1JRP

Crystal Structure of Xanthine Dehydrogenase inhibited by alloxanthine from Rhodobacter capsulatus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal structures of the active and alloxanthine-inhibited forms of xanthine dehydrogenase from Rhodobacter capsulatus

Truglio, J.J.Theis, K.Leimkuhler, S.Rappa, R.Rajagopalan, K.V.Kisker, C.

(2002) Structure 10: 115-125

  • Primary Citation of Related Structures:  1JRO
  • Also Cited By: 3BDJ

  • PubMed Abstract: 
  • Xanthine dehydrogenase (XDH), a complex molybdo/iron-sulfur/flavoprotein, catalyzes the oxidation of hypoxanthine to xanthine followed by oxidation of xanthine to uric acid with concomitant reduction of NAD+. The 2.7 A resolution structure of Rhodoba ...

    Xanthine dehydrogenase (XDH), a complex molybdo/iron-sulfur/flavoprotein, catalyzes the oxidation of hypoxanthine to xanthine followed by oxidation of xanthine to uric acid with concomitant reduction of NAD+. The 2.7 A resolution structure of Rhodobacter capsulatus XDH reveals that the bacterial and bovine XDH have highly similar folds despite differences in subunit composition. The NAD+ binding pocket of the bacterial XDH resembles that of the dehydrogenase form of the bovine enzyme rather than that of the oxidase form, which reduces O(2) instead of NAD+. The drug allopurinol is used to treat XDH-catalyzed uric acid build-up occurring in gout or during cancer chemotherapy. As a hypoxanthine analog, it is oxidized to alloxanthine, which cannot be further oxidized but acts as a tight binding inhibitor of XDH. The 3.0 A resolution structure of the XDH-alloxanthine complex shows direct coordination of alloxanthine to the molybdenum via a nitrogen atom. These results provide a starting point for the rational design of new XDH inhibitors.


    Organizational Affiliation

    Department of Pharmacological Sciences, Center for Structural Biology, State University of New York at Stony Brook, Stony Brook, NY 11794, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
xanthine dehydrogenase, chain A
A, C, E, G
462Rhodobacter capsulatusGene Names: xdhA
EC: 1.17.1.4
Find proteins for O54050 (Rhodobacter capsulatus)
Go to UniProtKB:  O54050
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
xanthine dehydrogenase, chain B
B, D, F, H
777Rhodobacter capsulatusGene Names: xdhB
EC: 1.17.1.4
Find proteins for O54051 (Rhodobacter capsulatus)
Go to UniProtKB:  O54051
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

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

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Download CCD File 
B, D, F, H
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MTE
Query on MTE

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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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Download CCD File 
A, C, E, G
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
141
Query on 141

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Download CCD File 
B, D, F, H
Oxypurinol
Alloxanthine
C5 H4 N4 O2
HXNFUBHNUDHIGC-UHFFFAOYSA-N
 Ligand Interaction
MOS
Query on MOS

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Download CCD File 
B, D, F, H
DIOXOTHIOMOLYBDENUM(VI) ION
H Mo O2 S
BDSRWPHSAKXXRG-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.193 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 92.617α = 109.59
b = 140.728β = 105.84
c = 157.665γ = 101.25
Software Package:
Software NamePurpose
X-PLORphasing
DENZOdata reduction
X-PLORmodel building
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-01-11
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2014-09-10
    Type: Non-polymer description
  • Version 1.4: 2015-04-22
    Type: Non-polymer description