2E3T

Crystal structure of rat xanthine oxidoreductase mutant (W335A and F336L)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.185 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Two mutations convert mammalian xanthine oxidoreductase to highly superoxide-productive xanthine oxidase

Asai, R.Nishino, T.Matsumura, T.Okamoto, K.Igarashi, K.Pai, E.F.Nishino, T.

(2007) J Biochem 141: 525-534

  • DOI: https://doi.org/10.1093/jb/mvm054
  • Primary Citation of Related Structures:  
    2E3T

  • PubMed Abstract: 

    Reactive oxygen species are generated by various systems, including NADPH oxidases, xanthine oxidoreductase (XOR) and mitochondrial respiratory enzymes, and contribute to many physiological and pathological phenomena. Mammalian xanthine dehydrogenase (XDH) can be converted to xanthine oxidase (XO), which produces both superoxide anion and hydrogen peroxide in a molar ratio of about 1:3, depending upon the conditions. Here, we present a mutant of rat XOR that displays mainly XO activity with a superoxide:hydrogen peroxide production ratio of about 6:1. In the mutant, tryptophan 335, which is a component of the amino acid cluster crucial for switching from the XDH to the XO conformation, was replaced with alanine, and phenylalanine 336, which modulates FAD's redox potential through stacking interactions with the flavin cofactor, was changed to leucine. When the mutant was expressed in Sf9 cells, it was obtained in the XO form, and dithiothreitol treatment only partially restored the pyridine nucleotide-binding capacity. The crystal structure of the dithiothreitol-treated mutant at 2.3 Angstroms resolution showed the enzyme's two subunits to be quite similar, but not identical: the cluster involved in conformation-switching was completely disrupted in one subunit, but remained partly associated in the other one. The chain trace of the active site loop in this mutant is very similar to that of the bovine XO form. These results are consistent with the idea that the XDH and XO forms of the mutant are in an equilibrium that greatly favours the XO form, but the equilibrium is partly shifted towards the XDH form upon incubation with dithiothreitol.


  • Organizational Affiliation

    Department of Biochemistry and Department of Molecular Biology, Nippon Medical School, 1-1-5 Sendagi, Tokyo, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Xanthine dehydrogenase/oxidase
A, B
1,331Rattus norvegicusMutation(s): 2 
EC: 1.17.1.4 (PDB Primary Data), 1.17.3.2 (PDB Primary Data)
UniProt
Find proteins for P22985 (Rattus norvegicus)
Explore P22985 
Go to UniProtKB:  P22985
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22985
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
N [auth A],
Z [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
FES
Query on FES

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L [auth A],
M [auth A],
X [auth B],
Y [auth B]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
URC
Query on URC

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AA [auth B],
O [auth A]
URIC ACID
C5 H4 N4 O3
LEHOTFFKMJEONL-UHFFFAOYSA-N
PO4
Query on PO4

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D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
BCT
Query on BCT

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C [auth A],
P [auth B]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
CA
Query on CA

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
V [auth B],
W [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.066α = 90
b = 139.513β = 90
c = 222.304γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
EPMRphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-10-25
    Changes: Data collection, Refinement description