N-acetylglucosamine-6-phosphate deacetylase: Difference between revisions
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GlcNAc-6-phosphate deacetylase is encoded by the gene NagA. |
GlcNAc-6-phosphate deacetylase is encoded by the gene NagA. |
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This enzyme belongs to the [[amidohydrolase]] superfamily. Amidohydrolases are a type of [[hydrolase]] that acts upon amide bonds. All members of the amidohydrolase family employ a [[TIM barrel]] structure, and a vast majority of members are [[Metalloprotein|metalloenzymes]].<ref>{{Citation|last=Liu|first=Aimin|title=Amidohydrolase Superfamily|date=2014-08-15|url=http://doi.wiley.com/10.1002/9780470015902.a0020546.pub2|work=eLS|editor-last=John Wiley & Sons Ltd|publisher=John Wiley & Sons, Ltd|language=en|doi=10.1002/9780470015902.a0020546.pub2|isbn=9780470015902|access-date=2019-03-09|last2=Huo|first2=Lu}}</ref> The family of enzymes is important in amino acid and nucleotide metabolism as well as biodegradation of agricultural and industrial compounds. NagA participates in amino-sugar metabolism, specifically in the biosynthesis of amino-sugar-nucleotides. |
This enzyme belongs to the [[amidohydrolase]] superfamily. Amidohydrolases are a type of [[hydrolase]] that acts upon amide bonds. All members of the amidohydrolase family employ a [[TIM barrel]] structure, and a vast majority of members are [[Metalloprotein|metalloenzymes]].<ref>{{Citation|last=Liu|first=Aimin|title=Amidohydrolase Superfamily|date=2014-08-15|url=http://doi.wiley.com/10.1002/9780470015902.a0020546.pub2|work=eLS|editor-last=John Wiley & Sons Ltd|publisher=John Wiley & Sons, Ltd|language=en|doi=10.1002/9780470015902.a0020546.pub2|isbn=9780470015902|access-date=2019-03-09|last2=Huo|first2=Lu}}</ref> The family of enzymes is important in amino acid and nucleotide metabolism as well as biodegradation of agricultural and industrial compounds. NagA participates in amino-sugar metabolism, specifically in the biosynthesis of amino-sugar-nucleotides.<ref>{{Cite journal|last=Kaplan|first=David L.|last2=Lee|first2=Kyongbum|last3=Numuta|first3=Keiji|last4=Shi|first4=Hai|last5=Panilaitis|first5=Bruce|last6=Yadav|first6=Vikas|date=2011-06-02|title=N-acetylglucosamine 6-Phosphate Deacetylase (nagA) Is Required for N-acetyl Glucosamine Assimilation in Gluconacetobacter xylinus|url=https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0018099|journal=PLOS ONE|language=en|volume=6|issue=6|pages=e18099|doi=10.1371/journal.pone.0018099|issn=1932-6203|pmc=PMC3107205|pmid=21655093}}</ref> |
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The systematic name of this enzyme class is '''N-acetyl-D-glucosamine-6-phosphate amidohydrolase'''. Other names in common use include '''acetylglucosamine phosphate deacetylase''', '''acetylaminodeoxyglucosephosphate acetylhydrolase''', and '''2-acetamido-2-deoxy-D-glucose-6-phosphate amidohydrolase'''. |
The systematic name of this enzyme class is '''N-acetyl-D-glucosamine-6-phosphate amidohydrolase'''. Other names in common use include '''acetylglucosamine phosphate deacetylase''', '''acetylaminodeoxyglucosephosphate acetylhydrolase''', and '''2-acetamido-2-deoxy-D-glucose-6-phosphate amidohydrolase'''. |
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=== PG Recycling Pathway === |
