MetaCyc Enzyme: D-xylose dehydrogenase

Gene: xdh Accession Number: G-12655 (MetaCyc)

Synonyms: rrnAC3034, gfo6

Species: Haloarcula marismortui

Subunit composition of D-xylose dehydrogenase = [Xdh]4
         D-xylose dehydrogenase subunit = Xdh

The native complex apparent molecular mass was determined to be 175 kDa by gel filtration chromatography and the enzyme was proposed to be a homotetramer [Johnsen04].

This enzyme showed a 41% amino acid sequence similarity to glucose-fructose oxidoreductase (GFOR) from Zymomonas mobilis [Johnsen04].

The enzyme was induced upon growth of cells on α-D-xylopyranose (D-xylose). Native enzyme was purified from cell extracts. Recombinant enzyme was expressed in inclusion bodies in Escherichia coli. It was activated by denaturation in urea followed by refolding in the presence of salts, glutathione and substrates, with subsequent purification and characterization [Johnsen04].
The native subunit apparent molecular mass was determined by SDS-PAGE to be 57 kDa. The discrepancy with the calculated molecular mass of 39.9 kDa is common in halophilic proteins [Johnsen04].

Map Position: [2,693,010 <- 2,694,092]

Molecular Weight of Polypeptide: 39.937 kD (from nucleotide sequence), 57.0 kD (experimental) [Johnsen04 ]

Molecular Weight of Multimer: 175.0 kD (experimental) [Johnsen04]

Unification Links: Entrez-gene:3130318 , Protein Model Portal:Q5UY95 , String:272569.rrnAC3034 , UniProt:Q5UY95

Relationship Links: InterPro:IN-FAMILY:IPR000683 , InterPro:IN-FAMILY:IPR004104 , InterPro:IN-FAMILY:IPR016040 , Pfam:IN-FAMILY:PF01408 , Pfam:IN-FAMILY:PF02894

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Created 21-Mar-2011 by Fulcher CA , SRI International

Enzymatic reaction of: D-xylose dehydrogenase

EC Number:

a D-xylopyranose + NADP+ <=> D-xylonolactone + NADPH + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

This reaction is reversible.

Alternative Substrates for NADP+: NAD+ [Johnsen04 ]

Alternative Substrates for a D-xylopyranose: D-ribose [Johnsen04 ] , D-glucose [Johnsen04 ] , D-galactose [Johnsen04 ]

In Pathways: superpathway of pentose and pentitol degradation , xylose degradation III

Kinetic parameters are for the native enzyme purified from cell extracts (the apparent Vmax of the recombinant enzyme was approximately 40% lower). The enzyme utilized both NADP+ and NAD+ as cosubstrate but had a 6-fold higher apparent Km for NAD+ indicating that NADP+ is the physiological electron acceptor [Johnsen04].

This enzyme efficiently utilized both α-D-xylopyranose and D-ribose as substrate but the highest catalytic efficiency was obtained using α-D-xylopyranose and NADP+. D-glucose showed a 70-fold lower catalytic efficiency and D-galactose was even less efficient as a substrate. D-arabinose and D-fructose were not significantly oxidized [Johnsen04].

This halophilic enzyme was strongly stimulated by 1.5 M potassium chloride, 1.5 M sodium chloride, or 100 mM MgCl2 The rate dependence on pH and temperature was assayed in the presence of 1.5 M potassium chloride [Johnsen04].

Activators (Unknown Mechanism): Mg2+ [Johnsen04] , potassium chloride [Johnsen04] , sodium chloride [Johnsen04]

Kinetic Parameters:

Km (μM)
a D-xylopyranose

T(opt): 50 °C [Johnsen04]

pH(opt): 8.3 [Johnsen04]


Drew98: Drew KN, Zajicek J, Bondo G, Bose B, Serianni AS (1998). "13C-labeled aldopentoses: detection and quantitation of cyclic and acyclic forms by heteronuclear 1D and 2D NMR spectroscopy." Carbohydrate Research 307(3-4);199-209.

Johnsen04: Johnsen U, Schonheit P (2004). "Novel xylose dehydrogenase in the halophilic archaeon Haloarcula marismortui." J Bacteriol 186(18);6198-207. PMID: 15342590

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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
Page generated by SRI International Pathway Tools version 19.0 on Tue Oct 6, 2015, biocyc14.