User:Mgood09/D-xylulose reductase
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| D-xylulose reductase | |||||||||
|---|---|---|---|---|---|---|---|---|---|
 D-xylulose reductase homotetramer, Gluconobacter oxydans | |||||||||
| Identifiers | |||||||||
| EC no. | 1.1.1.9 | ||||||||
| CAS no. | 9028-16-4 | ||||||||
| Databases | |||||||||
| IntEnz | IntEnz view | ||||||||
| BRENDA | BRENDA entry | ||||||||
| ExPASy | NiceZyme view | ||||||||
| KEGG | KEGG entry | ||||||||
| MetaCyc | metabolic pathway | ||||||||
| PRIAM | profile | ||||||||
| PDB structures | RCSB PDB PDBe PDBsum | ||||||||
| Gene Ontology | AmiGO / QuickGO | ||||||||
| |||||||||
The Enzyme
[edit]In enzymology, a D-xylulose reductase (EC 1.1.1.9) is an enzyme that is classified as an Oxidoreductase (EC 1) specifically acting on the CH-OH group of donors (EC 1.1.1) that uses NAD+ or NADP+ as an acceptor (EC 1.1.1.9).[1] This enzyme participates in pentose and glucuronate interconversions; a set of metabolic pathways that involve converting pentose sugars and glucuronate into other compounds.
The systematic name of this enzyme class is xylitol:NAD+ 2-oxidoreductase (D-xylulose-forming). Other common names used include NAD+-dependent xylitol dehydrogenase, xylitol dehydrogenase, erythritol dehydrogenase (as this enzyme also acts as an L-erythrylose reductase), 2,3-cis-polyol(DPN) dehydrogenase (C3-5), pentitol-DPN dehydrogenase, and xylitol-2-dehydrogenase.[2]
EC number
[edit]An Enzyme Commission (EC) number is a classification identifier given to all enzymes that helps identify their function and relationships to other enzymes. The EC number for D-xylulose reductase is 1.1.1.9, the breakdown is as follows:
EC 1: Oxidoreductase enzymes
EC 1.1.1: An oxidoreductase enzyme that acts on CH-OH group of donors
EC 1.1.1.9: An oxidoreductase enzyme that acts on the CH-OH group of donors that uses NAD+ or NADP+ as an acceptor[1]
The Reaction
[edit]D-xylulose reductase catalyzes the chemical reaction
xylitol + NAD+ ⇌ D-xylulose + NADH + H+
where xylitol and NAD are the substrates and D-xylulose, NADH and H+ are the products.
NAD+ acts as the coenzyme for the chemical reaction.
Catalysis
[edit]The enzyme is apart of a class called short-chain dehydrogenase/reductases (SDRs) enzyme class which are catalyzed by the amino acid tyrosine which acts as an acid or base. Additionally, hydrogen bonding within the enzyme is thought to help with catalysis by changing the surrounding environment to be favorable towards the reaction.[3]
D-xylulose Reductases Role In Cellular Metabolism
[edit]In cellular metabolism D-xylulose reductase is essential in various organisms. In bacteria, D-xylulose reductase is the second step of D-xylose metabolism which is necessary cellular growth. First, D-xylose is converted to xylitol which then is converted to D-xylulose when D-xylulose reductase exchanges NAD+ for NADH. D-xylulose then becomes phosphorylated, and proceeds through the rest of the cycle to create α-ketoglutarate which eventually enters the TCA cycle for energy production.[4]
Organisms and Function
[edit]D-xylulose reductase is found in both prokaryotes and eukaryotes; including molds, yeasts, and fungi.
One example of a mold that uses the enzyme is Aspergillus carbonarius; where the enzyme creates an intermediate for the pentose phosphate pathway. D-xylose is converted to xylitol by xylose reductase, then xylitol is converted to xylulose by D-xylulose reductase, afterwards xylulose is converted to xylulose-5-phosphate by xylulokinase and xylulose-5-P then goes into the pentose phosphate pathway for energy and intermediates production.[5]
In yeast, such as Hansenula polymorpha d-xylulose reductase has been found to help ferment xylose into ethanol, however it usually results in an accumulation of xylitol due to the imbalance between cofactor preferences in xylose reductase and xylulose reductase.[6]
In fungi d-xylulose reductase also ferments xylose into ethanol as a result of metabolic conditions (such as anaerobic conditions). [7]
Only one structure has been solved for this enzyme, under the Protein Data Bank accession code 1ZEM. The enzyme has 262 amino acid residues and is a tetramer. Each monomer has a Rossman fold domain made up of seven β sheets side by side with three short α helices on one end of the sheet and three longer α helices on the other. There are two shorter helices that stay outside of this Rossman fold.