=== PG Recycling Pathway === |
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In the PG Recycling pathway, once GlcNAc-6-P is metabolized by NagA, its product GlcN-6-P can then be converted to GlcN-1-P by the enzyme GlmM, followed by reacetylation and reaction with UTP by GlmU to form UDP-GlcNAc.<ref name=":3" /><ref name=":4" /> UDP-GlcNAc is the end product of this pathway, which is then used to make [[Glycosaminoglycan|glycosaminoglycans]], [[proteoglycans]], and [[glycolipids]], which are all necessary in order to replenish PG for the cell wall.<ref>{{Cite journal|last=Milewski|first=Sławomir|last2=Gabriel|first2=Iwona|last3=Olchowy|first3=Jarosław|date=2006-01-15|title=Enzymes of UDP-GlcNAc biosynthesis in yeast|url=http://doi.wiley.com/10.1002/yea.1337|journal=Yeast|language=en|volume=23|issue=1|pages=1–14|doi=10.1002/yea.1337|issn=0749-503X}}</ref> |
In the PG Recycling pathway, once GlcNAc-6-P is metabolized by NagA, its product, GlcN-6-P, can then be converted to GlcN-1-P by the enzyme GlmM, followed by reacetylation and reaction with UTP by GlmU to form UDP-GlcNAc.<ref name=":3" /><ref name=":4" /> UDP-GlcNAc is the end product of this pathway, which is then used to make [[Glycosaminoglycan|glycosaminoglycans]], [[proteoglycans]], and [[glycolipids]], which are all necessary in order to replenish PG for the cell wall.<ref>{{Cite journal|last=Milewski|first=Sławomir|last2=Gabriel|first2=Iwona|last3=Olchowy|first3=Jarosław|date=2006-01-15|title=Enzymes of UDP-GlcNAc biosynthesis in yeast|url=http://doi.wiley.com/10.1002/yea.1337|journal=Yeast|language=en|volume=23|issue=1|pages=1–14|doi=10.1002/yea.1337|issn=0749-503X}}</ref> |
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=== Glycolysis Pathway === |
=== Glycolysis Pathway === |
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Revision as of 07:34, 9 March 2019
| N-acetylglucosamine-6-phosphate deacetylase | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||
| EC no. | 3.5.1.25 | ||||||||
| CAS no. | 9027-50-3 | ||||||||
| 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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In enzymology, N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25), also known as GlcNAc-6-phosphate deacetylase or NagA, is an enzyme that catalyzes the deacetylation of N-acetylglucosamine-6-phosphate (GlcNAc-6-P) to glucosamine-6-phosphate (GlcN-6-P):
- H2O + N-acetyl-D-glucosamine 6-phosphate acetate + D-glucosamine 6-phosphate
NagA Reaction
GlcNAc-6-phosphate deacetylase is encoded by the gene NagA.
This enzyme belongs to the amidohydrolase superfamily. Amidohydrolases are a type of hydrolase that acts upon amide bonds. All members of the amidohydrolase family employ a TIM barrel structure, and a vast majority of members are metalloenzymes.[1] The family of enzymes is important in amino acid and nucleotide metabolism as well as biodegradation of agricultural and industrial compounds. NagA participates in amino-sugar metabolism, specifically in the biosynthesis of amino-sugar-nucleotides.[2]
The systematic name of this enzyme class is N-acetyl-D-glucosamine-6-phosphate amidohydrolase. Other names in common use include acetylglucosamine phosphate deacetylase, acetylaminodeoxyglucosephosphate acetylhydrolase, and 2-acetamido-2-deoxy-D-glucose-6-phosphate amidohydrolase.
