9EQF

Crystal structure of the L-arginine hydroxylase VioC MeHis316, bound to Fe(II), L-arginine, and succinate

  • Classification: OXIDOREDUCTASE
  • Organism(s): synthetic construct
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2024-03-21 Released: 2024-07-31 
  • Deposition Author(s): Hardy, F.J.
  • Funding Organization(s): European Research Council (ERC), Biotechnology and Biological Sciences Research Council (BBSRC), Engineering and Physical Sciences Research Council

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

Starting Model: experimental
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Literature

Probing Ferryl Reactivity in a Nonheme Iron Oxygenase Using an Expanded Genetic Code.

Hardy, F.J.Quesne, M.G.Gerard, E.F.Zhao, J.Ortmayer, M.Taylor, C.J.Ali, H.S.Slater, J.W.Levy, C.W.Heyes, D.J.Bollinger Jr., J.M.de Visser, S.P.Green, A.P.

(2024) ACS Catal 14: 11584-11590

  • DOI: https://doi.org/10.1021/acscatal.4c02365
  • Primary Citation of Related Structures:  
    9EQF

  • PubMed Abstract: 

    The ability to introduce noncanonical amino acids as axial ligands in heme enzymes has provided a powerful experimental tool for studying the structure and reactivity of their Fe IV =O ("ferryl") intermediates. Here, we show that a similar approach can be used to perturb the conserved Fe coordination environment of 2-oxoglutarate (2OG) dependent oxygenases, a versatile class of enzymes that employ highly-reactive ferryl intermediates to mediate challenging C-H functionalizations. Replacement of one of the cis-disposed histidine ligands in the oxygenase VioC with a less electron donating N δ -methyl-histidine (MeHis) preserves both catalytic function and reaction selectivity. Significantly, the key ferryl intermediate responsible for C-H activation can be accumulated in both the wildtype and the modified protein. In contrast to heme enzymes, where metal-oxo reactivity is extremely sensitive to the nature of the proximal ligand, the rates of C-H activation and the observed large kinetic isotope effects are only minimally affected by axial ligand replacement in VioC. This study showcases a powerful tool for modulating the coordination sphere of nonheme iron enzymes that will enhance our understanding of the factors governing their divergent activities.


  • Organizational Affiliation

    Department of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-ketoglutarate-dependent L-arginine hydroxylase394synthetic constructMutation(s): 0 
Gene Names: vioC
EC: 1.14.11.41
UniProt
Find proteins for Q6WZB0 (Streptomyces vinaceus)
Explore Q6WZB0 
Go to UniProtKB:  Q6WZB0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6WZB0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ARG (Subject of Investigation/LOI)
Query on ARG

Download Ideal Coordinates CCD File 
D [auth A]ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
SIN (Subject of Investigation/LOI)
Query on SIN

Download Ideal Coordinates CCD File 
C [auth A]SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE2 (Subject of Investigation/LOI)
Query on FE2

Download Ideal Coordinates CCD File 
B [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MHS
Query on MHS
A
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.145α = 90
b = 67.107β = 109.221
c = 62.945γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2024-07-31 
  • Deposition Author(s): Hardy, F.J.

Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union757991
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M027023/1
Engineering and Physical Sciences Research CouncilUnited KingdomEP/W524347/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-31
    Type: Initial release
  • Version 1.1: 2024-08-21
    Changes: Database references