3EUB

Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Substrate Orientation and Catalysis at the Molybdenum Site in Xanthine Oxidase: CRYSTAL STRUCTURES IN COMPLEX WITH XANTHINE AND LUMAZINE.

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

(2009) J Biol Chem 284: 8760-8767

  • DOI: https://doi.org/10.1074/jbc.M804517200
  • Primary Citation of Related Structures:  
    3ETR, 3EUB

  • PubMed Abstract: 

    Xanthine oxidoreductase is a ubiquitous cytoplasmic protein that catalyzes the final two steps in purine catabolism. We have previously investigated the catalytic mechanism of the enzyme by rapid reaction kinetics and x-ray crystallography using the poor substrate 2-hydroxy-6-methylpurine, focusing our attention on the orientation of substrate in the active site and the role of Arg-880 in catalysis. Here we report additional crystal structures of as-isolated, functional xanthine oxidase in the course of reaction with the pterin substrate lumazine at 2.2 A resolution and of the nonfunctional desulfo form of the enzyme in complex with xanthine at 2.6 A resolution. In both cases the orientation of substrate is such that the pyrimidine subnucleus is oriented opposite to that seen with the slow substrate 2-hydroxy-6-methylpurine. The mechanistic implications as to how the ensemble of active site functional groups in the active site work to accelerate reaction rate are discussed.


  • Organizational Affiliation

    Department of Biochemistry, University of California, Riverside, California 92521 and the Medical Scientist Program, The Ohio State University, Columbus, Ohio 43210, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Xanthine dehydrogenase/oxidaseA,
D [auth J],
G [auth S],
J [auth 2]
165Bos taurusMutation(s): 0 
EC: 1.17.1.4 (PDB Primary Data), 1.17.3.2 (PDB Primary Data)
UniProt
Find proteins for P80457 (Bos taurus)
Explore P80457 
Go to UniProtKB:  P80457
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80457
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Xanthine dehydrogenase/oxidaseB,
E [auth K],
H [auth T],
K [auth 3]
305Bos taurusMutation(s): 0 
EC: 1.17.1.4 (PDB Primary Data), 1.17.3.2 (PDB Primary Data)
UniProt
Find proteins for P80457 (Bos taurus)
Explore P80457 
Go to UniProtKB:  P80457
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80457
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Xanthine dehydrogenase/oxidaseC,
F [auth L],
I [auth U],
L [auth 4]
762Bos taurusMutation(s): 0 
EC: 1.17.1.4 (PDB Primary Data), 1.17.3.2 (PDB Primary Data)
UniProt
Find proteins for P80457 (Bos taurus)
Explore P80457 
Go to UniProtKB:  P80457
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80457
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
AA [auth T],
GA [auth 3],
O [auth B],
U [auth K]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
MTE
Query on MTE

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BA [auth U],
HA [auth 4],
P [auth C],
V [auth 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
FES
Query on FES

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EA [auth 2]
FA [auth 2]
M [auth A]
N [auth A]
S [auth J]
EA [auth 2],
FA [auth 2],
M [auth A],
N [auth A],
S [auth J],
T [auth J],
Y [auth S],
Z [auth S]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
XAN
Query on XAN

Download Ideal Coordinates CCD File 
DA [auth U],
JA [auth 4],
R [auth C],
X [auth L]
XANTHINE
C5 H4 N4 O2
LRFVTYWOQMYALW-UHFFFAOYSA-N
MOM
Query on MOM

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CA [auth U],
IA [auth 4],
Q [auth C],
W [auth L]
HYDROXY(DIOXO)MOLYBDENUM
H Mo O3
WEHYDZQUOLJPRX-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.298α = 96.88
b = 133.176β = 93.11
c = 142.633γ = 90.02
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-09-17
    Changes: Database references
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description