Enzyme Structure
Tertiary Structure
All NagA structures characterized to date reveal a similar overall architecture and arrangement of two domains.[3] Domain I comprises a (β/α)8 - barrel structural fold, also known as a TIM barrel, that forms the dimeric interface with domain I of the neighboring subunit.[3] This dimeric interface enables the formation of two identical active sites that are involved in substrate and metal co-factor recognition. The smaller second domain of NagA enzymes comprises a β-barrel with unknown biological functions.[3] While all members of the amidohydrolase superfamily employ a TIM-barrel structural fold, NagA in E.coli has a pseudo-TIM barrel enclosing the funnel-like catalytic site of the enzyme.[4]
Metal-Binding Capabilities
GlcNAc-6-P deacetylase in E.coli contains a mononuclear metal-binding site with a Zn2+ ion; in addition, NagA in E.coli shows a phosphate ion bound at the metal-binding site.[4] Unlike NagA of E.coli, NagA of Mycobacterium smegmatis (MSNagA), Thermotoga maritima, and Bacillus subtilis have binuclear metal-binding sites. MSNagA has two divalent metal ions located in each active site, which are both required for efficient catalysis and structural stability.[3] While the other bacteria species use Zn as their metal co-factor, NagA in Bacillus subtilis utilizes iron as the predominant metal in the metal-binding site.[5]
Active Site
A notable difference between mycobacterial NagA enzymes and NagA enzymes from other bacterial species is the presence of a cysteine at position 131. Other bacterial species have a lysine residue at this position.[3]
Enzyme Mechanism
The catalytic mechanism for NagA enzymes proposed utilizes nucleophilic attack via a metal-coordinated water molecule or hydroxide ion. The mechanism proceeds via a strictly conserved active-site aspartic acid residue that acts initially as a base to activate the hydrolytic water molecule and then as an acid to protonate the amine leaving group. Elimination NagA produces high levels of the allosteric activator GlcNAc-6-P, derived from the recycling of peptidoglycan of the bacterial cell walls. One proposed mechanism using the NagA from Bacillus subtilis and its two iron co-factors in the metal-binding site demonstrates the nucleophilic attack by an Fe-bridged hydroxide and then the stabilization of the carbonyl oxygen by one of the two Fe atoms.[5]
Biological Function and Involved Pathways
NagA is located in the cytoplasm of the cell. N-acetylglucosamine (GlcNAc) enters the cell as part of the breakdown of the cell wall. GlcNAc, a monosaccharide and derivative of glucose, is part of a biopolymer in the bacterial cell wall. This biopolymer forms a layered structure called peptidoglycan (PG). GlcNAc is then converted into GlcNAc-6-P by the enzyme NagE.[6] This substrate is then deacetylated into acetate and GlcN-6-P by NagA.[7] NagA is important for the production of GlcN-6-P, which is then used in two main pathways: PG recycling pathway and the glycolysis pathway.
PG Recycling Pathway
In the PG Recycling pathway, once GlcNAc-6-P is metabolized by NagA, its product, GlcN-6-P, can then be converted to GlcN-1-P by the enzyme GlmM, followed by reacetylation and reaction with UTP by GlmU to form UDP-GlcNAc.[6][7] UDP-GlcNAc is the end product of this pathway, which is then used to make glycosaminoglycans, proteoglycans, and glycolipids, which are all necessary in order to replenish PG for the cell wall.[8]
Glycolysis Pathway
Instead of entering the PG recycling pathway, GlcN-6-P can be converted into fructose-6-phosphate by NagB. This reaction is reversible by the enzyme GlmS.[6][7] The produced fructose-6-phosphate then enters the glycolysis pathway. Glycolysis catalyzes the production of pyruvate, leading to the citric acid cycle and allowing for the production of amino acids.
Disease Relevance
The gene NagA is a potential drug target of Mycobacterium tuberculosis (Mtb) because NagA represents the key enzymatic step in the generation of essential amino-sugar precursors required for Mtb cell wall biosynthesis and also influences recycling of cell wall peptidoglycan fragments.[3]
Structural studies
As of early 2019, 11 structures have been solved for this class of enzymes, with PDB accession codes 1O12, 1UN7, 1YMY, 1YRR, 2P50, 2P53, 6FV3, 6FV4, 3EGJ, 3IV8, and 2VHL.
