3BDJ

Crystal Structure of Bovine Milk Xanthine Dehydrogenase with a Covalently Bound Oxipurinol Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanism of inhibition of xanthine oxidoreductase by allopurinol: crystal structure of reduced bovine milk xanthine oxidoreductase bound with oxipurinol.

Okamoto, K.Eger, B.T.Nishino, T.Pai, E.F.Nishino, T.

(2008) Nucleosides Nucleotides Nucleic Acids 27: 888-893

  • DOI: 10.1080/15257770802146577

  • PubMed Abstract: 
  • Inhibitors of xanthine oxidoreductase block conversion of xanthine to uric acid and are therefore potentially useful for treatment of hyperuricemia or gout. We determined the crystal structure of reduced bovine milk xanthine oxidoreductase complexed ...

    Inhibitors of xanthine oxidoreductase block conversion of xanthine to uric acid and are therefore potentially useful for treatment of hyperuricemia or gout. We determined the crystal structure of reduced bovine milk xanthine oxidoreductase complexed with oxipurinol at 2.0 A resolution. Clear electron density was observed between the N2 nitrogen of oxipurinol and the molybdenum atom of the molybdopterin cofactor, indicating that oxipurinol coordinated directly to molybdenum. Oxipurinol forms hydrogen bonds with glutamate 802, arginine 880, and glutamate 1261, which have previously been shown to be essential for the enzyme reaction. We discuss possible differences in the hypouricemic effect of inhibitors, including allopurinol and newly developed inhibitors, based on their mode of binding in the crystal structures.


    Related Citations: 
    • Y-700[1-[3-CYANO-4-(2,2-DIMETHYLPROPOXY)PHENYL]-1H-PYRAZOLE-4-CARBOXYLIC ACID]: A Potent Xanthine Oxidoreductase Inhibitor with Hepatic excretion
      Fukunari, A.,Okamoto, K.,Nishino, T.,Eger, B.T.,Pai, E.F.,Kamezawa, M.,Yamada, I.,Kato, N.
      (2004) J.PHARMACOL.EXP.THER. 311: 519
    • An extremely potent inhibitor of Xanthine Oxidoreductase Crystal Structure of the enzyme-inhibitor complex and Mechanism of Inhibition
      Okamoto, K.,Eger, B.T.,Nishino, T.,Kondo, S.,Pai, E.F.,Nishino, T.
      (2003) J.Biol.Chem. 278: 1848
    • Crystal Structures of the Active and Alloxanthine-inhibited forms of Xanthine Dehydrogenase from Rhodobacter Capsulatusa
      Truglio, J.J.,Theis, K.,Leimkuhler, S.,Rappa, R.,Rajagopalan, K.V.,Kisker, C.
      (2002) Structure 10: 115
    • The Crystal Structure of Xanthine Oxidoreductase during catalysis: Implications for reaction mechanism and enzyme inhibition
      Okamoto, K.,Matsumoto, K.,Hille, R.,Eger, B.T.,Pai, E.F.,Nishino, T.
      (2004) Proc.Natl.Acad.Sci.USA 101: 7931


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Xanthine dehydrogenase/oxidase
A, B
1332Bos taurusMutation(s): 0 
Gene Names: XDH
Find proteins for P80457 (Bos taurus)
Go to Gene View: XDH
Go to UniProtKB:  P80457
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MOW
Query on MOW

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A, B
Oxo(sulfanyl)molybdenum(IV) ION
H Mo O S
LCFBNOLMHXMMKH-UHFFFAOYSA-M
 Ligand Interaction
FAD
Query on FAD

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A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
GOL
Query on GOL

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A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MTE
Query on MTE

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A, B
PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
C10 H14 N5 O6 P S2
HPEUEJRPDGMIMY-IFQPEPLCSA-N
 Ligand Interaction
FES
Query on FES

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A, B
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
141
Query on 141

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A, B
Oxypurinol
Alloxanthine
C5 H4 N4 O2
HXNFUBHNUDHIGC-UHFFFAOYSA-N
 Ligand Interaction
CO3
Query on CO3

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A, B
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 166.517α = 90.00
b = 124.074β = 91.01
c = 148.797γ = 90.00
Software Package:
Software NamePurpose
EPMRphasing
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2014-09-10
    Type: Non-polymer description