2W3S

Crystal Structure of Xanthine Dehydrogenase (desulfo form) from Rhodobacter capsulatus in Complex with Xanthine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mechanism of Substrate and Inhibitor Binding of Rhodobacter Capsulatus Xanthine Dehydrogenase.

Dietzel, U.Kuper, J.Doebbler, J.A.Schulte, A.Truglio, J.J.Leimkuhler, S.Kisker, C.

(2009) J Biol Chem 284: 8768

  • DOI: 10.1074/jbc.M808114200
  • Primary Citation of Related Structures:  
    2W3R, 2W3S, 2W54, 2W55

  • PubMed Abstract: 
  • Rhodobacter capsulatus xanthine dehydrogenase (XDH) is an (alphabeta)(2) heterotetrameric cytoplasmic enzyme that resembles eukaryotic xanthine oxidoreductases in respect to both amino acid sequence and structural fold. To obtain a detailed understan ...

    Rhodobacter capsulatus xanthine dehydrogenase (XDH) is an (alphabeta)(2) heterotetrameric cytoplasmic enzyme that resembles eukaryotic xanthine oxidoreductases in respect to both amino acid sequence and structural fold. To obtain a detailed understanding of the mechanism of substrate and inhibitor binding at the active site, we solved crystal structures of R. capsulatus XDH in the presence of its substrates hypoxanthine, xanthine, and the inhibitor pterin-6-aldehyde using either the inactive desulfo form of the enzyme or an active site mutant (E(B)232Q) to prevent substrate turnover. The hypoxanthine- and xanthine-bound structures reveal the orientation of both substrates at the active site and show the importance of residue Glu(B)-232 for substrate positioning. The oxygen atom at the C-6 position of both substrates is oriented toward Arg(B)-310 in the active site. Thus the substrates bind in an orientation opposite to the one seen in the structure of the reduced enzyme with the inhibitor oxypurinol. The tightness of the substrates in the active site suggests that the intermediate products must exit the binding pocket to allow first the attack of the C-2, followed by oxidation of the C-8 atom to form the final product uric acid. Structural studies of pterin-6-aldehyde, a potent inhibitor of R. capsulatus XDH, contribute further to the understanding of the relative positioning of inhibitors and substrates in the binding pocket. Steady state kinetics reveal a competitive inhibition pattern with a K(i) of 103.57 +/- 18.96 nm for pterin-6-aldehyde.


    Organizational Affiliation

    Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg, Versbacher Strasse 9, 97078 Würzburg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
XANTHINE DEHYDROGENASEA, C, E, G462Rhodobacter capsulatusMutation(s): 0 
Gene Names: xdhA
EC: 1.1.1.204
Find proteins for O54050 (Rhodobacter capsulatus)
Explore O54050 
Go to UniProtKB:  O54050
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
XANTHINE DEHYDROGENASEB, D, F, H777Rhodobacter capsulatusMutation(s): 0 
Gene Names: xdhB
EC: 1.1.1.204
Find proteins for O54051 (Rhodobacter capsulatus)
Explore O54051 
Go to UniProtKB:  O54051
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download CCD File 
A, C, E, G
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
MTE
Query on MTE

Download CCD File 
B, D, F, H
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, C, E, G
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
XAN
Query on XAN

Download CCD File 
B, D, F, H
XANTHINE
C5 H4 N4 O2
LRFVTYWOQMYALW-UHFFFAOYSA-N
 Ligand Interaction
MOM
Query on MOM

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B, D, F, H
HYDROXY(DIOXO)MOLYBDENUM
H Mo O3
WEHYDZQUOLJPRX-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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B, D, F, H
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.83α = 109.6
b = 140.56β = 105.89
c = 158.17γ = 101.18
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-23
    Type: Initial release
  • Version 1.1: 2015-04-22
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance