Biology:D-xylulose reductase
| D-xylulose reductase | |||||||||
|---|---|---|---|---|---|---|---|---|---|
 D-xylulose reductase homotetramer, Gluconobacter oxydans | |||||||||
| Identifiers | |||||||||
| EC number | 1.1.1.9 | ||||||||
| CAS number | 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 | ||||||||
| |||||||||
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.
Nomenclature
The systematic name of this enzyme class is xylitol:NAD+ 2-oxidoreductase (D-xylulose-forming). Other common names used include :[2]
- 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
EC number
An Enzyme Commission (EC) number is a classification identifier given to all enzymes that helps identify their function and relationships to other enzymes.[3] 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]
Catalyzed reaction
D-xylulose reductase catalyzes the chemical reaction
xylitol + NAD+ ⇌ D-xylulose + NADH + H+[4]
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.
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.[5]
Role in metabolism
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.[6]
Species distribution
D-xylulose reductase is found in both prokaryotes and eukaryotes; including molds, yeasts, and fungi.
Structure
Only one structure has been solved for this enzyme, under the Protein Data Bank accession code 1ZEM.[5] 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.
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.[5]
Function
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.[7]
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.[8]
In fungi d-xylulose reductase also ferments xylose into ethanol as a result of metabolic conditions (such as anaerobic conditions).[9]
References
- ↑ 1.0 1.1 "EC 1.1.1.9". Enzyme Nomenclature. International Union of Biochemistry and Molecular Biology (IUBMB). 2023-07-26. https://iubmb.qmul.ac.uk/enzyme/EC1/1/1/9.html.
- ↑ EMBL-EBI. "IntEnz - EC 1.1.1.9". https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=1.1.1.9.
- ↑ "Assignment of EC numbers to enzymatic reactions with reaction difference fingerprints". PLOS ONE 7 (12): e52901. 2012-12-28. doi:10.1371/journal.pone.0052901. PMID 23285222.
- ↑ "1.1.1.9: D-xylulose reductase - BRENDA Enzyme Database". https://www.brenda-enzymes.info/all_enzymes.php?ecno=1.1.1.9&table=Reaction.
- ↑ 5.0 5.1 5.2 "Structure-guided engineering of xylitol dehydrogenase cosubstrate specificity". Structure 14 (3): 567–575. March 2006. doi:10.1016/j.str.2005.11.016. PMID 16531240.
- ↑ "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. November 2018. doi:10.1007/s00253-018-9353-2. PMID 30238140.
- ↑ "Point mutation of the xylose reductase (XR) gene reduces xylitol accumulation and increases citric acid production in Aspergillus carbonarius". Journal of Industrial Microbiology & Biotechnology 41 (4): 733–739. April 2014. doi:10.1007/s10295-014-1415-6. PMID 24570325.
- ↑ "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. February 2008. doi:10.1111/j.1567-1364.2007.00289.x. PMID 17662053.
- ↑ "Molecular analysis of NAD⁺-dependent xylitol dehydrogenase from the zygomycetous fungus Rhizomucor pusillus and reversal of the coenzyme preference". Bioscience, Biotechnology, and Biochemistry 78 (11): 1943–53. 2014. doi:10.1080/09168451.2014.943646. PMID 25082263.
Further reading
- "A new pathway of pentose metabolism". Biochemical and Biophysical Research Communications 3 (5): 554–559. November 1960. doi:10.1016/0006-291X(60)90174-1. PMID 13692998.
- "A sensitive and stereospecific enzymatic assay for xylulose". The Journal of Biological Chemistry 234 (4): 758–761. April 1959. doi:10.1016/s0021-9258(18)70169-5. PMID 13654257.
- "Erythritol dehydrogenase from Aerobacter aerogenes". Biochimica et Biophysica Acta 48 (1): 26–32. March 1961. doi:10.1016/0006-3002(61)90511-X. PMID 13789254.
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