BRENDA - Enzyme Database

Protonation and sulfido versus oxo ligation changes at the molybdenum cofactor in xanthine dehydrogenase (XDH) variants studied by X-ray absorption spectroscopy

Reschke, S.; Mebs, S.; Sigfridsson-Clauss, K.G.; Kositzki, R.; Leimkuehler, S.; Haumann, M.; Inorg. Chem. 56, 2165-2176 (2017)

Data extracted from this reference:

Engineering
EC Number
Amino acid exchange
Commentary
Organism
1.17.1.4
E730A
crystal structure determination and analysis, comparison with wild-type enzyme structure, the sulfido is replaced with an oxo ligand in the inactive E730A mutant, further showing another oxo and one Mo-OH ligand at Mo, which are independent of pH
Rhodobacter capsulatus
1.17.1.4
additional information
the enzyme mutants show alterations in the Mo site structure, which changes in a pH range of 5-10, and in the influence of amino acids (Glu730 and Gln179) close to molybdenum cofactor in wild-type, and Q179A and E730A mutants, enzyme kinetics and quantum chemical studies, overview
Rhodobacter capsulatus
1.17.1.4
Q179A
crystal structure determination and analysis, comparison with wild-type enzyme structure, a similar acidic pK for the wild-type and Q179A variants, as well as the metrical parameters of the Mo site and density functional theory calculations, suggested protonation at the equatorial oxo group. Oxidized wild-type and mutant Q179A reveal a similar Mo(VI) ion with each one molybdopterin, Mo=O, Mo-O-, and Mo=S ligand, and a weak Mo-O(E730) bond at alkaline pH
Rhodobacter capsulatus
Metals/Ions
EC Number
Metals/Ions
Commentary
Organism
Structure
1.17.1.4
Molybdenum
in the molybdenum cofactor, the metal ion binds a molybdopterin (MPT) molecule via its dithiolene function and terminal sulfur and oxygen groups. Oxidized wild-type and mutant Q179A reveal a similar Mo(VI) ion with each one molybdopterin, Mo=O, Mo-O-, and Mo=S ligand, and a weak Mo-O(E730) bond at alkaline pH
Rhodobacter capsulatus
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
1.17.1.4
xanthine + NAD+ + H2O
Rhodobacter capsulatus
-
urate + NADH + H+
-
-
?
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
1.17.1.4
Rhodobacter capsulatus
-
-
-
Reaction
EC Number
Reaction
Commentary
Organism
1.17.1.4
xanthine + NAD+ + H2O = urate + NADH + H+
a reaction mechanism for XDH is suggested in which an initial oxo rather than a hydroxo group and the sulfido ligand are essential for xanthine oxidation
Rhodobacter capsulatus
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.17.1.4
xanthine + NAD+ + H2O
-
745069
Rhodobacter capsulatus
urate + NADH + H+
-
-
-
?
Cofactor
EC Number
Cofactor
Commentary
Organism
Structure
1.17.1.4
molybdenum cofactor
MoCo, the metal ion binds a molybdopterin (MPT) molecule via its dithiolene function and terminal sulfur and oxygen groups
Rhodobacter capsulatus
1.17.1.4
[2Fe-2S]-center
-
Rhodobacter capsulatus
Cofactor (protein specific)
EC Number
Cofactor
Commentary
Organism
Structure
1.17.1.4
molybdenum cofactor
MoCo, the metal ion binds a molybdopterin (MPT) molecule via its dithiolene function and terminal sulfur and oxygen groups
Rhodobacter capsulatus
1.17.1.4
[2Fe-2S]-center
-
Rhodobacter capsulatus
Engineering (protein specific)
EC Number
Amino acid exchange
Commentary
Organism
1.17.1.4
E730A
crystal structure determination and analysis, comparison with wild-type enzyme structure, the sulfido is replaced with an oxo ligand in the inactive E730A mutant, further showing another oxo and one Mo-OH ligand at Mo, which are independent of pH
Rhodobacter capsulatus
1.17.1.4
additional information
the enzyme mutants show alterations in the Mo site structure, which changes in a pH range of 5-10, and in the influence of amino acids (Glu730 and Gln179) close to molybdenum cofactor in wild-type, and Q179A and E730A mutants, enzyme kinetics and quantum chemical studies, overview
Rhodobacter capsulatus
1.17.1.4
Q179A
crystal structure determination and analysis, comparison with wild-type enzyme structure, a similar acidic pK for the wild-type and Q179A variants, as well as the metrical parameters of the Mo site and density functional theory calculations, suggested protonation at the equatorial oxo group. Oxidized wild-type and mutant Q179A reveal a similar Mo(VI) ion with each one molybdopterin, Mo=O, Mo-O-, and Mo=S ligand, and a weak Mo-O(E730) bond at alkaline pH
Rhodobacter capsulatus
Metals/Ions (protein specific)
EC Number
Metals/Ions
Commentary
Organism
Structure
1.17.1.4
Molybdenum
in the molybdenum cofactor, the metal ion binds a molybdopterin (MPT) molecule via its dithiolene function and terminal sulfur and oxygen groups. Oxidized wild-type and mutant Q179A reveal a similar Mo(VI) ion with each one molybdopterin, Mo=O, Mo-O-, and Mo=S ligand, and a weak Mo-O(E730) bond at alkaline pH
Rhodobacter capsulatus
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
1.17.1.4
xanthine + NAD+ + H2O
Rhodobacter capsulatus
-
urate + NADH + H+
-
-
?
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.17.1.4
xanthine + NAD+ + H2O
-
745069
Rhodobacter capsulatus
urate + NADH + H+
-
-
-
?
General Information
EC Number
General Information
Commentary
Organism
1.17.1.4
evolution
the enzyme belongs to the xanthine oxidase family
Rhodobacter capsulatus
1.17.1.4
additional information
analysis of the mechanism of transfer of an oxygen atom to the substrate
Rhodobacter capsulatus
General Information (protein specific)
EC Number
General Information
Commentary
Organism
1.17.1.4
evolution
the enzyme belongs to the xanthine oxidase family
Rhodobacter capsulatus
1.17.1.4
additional information
analysis of the mechanism of transfer of an oxygen atom to the substrate
Rhodobacter capsulatus