Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 298098.16 
• Atom Count: 20355 
• Residue Count: 2664 
• Unique protein chains: 1

1FO4

CRYSTAL STRUCTURE OF XANTHINE DEHYDROGENASE ISOLATED FROM BOVINE MILK

• DOI: 10.2210/pdb1FO4/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bos taurus


• Deposited: 2000-08-24 Released: 2000-10-25 
• Deposition Author(s): Enroth, C., Eger, B.T., Okamoto, K., Nishino, T., Nishino, T., Pai, E.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.238 
• R-Value Work: 0.198 

Literature

Crystal structures of bovine milk xanthine dehydrogenase and xanthine oxidase: structure-based mechanism of conversion.

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

(2000) Proc.Natl.Acad.Sci.USA 97: 10723-10728

• PubMed: 11005854 
• Primary Citation of Related Structures:  
  1FIQ


• PubMed Abstract: 
  

Mammalian xanthine oxidoreductases, which catalyze the last two steps in the formation of urate, are synthesized as the dehydrogenase form xanthine dehydrogenase (XDH) but can be readily converted to the oxidase form xanthine oxidase (XO) by oxidation of sulfhydryl residues or by proteolysis. Here, we present the crystal structure of the dimeric (M(r), 290,000) bovine milk XDH at 2.1-A resolution and XO at 2.5-A resolution and describe the major changes that occur on the proteolytic transformation of XDH to the XO form. Each molecule is composed of an N-terminal 20-kDa domain containing two iron sulfur centers, a central 40-kDa flavin adenine dinucleotide domain, and a C-terminal 85-kDa molybdopterin-binding domain with the four redox centers aligned in an almost linear fashion. Cleavage of surface-exposed loops of XDH causes major structural rearrangement of another loop close to the flavin ring (Gln 423Lys 433). This movement partially blocks access of the NAD substrate to the flavin adenine dinucleotide cofactor and changes the electrostatic environment of the active site, reflecting the switch of substrate specificity observed for the two forms of this enzyme.

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Organizational Affiliation: 

Ontario Cancer Institute/Princess Margaret Hospital, Division of Molecular and Structural Biology, 610 University Avenue, Toronto, ON, Canada M5G 2M9.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
XANTHINE DEHYDROGENASE	A, B	1332	Bos taurus	Mutation(s): 0  Gene Names: XDH
Find proteins for P80457 (Bos taurus) Go to Gene View: XDH Go to UniProtKB:  P80457

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
FAD	A, B	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
GOL	A, B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	A, B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MTE	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
FES	A, B	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
SAL	A, B	2-HYDROXYBENZOIC ACID SALICYLIC ACID C7 H6 O3 YGSDEFSMJLZEOE-UHFFFAOYSA-N
MOS	A, B	DIOXOTHIOMOLYBDENUM(VI) ION H Mo O2 S BDSRWPHSAKXXRG-UHFFFAOYSA-M

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
SAL	Ki: 100000000 nM (99) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.238 
• R-Value Work: 0.198 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 169.451	α = 90.00
b = 124.493	β = 90.94
c = 148.327	γ = 90.00

Software Package:

Software Name	Purpose
EPMR	phasing
SIGMAA	model building
SHARP	phasing
SCALEPACK	data scaling
CNS	phasing
DENZO	data reduction
DM	phasing
SOLVE	phasing
SIGMAA	phasing
DM	model building
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-08-24 
• Released Date: 2000-10-25 
• Deposition Author(s): Enroth, C., Eger, B.T., Okamoto, K., Nishino, T., Nishino, T., Pai, E.F.

Revision History 

• Version 1.0: 2000-10-25
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance
• Version 1.3: 2017-02-01
  Type: Structure summary
• Version 1.4: 2017-10-04
  Type: Refinement description