MetaCyc Enzyme: D-xylose dehydrogenase

Gene: xdh Accession Number: G-12642 (MetaCyc)

Synonyms: HVO_B0028

Species: Haloferax volcanii

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

The native apparent molecular mass was determined by gel filtration chromatography [Johnsen09].

This enzyme was shown to catalyze the first reaction in the oxidative xylose degradation pathway of the halophilic archaeon Haloferax volcanii (see pathway xylose degradation III). It showed 59% amino acid sequence identity to a functionally characterized xylose dehydrogenase from Haloarcula marismortui and 56% identity to an ortholog in Halorubrum lacusprofundi, but was only 11% identical to the bacterial NAD+-dependent xylose dehydrogenase from Caulobacter crescentus CB15 [Johnsen09, Johnsen04].

The enzyme was induced by growth of cells on α-D-xylopyranose (D-xylose). Native enzyme was purified from cell extracts. Recombinant, His-tagged enzyme was expressed in Escherichia coli, but it was catalytically inactive due to misfolding after expression in a nonhalophilic organism. The enzyme was reactivated by denaturation in urea followed by refolding in the presence of salts and substrates, and was purified and characterized [Johnsen09].
The subunit apparent molecular mass was determined by SDS-PAGE to be 55.5 kDa. The discrepancy with the calculated molecular mass of 42.3 kDa is common in halophilic proteins [Johnsen09].
The genome of this organism is composed of a main chromosome of 2.848 Mb, three smaller chromosomes (pHV4, pHV3 and pHV1) and a plasmid pHV2 [Hartman10]. This gene is located on pHV3.

Map Position: [30,784 -> 31,956]

Molecular Weight of Polypeptide: 42.307 kD (from nucleotide sequence), 55.5 kD (experimental) [Johnsen09 ]

Molecular Weight of Multimer: 165.0 kD (experimental) [Johnsen09]

Unification Links: Entrez-gene:8919161 , Protein Model Portal:D4GP29 , UniProt:D4GP29

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 18-Mar-2011 by Fulcher CA , SRI International

Enzymatic reaction of: D-xylose dehydrogenase

Synonyms: 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.

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

This enzyme was highly specific for α-D-xylopyranose as substrate. D-glucose showed a 130-fold lower catalytic efficiency. L-arabinose, D-arabinose, D-ribose, D-mannose and L-mannose were not significantly oxidized. The enzyme was also specific for NADP+ as cofactor and no activity was found with NAD+ [Johnsen09].

Kinetic Parameters:

Km (μM)
a D-xylopyranose


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.

Hartman10: Hartman AL, Norais C, Badger JH, Delmas S, Haldenby S, Madupu R, Robinson J, Khouri H, Ren Q, Lowe TM, Maupin-Furlow J, Pohlschroder M, Daniels C, Pfeiffer F, Allers T, Eisen JA (2010). "The complete genome sequence of Haloferax volcanii DS2, a model archaeon." PLoS One 5(3);e9605. PMID: 20333302

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

Johnsen09: Johnsen U, Dambeck M, Zaiss H, Fuhrer T, Soppa J, Sauer U, Schonheit P (2009). "D-xylose degradation pathway in the halophilic archaeon Haloferax volcanii." J Biol Chem 284(40);27290-303. PMID: 19584053

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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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