Glycosyltransferase Family 1 - Revision history

David Teze at 14:26, 11 July 2024

2024-07-11T14:26:09Z

David Teze at 14:23, 11 July 2024

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David Teze at 14:21, 11 July 2024

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David Teze at 14:20, 11 July 2024

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David Teze at 14:12, 11 July 2024

2024-07-11T14:12:41Z

David Teze at 14:11, 11 July 2024

2024-07-11T14:11:58Z

David Teze at 14:07, 11 July 2024

2024-07-11T14:07:51Z

David Teze at 14:07, 11 July 2024

2024-07-11T14:07:24Z

David Teze at 14:06, 11 July 2024

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David Teze at 14:06, 11 July 2024

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 == Catalytic Residues ==
-The large majority of GT1 presents a His-Asp catalytic dyad, acting as a general base. The histidine abstract a proton, increasing the nucleophilicity of the glycosyl acceptor. The aspartate activates the histidine, the abstracted proton being shared almost equally between these two residues <cite>ONS</cite>. However, this His-Asp dyad is not completely conserved, and among the earliest GT1 studied, GtfA, GtfB, and GtfD present an aspartate as a base.
+The large majority of GT1 presents a His-Asp catalytic dyad <cite>Hisfirst</cite>, acting as a general base. The histidine abstract a proton, increasing the nucleophilicity of the glycosyl acceptor. The aspartate activates the histidine, the abstracted proton being shared almost equally between these two residues <cite>ONS</cite>. However, this His-Asp dyad is not completely conserved, and among the earliest GT1 studied, GtfA, GtfB <cite>Mulichak2001</cite>, and GtfD present an aspartate as a base.
 == Three-dimensional structures ==

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 First 3D structure, GtfB (Amycolatopsis orientalis) PDB ID 1IIR in 2001 <cite>Mulichak2001</cite>.
-First His as catalytic base <cite>Hisfirst</cite>.
+First His-Asp as catalytic dyad (His20 Asp119) <cite>Hisfirst</cite>.
 First Asp as catalytic base <cite>Mulichak2001</cite>.

← Older revision		Revision as of 14:21, 11 July 2024
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	First His as catalytic base <cite>Hisfirst</cite>.		First His as catalytic base <cite>Hisfirst</cite>.
		+	First Asp as catalytic base <cite>Mulichak2001</cite>.

	== References ==		== References ==

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 == Kinetics and Mechanism ==
-The overall mechanism of GT1 enzymes features a catalytic base which activates the glycosyl acceptor, while the nucleotide glycosyl donor dissociate into an ion-pair between an oxocarbenium-like glycosyl and the phosphate of the nucleotide <cite>ONS</cite>. Classically, GT1s have ''k''<sub>cat</sub> in the order of magnitude of 1 per second, corresponding to an energy barrier of 17 kcal/mol, and ''K''<sub>M</sub> in the order of the tens of µM. GT1s very often present an acceptor substrate inhibition, which can intriguingly be alleviated with higher enzymes concentrations <cite>Chemostab</cite>.
+The overall mechanism of GT1 enzymes features a catalytic base which activates the glycosyl acceptor, while the nucleotide glycosyl donor dissociate into an ion-pair between an oxocarbenium-like glycosyl and the phosphate of the nucleotide <cite>ONS</cite>. The mechanism is metal ion-independent. Classically, GT1s have ''k''<sub>cat</sub> in the order of magnitude of 1 per second, corresponding to an energy barrier of 17 kcal/mol, and ''K''<sub>M</sub> in the order of the tens of µM. GT1s very often present an acceptor substrate inhibition, which can intriguingly be alleviated with higher enzymes concentrations <cite>Chemostab</cite>.
 == Catalytic Residues ==
-The large majority of GT1 presents a His-Asp catalytic dyad, acting as a general base. The histidine abstract a proton, increasing the nucleophilicity of the glycosyl acceptor. The aspartate activates the histidine, the abstracted proton being shared almost equally between these two residues <cite>ONS</cite>.
+The large majority of GT1 presents a His-Asp catalytic dyad, acting as a general base. The histidine abstract a proton, increasing the nucleophilicity of the glycosyl acceptor. The aspartate activates the histidine, the abstracted proton being shared almost equally between these two residues <cite>ONS</cite>. However, this His-Asp dyad is not completely conserved, and among the earliest GT1 studied, GtfA, GtfB, and GtfD present an aspartate as a base.
 == Three-dimensional structures ==
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 First 3D structure, GtfB (Amycolatopsis orientalis) PDB ID 1IIR in 2001 <cite>Mulichak2001</cite>.
 == References ==
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 #GTfirst pmid=9334165
 #GTsecond pmid=12691742

