9EQF | pdb_00009eqf

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 (Depositor), 0.186 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 
    0.159 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

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 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.

Macromolecule Content 

  • Total Structure Weight: 43.84 kDa 
  • Atom Count: 3,187 
  • Modeled Residue Count: 335 
  • Deposited Residue Count: 394 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 (Depositor), 0.186 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 0.159 (Depositor) 
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