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MetaCyc Enzyme: D-uronate dehydrogenase

Gene: udh Accession Numbers: G-11981 (MetaCyc), Atu3143

Species: Agrobacterium fabrum C58

Subunit composition of D-uronate dehydrogenase = [Udh]6
         D-uronate dehydrogenase moomer = Udh

Summary:
The enzyme was induced by growth of the organism on D-galacturonate [Boer10]. In earlier work using Agrobacterium tumefaciens strain II BN V6 the enzyme was shown to be induced by growth of the organism on both D-galacturonate and D-glucuronate [Chang69].

The recombinant, six-His tagged polypeptide was expressed in Escherichia coli and purified. Its apparent molecular mass was determined by SDS-PAGE [Yoon09]. A recombinant, N-terminal six-His tagged enzyme has also been expressed in a yeast expression system [Boer10]. The protein forms a hexamer in solution [Parkkinen11].

In earlier work using Agrobacterium tumefaciens strain II BN V6 the enzyme was shown to be induced by growth of the organism on D-galacturonate or D-glucuronate [Chang69].

The recombinant enzyme from Agrobacterium tumefaciens has also been used to develop an assay for D-glucuronate [Moon09a].

The enzyme was shown to accept both α and β anomers of the pyranose form of the substrate D-galacturonate [Boer10]. Using D-glucuronate as substrate, a sudy using circular dichroism analysis suggested that the reaction product was D-glucarate [Yoon09]. A subsequent study using NMR analysis of reactants and products suggested that the actual product of the enzyme's action on galacturonate was D-galactaro-1,4-lactone, which was shown to be stable at cytosolic pH [Boer10]. However, later work showed that the actual product is D-galactaro-1,5-lactone [Andberg12].

Neither D-galactose nor D-galactonate were substrates [Boer10].

Crystal structures have been reported for an apo-form, a ternary form in complex with NADH and product (substrate-soaked structure), and an inactive Y136A mutant in complex with NAD [Parkkinen11]. The crystal structure showed that the enzyme can accept only the β form of D-galacturonate as a substrate, as the O1 hydroxyl group of α-D-galacturonate would clash with the nicotinamide ring of NAD+. This was corroborated by the observation that the β-anomeric form is consumed faster than the α-anomer. Once consumed, the rate of the reaction matches that of the mutarotation from the α to the β from [Parkkinen11].

In earlier work using Agrobacterium tumefaciens strain II BN V6 the enzyme was shown to be induced by growth of the organism on D-galacturonate or D-glucuronate. The reaction was irreversible and NADP+ could not serve as cofactor [Chang69].

Molecular Weight of Polypeptide: 29.047 kD (from nucleotide sequence), 32.0 kD (experimental) [Yoon09 ]

Unification Links: Entrez-Nucleotide:BK006462 , Protein Model Portal:Q7CRQ0 , String:176299.Atu3143 , UniProt:Q7CRQ0

Relationship Links: InterPro:IN-FAMILY:IPR001509 , InterPro:IN-FAMILY:IPR016040 , PDB:Structure:3RFT , PDB:Structure:3RFV , PDB:Structure:3RFX , Pfam:IN-FAMILY:PF01370

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Credits:
Created 21-Apr-2010 by Fulcher CA , SRI International
Revised 23-Mar-2015 by Caspi R , SRI International


Enzymatic reaction of: D-glucuronate dehydrogenase (D-uronate dehydrogenase)

Synonyms: D-glucuronic acid dehydrogenase

EC Number: 1.1.1.203

β-D-glucuronate + NAD+ <=> D-glucaro-1,5-lactone + NADH + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown. [Boer10]

Alternative Substrates for β-D-glucuronate: β-D-galacturonate [Yoon09 ]

In Pathways: superpathway of microbial D-galacturonate and D-glucuronate degradation , D-glucuronate degradation II

Kinetic Parameters:

Substrate
Km (μM)
Citations
NAD+
180.0
[Yoon09]
β-D-glucuronate
370.0
[Yoon09]


Enzymatic reaction of: D-galacturonate dehydrogenase (D-uronate dehydrogenase)

Synonyms: D-galacturonic acid dehydrogenase

EC Number: 1.1.1.203

β-D-galacturonate + NAD+ <=> D-galactaro-1,5-lactone + NADH + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown. [Boer10]

Alternative Substrates for β-D-galacturonate: β-D-glucuronate [Yoon09 ]

In Pathways: superpathway of microbial D-galacturonate and D-glucuronate degradation , D-galacturonate degradation II

Kinetic Parameters:

Substrate
Km (μM)
Citations
NAD+
180.0
[Yoon09]

pH(opt): 8.0 [Yoon09]


References

Andberg12: Andberg M, Maaheimo H, Boer H, Penttila M, Koivula A, Richard P (2012). "Characterization of a novel Agrobacterium tumefaciens galactarolactone cycloisomerase enzyme for direct conversion of D-galactarolactone to 3-deoxy-2-keto-L-threo-hexarate." J Biol Chem 287(21);17662-71. PMID: 22493433

Boer10: Boer H, Maaheimo H, Koivula A, Penttila M, Richard P (2010). "Identification in Agrobacterium tumefaciens of the D-galacturonic acid dehydrogenase gene." Appl Microbiol Biotechnol 86(3);901-9. PMID: 19921179

Chang69: Chang YF, Feingold DS (1969). "Hexuronic acid dehydrogenase of Agrobacterium tumefaciens." J Bacteriol 99(3);667-73. PMID: 4313130

Moon09a: Moon TS, Yoon SH, Tsang Mui Ching MJ, Lanza AM, Prather KL (2009). "Enzymatic assay of D-glucuronate using uronate dehydrogenase." Anal Biochem 392(2);183-5. PMID: 19481054

Parkkinen11: Parkkinen T, Boer H, Janis J, Andberg M, Penttila M, Koivula A, Rouvinen J (2011). "Crystal structure of uronate dehydrogenase from Agrobacterium tumefaciens." J Biol Chem 286(31);27294-300. PMID: 21676870

Richard09: Richard P, Hilditch S (2009). "D-galacturonic acid catabolism in microorganisms and its biotechnological relevance." Appl Microbiol Biotechnol 82(4);597-604. PMID: 19159926

Yoon09: Yoon SH, Moon TS, Iranpour P, Lanza AM, Prather KJ (2009). "Cloning and characterization of uronate dehydrogenases from two pseudomonads and Agrobacterium tumefaciens strain C58." J Bacteriol 191(5);1565-73. PMID: 19060141


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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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