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Overview for MACiE Entry M0139

Version history

General Information

EC Number: 1.17.1.4 (A member of the Oxidoreductases, Acting on CH or CH2 groups, With NAD+ or NADP+ as acceptor)

Enzyme Name: xanthine dehydrogenase

Biological Species: Bos taurus (Cow)

Catalytic Chain UniprotKB Accession Codes:

Representative PDB Code: 1v97 - CRYSTAL STRUCTURE OF BOVINE MILK XANTHINE DEHYDROGENASE FYX-051 BOUND FORM (Resolution = 1.94 Å).

Catalytic CATH Codes:

  • Unassigned Domain

Display structure information

Overall Reaction:

Image of xanthine

Image of water

Image of NAD

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Image of proton

Image of urate

Image of NADH

xanthine
C00385
CHEBI:15318
water
C00001
CHEBI:15377
NAD
C00003
CHEBI:15846
proton
C00080
CHEBI:24636
urate
C00366
CHEBI:17775
NADH
C00004
CHEBI:16908

Overall Comment: Xanthine dehydrogenase (EC 1.17.1.4) and xanthine oxidase (EC 1.17.3.2) are two variants of the same gene product. The former prefers NAD+ as the oxidising substrate whereas the latter uses dioxygen exclusively [1]. The mechanism shown in MACiE strongly supports all the available evidence. The pH dependence of the reaction strongly suggests that the active site base (Glu1261A) is initially in its unprotonated state and that the enzyme only works on the substrate in its neutral state [3]. The mechanism shown in here is supported by mutational spectroscopic computational and crystallographic studies [1,2,3,4]. There has been some debate as to whether the catalytically labile oxygen is from the Mo=O or Mo-OH groups. Isotope labelling experiments of solvent shows that the catalytically labile group is the Mo-OH and that it is replenished from solvent at the end of the catalytic cycle [1 2].


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Stepwise Description of the Reaction

Step 1Glu1261 deprotonates the MTE bound hydroxide, activating it for nucleophilic attack upon the xanthine substrate, resulting in a nucleophilic addition of the substrate to the cofactor. Xanthine then transfers a hydride to the sulfur bound to the molybdenum ion (Mo=S) resulting in a two electron reduction of the Mo(VI) to Mo(IV) and a thiol bound to molybdenum.
Step 2Water deprotonates the molybdenum bound thiol, reforming the Mo=S species and a single electron transfer from the Mo(IV) through the rest of the cofactor and two iron-sulfur clusters to a bound FAD cofactor, forming Mo(V) and a radical on the FAD cofactor.
Step 3A free hydroxide ion attacks the Mo(V), releasing the urate product (oxidised xanthine), which is re-protonated from the Glu1261, in a nucleophilic substitution reaction. This also results in the second electron transfer from the Mo(V) through the rest of the cofactor and two iron-sulfur clusters to a bound FAD cofactor, which then deprotonates a hydroxonium ion.
Step 4FAD is regenerated through a hydroxide transfer from the FAD cofactor to the substrate NAD

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Catalytic Residues Involved

Type Number Chain Location of Function
Glu 802 A Side Chain
Arg 880 A Side Chain
Glu 1261 A Side Chain

Organic Cofactors for M0139

Type Identity Chain
MTE MTE 3003 Overview
FAD FAD 3005 Overview

Metal Cofactors for M0139

Type Het group Number Chain
iron FES 3001 A Overview
iron FES 3002 A Overview
molybdenum MOS 3004 x Overview

References

  1. K. Okamoto et al. (2004), Proc. Natl Acad. Sci. USA, 101, 7931-7936. The crystal structure of xanthine oxidoreductase during catalysis: implications for reaction mechanism and enzyme inhibition.
    Medline: 15148401
  2. R. Hille (2005), Arch. Biochem. Biophys., 433, 107-116. Molybdenum-containing hydroxylases.
    Medline: 15581570
  3. E.-Y. Choi et al. (2004), J. Inorg. Biochem., 98, 841-848. Studies on the mechanism of action of xanthine oxidase.
    Medline: 15134930
  4. S. Leimkuhler et al. (2004), J. Biol. Chem., 279, 40437-40444. The role of active site glutamate residues in catalysis of Rhodobacter capsulatus xanthine dehydrogenase.
    Medline: 15265866
  5. X.-H. Zhang et al. (2005), Inorg. Chem., 44, 1466-1471. A theoretical study on the mechanism of the reductive half-reaction of xanthine oxidase.
    Medline: 15732988

Homologue information for M0139 (1v97)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)


Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
Link to MetaCyc Link to KEGG Link to BRENDA Link to ExplorENZ

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catalytic activity (molecular function)
xanthine dehydrogenase activity (molecular function)
xanthine oxidase activity (molecular function)
binding (molecular function)
iron ion binding (molecular function)
extracellular region (cellular component)
cytoplasm (cellular component)
peroxisome (cellular component)
UDP-N-acetylmuramate dehydrogenase activity (molecular function)
electron carrier activity (molecular function)
xanthine catabolic process (biological process)
oxidoreductase activity (molecular function)
oxidoreductase activity, acting on CH-OH group of donors (molecular function)
protein homodimerization activity (molecular function)
molybdopterin cofactor binding (molecular function)
metal ion binding (molecular function)
flavin adenine dinucleotide binding (molecular function)
iron-sulfur cluster binding (molecular function)
2 iron, 2 sulfur cluster binding (molecular function)
oxidation-reduction process (biological process)
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