. However, relatively few radical halogenases have been identified to date, limiting their synthetic utility. Here, we report a strategy to expand the palette of enzymatic halogenation by engineering a reaction pathway rather than substrate selectivity. This approach could allow us to tap the broader class of Fe II /αKG-dependent hydroxylases as catalysts by their conversion to halogenases. Toward this goal, we discovered active halogenases from a DNA shuffle library generated from a halogenase-hydroxylase pair using a high-throughput in vivo fluorescent screen coupled to an alkyne-producing biosynthetic pathway. Insights from sequencing halogenation-active variants along with the crystal structure of the hydroxylase enabled engineering of a hydroxylase to perform halogenation with comparable activity and higher selectivity than the wild-type halogenase, showcasing the potential of harnessing hydroxylases for biocatalytic halogenation.


  • Organizational Affiliation

    Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine hydroxylase
A, B, C, D
263Streptomyces roseifaciensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4 (Subject of Investigation/LOI)
Query on PG4

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
LYS (Subject of Investigation/LOI)
Query on LYS

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
M [auth C]
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
AKG (Subject of Investigation/LOI)
Query on AKG

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
N [auth C],
P [auth D]
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
FE2 (Subject of Investigation/LOI)
Query on FE2

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
O [auth C],
Q [auth D]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.626α = 90
b = 93.53β = 107.56
c = 91.339γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesLBNL DEAC02-05CH11231, FWP CH030201

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-25
    Type: Initial release
  • Version 1.1: 2022-03-09
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description