6VIA

Observing a ring-cleaving dioxygenase in action through a crystalline lens - a seven-membered lactone bound structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

Starting Model: experimental
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This is version 2.2 of the entry. See complete history


Literature

Observing 3-hydroxyanthranilate-3,4-dioxygenase in action through a crystalline lens.

Wang, Y.Liu, K.F.Yang, Y.Davis, I.Liu, A.

(2020) Proc Natl Acad Sci U S A 117: 19720-19730

  • DOI: https://doi.org/10.1073/pnas.2005327117
  • Primary Citation of Related Structures:  
    6VI5, 6VI6, 6VI7, 6VI8, 6VI9, 6VIA, 6VIB, 6X11

  • PubMed Abstract: 

    The synthesis of quinolinic acid from tryptophan is a critical step in the de novo biosynthesis of nicotinamide adenine dinucleotide (NAD + ) in mammals. Herein, the nonheme iron-based 3-hydroxyanthranilate-3,4-dioxygenase responsible for quinolinic acid production was studied by performing time-resolved in crystallo reactions monitored by UV-vis microspectroscopy, electron paramagnetic resonance (EPR) spectroscopy, and X-ray crystallography. Seven catalytic intermediates were kinetically and structurally resolved in the crystalline state, and each accompanies protein conformational changes at the active site. Among them, a monooxygenated, seven-membered lactone intermediate as a monodentate ligand of the iron center at 1.59-Å resolution was captured, which presumably corresponds to a substrate-based radical species observed by EPR using a slurry of small-sized single crystals. Other structural snapshots determined at around 2.0-Å resolution include monodentate and subsequently bidentate coordinated substrate, superoxo, alkylperoxo, and two metal-bound enol tautomers of the unstable dioxygenase product. These results reveal a detailed stepwise O-atom transfer dioxygenase mechanism along with potential isomerization activity that fine-tunes product profiling and affects the production of quinolinic acid at a junction of the metabolic pathway.


  • Organizational Affiliation

    Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-hydroxyanthranilate 3,4-dioxygenase195Cupriavidus metallidurans CH34Mutation(s): 0 
Gene Names: nbaCRmet_5193
EC: 1.13.11.6
UniProt
Find proteins for Q1LCS4 (Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34))
Explore Q1LCS4 
Go to UniProtKB:  Q1LCS4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1LCS4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EAY (Subject of Investigation/LOI)
Query on EAY

Download Ideal Coordinates CCD File 
G [auth A](2R,3E)-2-hydroxy-3-imino-2,3-dihydrooxepine-4-carboxylic acid
C7 H7 N O4
UYPQDLOIVBUHNZ-KBUNYLKBSA-N
TRS
Query on TRS

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B [auth A],
C [auth A]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
FE (Subject of Investigation/LOI)
Query on FE

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E [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
FE2
Query on FE2

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D [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
OH (Subject of Investigation/LOI)
Query on OH

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F [auth A]HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.517α = 90
b = 58.517β = 90
c = 231.902γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM108988
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesR21MH107985
National Science Foundation (NSF, United States)United StatesCHE-1623856
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM107529

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 2.0: 2020-08-05
    Changes: Atomic model
  • Version 2.1: 2021-10-06
    Changes: Database references
  • Version 2.2: 2023-10-11
    Changes: Data collection, Refinement description