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 == Substrate specificities ==
-'''Glycosyl donor: nucleotide sugar.''' Family 1 glycosyltransferases or GT1s <cite>DaviesSinnott2008 Cantarel2009</cite> are more often refered to as UGTs, for UDP-dependent glycosyltransferases. Indeed, the most common glycosyl donnor substrates are UDP-α-<small><small>D</small></small>-glycosyl, but other nucleotide sugars can be found as well. They are thus also part of the Leloir glycosyltransferases.
+'''Glycosyl donor: nucleotide sugar.''' Family 1 glycosyltransferases or GT1s <cite>GTfirst DaviesSinnott2008 Cantarel2009</cite> are more often refered to as UGTs, for UDP-dependent glycosyltransferases. Indeed, the most common glycosyl donnor substrates are UDP-α-<small><small>D</small></small>-glycosyl, but other nucleotide sugars can be found as well. They are thus also part of the Leloir glycosyltransferases.
 To date (July 2024), there are no described CAZy subfamilies of GT1s. On the other hand, over hundred subfamilies of GT1s are described in the UGT naming convention system, which organise the enzymes in funtion of the kingdom of their provenance (plant, animal, bacteria) and by phylogeny, based on a system developped for UDP-glucuronyltransferases <cite>Ross2001</cite>. This convention is widely used to name the individual enzymes as well, allowing from the name of the enzyme to know which subfamily it belongs to.

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 == Family Firsts ==
-The GT1 family was first proposed in 2003 <cite>GTfirst</cite>.
+The GT1 family was first proposed in 1997 <cite>GTfirst GTsecond</cite>.
 First 3D structure, GtfB (Amycolatopsis orientalis) PDB ID 1IIR in 2001 <cite>Mulichak2001</cite>.
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 #Ross2001 pmid=11182895
-#GTfirst pmid=12691742
+#GTfirst pmid=9334165
 #Chemostab pmid=35936788

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 == Three-dimensional structures ==
-From 2001 to July 2024, experimental structures of 75 different GT1 enzymes have been deposited, including with donors and acceptors. GT1 present a GT-B fold <cite>Bourne2001</cite>, characterized by two Rossman domains. The N-terminal domain binds the glycosyl acceptor site (+1), and the C-terminal one (-1) binds the glycosyl donor, usually a UDP alpha glycosyl.
+From 2001 to July 2024, experimental structures of 75 different GT1 enzymes have been deposited into the PDB, including with donors and acceptors. GT1 present a GT-B fold <cite>Bourne2001</cite>, characterized by two Rossman domains. The N-terminal domain binds the glycosyl acceptor site (+1), and the C-terminal one (-1) binds the glycosyl donor, usually a UDP alpha glycosyl.
 [[File:GT1---.png]]

← Older revision		Revision as of 14:06, 11 July 2024
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	The GT1 family was first proposed in 2003 <cite>GTfirst</cite>.		The GT1 family was first proposed in 2003 <cite>GTfirst</cite>.
		+
	First 3D structure, GtfB (Amycolatopsis orientalis) PDB ID 1IIR in 2001 <cite>Mulichak2001</cite>.		First 3D structure, GtfB (Amycolatopsis orientalis) PDB ID 1IIR in 2001 <cite>Mulichak2001</cite>.