D-xylulose reductase

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D-xylulose reductase
1zem.jpg
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
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PMC articles
PubMed articles
NCBI proteins

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.

Contents

Nomenclature

The systematic name of this enzyme class is xylitol:NAD+ 2-oxidoreductase (D-xylulose-forming). Other common names used include : [2]

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:

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 a part 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]

Related Research Articles

A dehydrogenase is an enzyme belonging to the group of oxidoreductases that oxidizes a substrate by reducing an electron acceptor, usually NAD+/NADP+ or a flavin coenzyme such as FAD or FMN. Like all catalysts, they catalyze reverse as well as forward reactions, and in some cases this has physiological significance: for example, alcohol dehydrogenase catalyzes the oxidation of ethanol to acetaldehyde in animals, but in yeast it catalyzes the production of ethanol from acetaldehyde.

<span class="mw-page-title-main">Nicotinamide adenine dinucleotide phosphate</span> Chemical compound

Nicotinamide adenine dinucleotide phosphate, abbreviated NADP+ or, in older notation, TPN (triphosphopyridine nucleotide), is a cofactor used in anabolic reactions, such as the Calvin cycle and lipid and nucleic acid syntheses, which require NADPH as a reducing agent ('hydrogen source'). NADPH is the reduced form, whereas NADP+ is the oxidized form. NADP+ is used by all forms of cellular life.

<span class="mw-page-title-main">6-phosphogluconolactonase</span> Cytosolic enzyme

6-Phosphogluconolactonase (EC 3.1.1.31, 6PGL, PGLS, systematic name 6-phospho-D-glucono-1,5-lactone lactonohydrolase) is a cytosolic enzyme found in all organisms that catalyzes the hydrolysis of 6-phosphogluconolactone to 6-phosphogluconic acid in the oxidative phase of the pentose phosphate pathway:

<span class="mw-page-title-main">L-xylulose reductase</span> Enzyme

Dicarbonyl/L-xylulose reductase, also known as carbonyl reductase II, is an enzyme that in human is encoded by the DCXR gene located on chromosome 17.

<span class="mw-page-title-main">Saccharopine dehydrogenase</span>

In molecular biology, the protein domain Saccharopine dehydrogenase (SDH), also named Saccharopine reductase, is an enzyme involved in the metabolism of the amino acid lysine, via an intermediate substance called saccharopine. The Saccharopine dehydrogenase enzyme can be classified under EC 1.5.1.7, EC 1.5.1.8, EC 1.5.1.9, and EC 1.5.1.10. It has an important function in lysine metabolism and catalyses a reaction in the alpha-Aminoadipic acid pathway. This pathway is unique to fungal organisms therefore, this molecule could be useful in the search for new antibiotics. This protein family also includes saccharopine dehydrogenase and homospermidine synthase. It is found in prokaryotes, eukaryotes and archaea.

<span class="mw-page-title-main">Formate dehydrogenase</span>

Formate dehydrogenases are a set of enzymes that catalyse the oxidation of formate to carbon dioxide, donating the electrons to a second substrate, such as NAD+ in formate:NAD+ oxidoreductase (EC 1.17.1.9) or to a cytochrome in formate:ferricytochrome-b1 oxidoreductase (EC 1.2.2.1). This family of enzymes has attracted attention as inspiration or guidance on methods for the carbon dioxide fixation, relevant to global warming.

<span class="mw-page-title-main">Xylose metabolism</span>

D-Xylose is a five-carbon aldose that can be catabolized or metabolized into useful products by a variety of organisms.

In enzymology, a D-arabinitol 4-dehydrogenase (EC 1.1.1.11) is an enzyme that catalyzes the chemical reaction

In enzymology, a D-xylose 1-dehydrogenase (EC 1.1.1.175) is an enzyme that catalyzes the chemical reaction

In enzymology, a fructuronate reductase (EC 1.1.1.57) is an enzyme that catalyzes the chemical reaction

In enzymology, a glucuronate reductase (EC 1.1.1.19) is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">Glycerate dehydrogenase</span>

In enzymology, a glycerate dehydrogenase (EC 1.1.1.29) is an enzyme that catalyzes the chemical reaction

In enzymology, a hydroxypyruvate reductase (EC 1.1.1.81) is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">L-arabinitol 4-dehydrogenase</span>

In enzymology, a L-arabinitol 4-dehydrogenase (EC 1.1.1.12) is an enzyme that catalyzes the chemical reaction

In enzymology, a ribitol 2-dehydrogenase (EC 1.1.1.56) is an enzyme that catalyzes the chemical reaction

In enzymology, a 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase (EC 1.1.1.127) is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">3-hydroxyacyl-CoA dehydrogenase</span> Enzyme

In enzymology, a 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) is an enzyme that catalyzes the chemical reaction

In enzymology, 3-hydroxybutyrate dehydrogenase (EC 1.1.1.30) is an enzyme that catalyzes the chemical reaction:

<span class="mw-page-title-main">Xylulokinase</span>

In enzymology, a xylulokinase is an enzyme that catalyzes the chemical reaction

D-xylose reductase (EC 1.1.1.307, XylR, XyrA, msXR, dsXR, monospecific xylose reductase, dual specific xylose reductase, NAD(P)H-dependent xylose reductase, xylose reductase) is an enzyme with systematic name xylitol:NAD(P)+ oxidoreductase. This enzyme catalyses the following chemical reaction

References

  1. 1 2 Moss G (2023-07-26). "EC 1.1.1.9". Enzyme Nomenclature. International Union of Biochemistry and Molecular Biology (IUBMB). Retrieved 2023-10-01 via School of Physical and Chemical Sciences, Queen Mary, University of London.
  2. EMBL-EBI. "IntEnz - EC 1.1.1.9". www.ebi.ac.uk. Retrieved 2023-10-03.
  3. Hu QN, Zhu H, Li X, Zhang M, Deng Z, Yang X, Deng Z (2012-12-28). "Assignment of EC numbers to enzymatic reactions with reaction difference fingerprints". PLOS ONE. 7 (12): e52901. doi: 10.1371/journal.pone.0052901 . PMC   3532301 . PMID   23285222.
  4. "1.1.1.9: D-xylulose reductase - BRENDA Enzyme Database". www.brenda-enzymes.info. Retrieved 2023-10-23.
  5. 1 2 3 Ehrensberger AH, Elling RA, Wilson DK (March 2006). "Structure-guided engineering of xylitol dehydrogenase cosubstrate specificity". Structure. 14 (3): 567–575. doi: 10.1016/j.str.2005.11.016 . PMID   16531240.
  6. Kim D, Woo HM (November 2018). "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. PMID   30238140. S2CID   52307667.
  7. Weyda I, Lübeck M, Ahring BK, Lübeck PS (April 2014). "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. doi:10.1007/s10295-014-1415-6. PMC   3953602 . PMID   24570325.
  8. Dmytruk OV, Voronovsky AY, Abbas CA, Dmytruk KV, Ishchuk OP, Sibirny AA (February 2008). "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 . PMID   17662053.
  9. Yamasaki-Yashiki S, Komeda H, Hoshino K, Asano Y (2014). "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. doi: 10.1080/09168451.2014.943646 . PMID   25082263. S2CID   12604939.

Further reading