3NRZ

Crystal Structure of Bovine Xanthine Oxidase in Complex with Hypoxanthine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Substrate orientation and catalytic specificity in the action of xanthine oxidase: the sequential hydroxylation of hypoxanthine to uric acid.

Cao, H.Pauff, J.M.Hille, R.

(2010) J.Biol.Chem. 285: 28044-28053

  • DOI: 10.1074/jbc.M110.128561
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Xanthine oxidase is a molybdenum-containing enzyme catalyzing the hydroxylation of a sp(2)-hybridized carbon in a broad range of aromatic heterocycles and aldehydes. Crystal structures of the bovine enzyme in complex with the physiological substrate ...

    Xanthine oxidase is a molybdenum-containing enzyme catalyzing the hydroxylation of a sp(2)-hybridized carbon in a broad range of aromatic heterocycles and aldehydes. Crystal structures of the bovine enzyme in complex with the physiological substrate hypoxanthine at 1.8 A resolution and the chemotherapeutic agent 6-mercaptopurine at 2.6 A resolution have been determined, showing in each case two alternate orientations of substrate in the two active sites of the crystallographic asymmetric unit. One orientation is such that it is expected to yield hydroxylation at C-2 of substrate, yielding xanthine. The other suggests hydroxylation at C-8 to give 6,8-dihydroxypurine, a putative product not previously thought to be generated by the enzyme. Kinetic experiments demonstrate that >98% of hypoxanthine is hydroxylated at C-2 rather than C-8, indicating that the second crystallographically observed orientation is significantly less catalytically effective than the former. Theoretical calculations suggest that enzyme selectivity for the C-2 over C-8 of hypoxanthine is largely due to differences in the intrinsic reactivity of the two sites. For the orientation of hypoxanthine with C-2 proximal to the molybdenum center, the disposition of substrate in the active site is such that Arg(880) and Glu(802), previous shown to be catalytically important for the conversion of xanthine to uric acid, play similar roles in hydroxylation at C-2 as at C-8. Contrary to the literature, we find that 6,8-dihydroxypurine is effectively converted to uric acid by xanthine oxidase.


    Organizational Affiliation

    Department of Biochemistry, University of California at Riverside, Riverside, California 92521, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Xanthine dehydrogenase/oxidase
A, J
164Bos taurusMutation(s): 0 
Gene Names: XDH
Find proteins for P80457 (Bos taurus)
Go to Gene View: XDH
Go to UniProtKB:  P80457
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Xanthine dehydrogenase/oxidase
B, K
305Bos taurusMutation(s): 0 
Gene Names: XDH
Find proteins for P80457 (Bos taurus)
Go to Gene View: XDH
Go to UniProtKB:  P80457
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Xanthine dehydrogenase/oxidase
C, L
756Bos taurusMutation(s): 0 
Gene Names: XDH
Find proteins for P80457 (Bos taurus)
Go to Gene View: XDH
Go to UniProtKB:  P80457
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

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Download CCD File 
B, K
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
MTE
Query on MTE

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Download CCD File 
C, L
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
HPA
Query on HPA

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C, L
HYPOXANTHINE
C5 H4 N4 O
FDGQSTZJBFJUBT-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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Download CCD File 
A, J
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
MOS
Query on MOS

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Download CCD File 
C, L
DIOXOTHIOMOLYBDENUM(VI) ION
H Mo O2 S
BDSRWPHSAKXXRG-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HPAKd: 4600 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 133.016α = 90.00
b = 73.645β = 97.05
c = 138.696γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOLREPphasing
MOSFLMdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance