7JSD | pdb_00007jsd

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 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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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 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.

Macromolecule Content 

  • Total Structure Weight: 121.95 kDa 
  • Atom Count: 8,351 
  • Modeled Residue Count: 989 
  • Deposited Residue Count: 1,052 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lysine hydroxylase
A, B, C, D
263Streptomyces roseifaciensMutation(s): 0 
UniProt
Find proteins for A0A8M0FGT0 (Streptomyces roseifaciens)
Explore A0A8M0FGT0 
Go to UniProtKB:  A0A8M0FGT0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8M0FGT0
Sequence Annotations
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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 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
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

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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