3B9J | pdb_00003b9j

Structure of Xanthine Oxidase with 2-hydroxy-6-methylpurine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.263 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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Literature

Substrate orientation in xanthine oxidase: crystal structure of enzyme in reaction with 2-hydroxy-6-methylpurine.

Pauff, J.M.Zhang, J.Bell, C.E.Hille, R.

(2008) J Biological Chem 283: 4818-4824

  • DOI: https://doi.org/10.1074/jbc.M707918200
  • Primary Citation Related Structures: 
    3B9J

  • PubMed Abstract: 

    Xanthine oxidoreductase catalyzes the final two steps of purine catabolism and is involved in a variety of pathological states ranging from hyperuricemia to ischemia-reperfusion injury. The human enzyme is expressed primarily in its dehydrogenase form utilizing NAD+ as the final electron acceptor from the enzyme's flavin site but can exist as an oxidase that utilizes O2 for this purpose. Central to an understanding of the enzyme's function is knowledge of purine substrate orientation in the enzyme's molybdenum-containing active site. We report here the crystal structure of xanthine oxidase, trapped at the stage of a critical intermediate in the course of reaction with the slow substrate 2-hydroxy-6-methylpurine at 2.3A. This is the first crystal structure of a reaction intermediate with a purine substrate that is hydroxylated at its C8 position as is xanthine and confirms the structure predicted to occur in the course of the presently favored reaction mechanism. The structure also corroborates recent work suggesting that 2-hydroxy-6-methylpurine orients in the active site with its C2 carbonyl group interacting with Arg-880 and extends our hypothesis that xanthine binds opposite this orientation, with its C6 carbonyl positioned to interact with Arg-880 in stabilizing the MoV transition state.


  • Organizational Affiliation
    • Department of Biochemistry, University of California, Riverside, California 92521, USA.

Macromolecule Content 

  • Total Structure Weight: 297.74 kDa 
  • Atom Count: 19,847 
  • Modeled Residue Count: 2,439 
  • Deposited Residue Count: 2,664 
  • Unique protein chains: 3

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
xanthine oxidaseA,
D [auth I]
219Bos taurusMutation(s): 0 
EC: 1.17.3.2 (PDB Primary Data), 1.17.1.4 (UniProt)
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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
xanthine oxidaseB,
E [auth J]
350Bos taurusMutation(s): 0 
EC: 1.17.3.2 (PDB Primary Data), 1.17.1.4 (UniProt)
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
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
xanthine oxidaseC,
F [auth K]
763Bos taurusMutation(s): 0 
EC: 1.17.3.2 (PDB Primary Data), 1.17.1.4 (UniProt)
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
Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD



Download:Ideal Coordinates CCD File
I [auth B],
P [auth J]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
MTE

Query on MTE



Download:Ideal Coordinates CCD File
K [auth C],
Q [auth K]
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



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
N [auth I],
O [auth I]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
MOS

Query on MOS



Download:Ideal Coordinates CCD File
L [auth C],
R [auth K]
DIOXOTHIOMOLYBDENUM(VI) ION
H Mo O2 S
BDSRWPHSAKXXRG-UHFFFAOYSA-M
290

Query on 290



Download:Ideal Coordinates CCD File
M [auth C],
S [auth K]
6-methyl-3,9-dihydro-2H-purin-2-one
C6 H6 N4 O
PTQIZCPBAIYYII-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
J [auth C]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.263 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.187α = 90
b = 73.794β = 98.87
c = 146.498γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Atdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description