References
- ^ Liu, Aimin; Huo, Lu (2014-08-15), John Wiley & Sons Ltd (ed.), "Amidohydrolase Superfamily", eLS, John Wiley & Sons, Ltd, doi:10.1002/9780470015902.a0020546.pub2, ISBN 9780470015902, retrieved 2019-03-09
- ^ Kaplan, David L.; Lee, Kyongbum; Numuta, Keiji; Shi, Hai; Panilaitis, Bruce; Yadav, Vikas (2011-06-02). "N-acetylglucosamine 6-Phosphate Deacetylase (nagA) Is Required for N-acetyl Glucosamine Assimilation in Gluconacetobacter xylinus". PLOS ONE. 6 (6): e18099. doi:10.1371/journal.pone.0018099. ISSN 1932-6203. PMC 3107205. PMID 21655093.
{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link) - ^ a b c d e f Ahangar, Mohd Syed; Furze, Christopher M.; Guy, Collette S.; Cooper, Charlotte; Maskew, Kathryn S.; Graham, Ben; Cameron, Alexander D.; Fullam, Elizabeth (2018-06-22). "Structural and functional determination of homologs of the Mycobacterium tuberculosis N -acetylglucosamine-6-phosphate deacetylase (NagA)". Journal of Biological Chemistry. 293 (25): 9770–9783. doi:10.1074/jbc.RA118.002597. ISSN 0021-9258. PMC 6016474. PMID 29728457.
{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link) - ^ a b "ScienceDirect". www.sciencedirect.com. doi:10.1016/j.jmb.2006.03.024. Retrieved 2019-03-09.
- ^ a b Vincent, Florence; Yates, David; Garman, Elspeth; Davies, Gideon J.; Brannigan, James A. (2004-01-23). "The Three-dimensional Structure of the N -Acetylglucosamine-6-phosphate Deacetylase, NagA, from Bacillus subtilis: A MEMBER OF THE UREASE SUPERFAMILY". Journal of Biological Chemistry. 279 (4): 2809–2816. doi:10.1074/jbc.M310165200. ISSN 0021-9258.
{{cite journal}}: CS1 maint: unflagged free DOI (link) - ^ a b c Park, J. T.; Uehara, T. (2008-06-01). "How Bacteria Consume Their Own Exoskeletons (Turnover and Recycling of Cell Wall Peptidoglycan)". Microbiology and Molecular Biology Reviews. 72 (2): 211–227. doi:10.1128/MMBR.00027-07. ISSN 1092-2172. PMC 2415748. PMID 18535144.
{{cite journal}}: CS1 maint: PMC format (link) - ^ a b c Plumbridge, J. (2009-09-15). "An Alternative Route for Recycling of N-Acetylglucosamine from Peptidoglycan Involves the N-Acetylglucosamine Phosphotransferase System in Escherichia coli". Journal of Bacteriology. 191 (18): 5641–5647. doi:10.1128/JB.00448-09. ISSN 0021-9193. PMC 2737974. PMID 19617367.
{{cite journal}}: CS1 maint: PMC format (link) - ^ Milewski, Sławomir; Gabriel, Iwona; Olchowy, Jarosław (2006-01-15). "Enzymes of UDP-GlcNAc biosynthesis in yeast". Yeast. 23 (1): 1–14. doi:10.1002/yea.1337. ISSN 0749-503X.
- White RJ, Pasternak CA (1967). "The purification and properties of N-acetylglucosamine 6-phosphate deacetylase from Escherichia coli". Biochem. J. 105 (1): 121–5. PMC 1198282. PMID 4861885.
- Yamano N, Matsushita Y, Kamada Y, Fujishima S, Arita M (1996). "Purification and characterization of N-acetylglucosamine 6-phosphate deacetylase with activity against N-acetylglucosamine from Vibrio cholerae non-O1". Biosci. Biotechnol. Biochem. 60 (8): 1320–3. doi:10.1271/bbb.60.1320. PMID 8987551.