The N-terminal region of the primary sequence has been found to be responsible for the selectivity of binding NAD+, and the active site is located between helices αFG1, αFG2 and the C-terminal end of the β sheet.
Structure and Function
[edit]Some images of D-xylulose reductase show magnesium bound, this is because the solution used to grow the protein crystals for visualization that were used contained 100mM of MgCl2. However it has been found that D-xylulose reductase is not inhibited by magnesium; it has even been suggested that magnesium may be important for stabilization and formation of the oligomers.
Additional references[9][10][11]
References
[edit]- ^ a b Moss, Gerry (7-26-2023). "Enzyme Nomenclature". iubmb. Retrieved 10-1-2023.
{{cite web}}: Check date values in:|access-date=and|date=(help)CS1 maint: url-status (link) - ^ EMBL-EBI. "IntEnz - EC 1.1.1.9". www.ebi.ac.uk. Retrieved 2023-10-03.
- ^ Ehrensberger, Andreas H.; Elling, Robert A.; Wilson, David K. (2006-03). "Structure-Guided Engineering of Xylitol Dehydrogenase Cosubstrate Specificity". Structure. 14 (3): 567–575. doi:10.1016/j.str.2005.11.016. ISSN 0969-2126.
{{cite journal}}: Check date values in:|date=(help) - ^ Kim, Donghyuk; Woo, Han Min (2018-11-01). "Deciphering bacterial xylose metabolism and metabolic engineering of industrial microorganisms for use as efficient microbial cell factories". Applied Microbiology and Biotechnology. 102 (22): 9471–9480. doi:10.1007/s00253-018-9353-2. ISSN 1432-0614.
- ^ Weyda, István; Lübeck, Mette; Ahring, Birgitte K; Lübeck, Peter S (2014-04-01). "Point mutation of the xylose reductase (XR) gene reduces xylitol accumulation and increases citric acid production in Aspergillus carbonarius". Journal of Industrial Microbiology and Biotechnology. 41 (4): 733–739. doi:10.1007/s10295-014-1415-6. ISSN 1476-5535. PMC 3953602. PMID 24570325.
{{cite journal}}: CS1 maint: PMC format (link) - ^ Dmytruk, Olena V.; Voronovsky, Andriy Y.; Abbas, Charles A.; Dmytruk, Kostyantyn V.; Ishchuk, Olena P.; Sibirny, Andriy A. (2008-02). "Overexpression of bacterial xylose isomerase and yeast host xylulokinase improves xylose alcoholic fermentation in the thermotolerant yeast Hansenula polymorpha". FEMS Yeast Research. 8 (1): 165–173. doi:10.1111/j.1567-1364.2007.00289.x.
{{cite journal}}: Check date values in:|date=(help) - ^ academic.oup.com. doi:10.1080/09168451.2014.943646 https://academic.oup.com/bbb/article/78/11/1943/5938359. Retrieved 2023-10-03.
{{cite web}}: Missing or empty|title=(help) - ^ Ehrensberger, Andreas H.; Elling, Robert A.; Wilson, David K. (2006-03). "Structure-Guided Engineering of Xylitol Dehydrogenase Cosubstrate Specificity". Structure. 14 (3): 567–575. doi:10.1016/j.str.2005.11.016. ISSN 0969-2126.
{{cite journal}}: Check date values in:|date=(help) - ^ Chiang, Ching; Knight, S. G. (1960-11-01). "A new pathway of pentose metabolism". Biochemical and Biophysical Research Communications. 3 (5): 554–559. doi:10.1016/0006-291X(60)90174-1. ISSN 0006-291X.
- ^ Hickman, Jean; Ashwell, Gilbert (1959-04). "A Sensitive and Stereospecific Enzymatic Assay for Xylulose". Journal of Biological Chemistry. 234 (4): 758–761. doi:10.1016/s0021-9258(18)70169-5. ISSN 0021-9258.
{{cite journal}}: Check date values in:|date=(help) - ^ Jakoby, William B.; Fredericks, Joan (1961-03-18). "Erythritol dehydrogenase from Aerobacter aerogenes". Biochimica et Biophysica Acta. 48 (1): 26–32. doi:10.1016/0006-3002(61)90511-X. ISSN 0006-3002.