Glycosyltransferases - Revision history

Spencer Williams: /* References */

2021-01-07T11:47:01Z

References

Spencer Williams: /* Leloir GTs */

2021-01-07T11:45:52Z

Leloir GTs

Spencer Williams: /* 3-D folds */

2017-03-19T04:43:22Z

3-D folds

Spencer Williams: /* Example structures */

2017-03-19T04:43:01Z

Example structures

Spencer Williams: /* Example structures */

2017-03-19T04:41:06Z

Example structures

Spencer Williams at 04:48, 9 December 2013

2013-12-09T04:48:31Z

Harry Brumer: fixed broken Unligil2000 reference

2013-10-16T15:17:26Z

fixed broken Unligil2000 reference

Spencer Williams: /* Retaining glycosyltransferases */

2013-06-27T05:42:44Z

Retaining glycosyltransferases

Spencer Williams: /* Retaining glycosyltransferases */

2013-06-27T03:56:46Z

Retaining glycosyltransferases

Spencer Williams at 03:56, 27 June 2013

2013-06-27T03:56:33Z

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 #Lizak2011 pmid=21677752
 #Lee2011 pmid=21822275
 </biblio>
 [[Category:Definitions and explanations]]

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 === Leloir GTs ===
-Sugar nucleotide-dependent (Leloir) glycosyltransferases have been found to possess only two different folds, termed the GT-A and GT-B folds <cite>Unligil2000</cite>. The GT-A fold is typified by the first member to have its X-ray structure determined, SpsA from''Bacillus subtilus'' <cite>Charnock1999</cite>. The GT-A fold consists of two dissimilar domains, one involved in nucleotide binding and the other binding the acceptor. The GT-B fold was exemplified by its first member, the beta-glucosyltransferase from bacteriophage T4 <cite>Vrielink1994</cite>. The GT-B fold consists of two similar Rossmann fold subdomains.
+Sugar nucleotide-dependent (Leloir) glycosyltransferases have been found to possess a range of different folds. The main folds are termed the GT-A and GT-B folds <cite>Unligil2000</cite>. The GT-A fold is typified by the first member to have its X-ray structure determined, SpsA from''Bacillus subtilus'' <cite>Charnock1999</cite>. The GT-A fold consists of two dissimilar domains, one involved in nucleotide binding and the other binding the acceptor. The GT-B fold was exemplified by its first member, the beta-glucosyltransferase from bacteriophage T4 <cite>Vrielink1994</cite>. The GT-B fold consists of two similar Rossmann fold subdomains. The mannosyltransferases of family [[GT108]] possess a 5-bladed beta-propeller fold, similar to family [[GH130]] glycoside phosphorylases <cite>Sernee2019</cite>.
 === Non-Leloir GTs ===

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 === Non-Leloir GTs ===
 Non-Leloir glycosyltransferases possess non-GT-A and -B folds. For example, the polymerizing glycosyltransferase transglycosylase, which catalyzes the condensation of oligosaccharyl polyprenolphosphate to generate the carbohydrate backbone of peptidoglycan has a bacteriophage-lysozyme-like fold <cite>Lovering2007</cite>. The ''Pyrococcus furiosius'' oligosaccharyltransferase STT3, which catalyzes the transfer of a preformed oligosaccharide from a dolichol phosphate glycosyl donor to form asparagine-linked glycoproteins, possesses a novel fold; however, this crystallized fragment is catalytically-inactive and may not represent the structure of the complete glycosyltransferase <cite>Igura2008</cite>. The same fold is also observed in the periplasmic domain of the PglB  oligosaccharyltransferase of ''Camplyobacter lari''; this latter protein was been crystallized as a full length protein incorporating a transmembrane domain that retains transferase activity <cite>Lizak2011</cite>. A structure of PglB oligosaccharyltransferase in complex with a hexapeptide substrate showed that the peptide binds to both the periplasmic domain and the transmembrane domain. These data demonstrate that the transmembrane domain of this bacterial oligosaccharyltransferase is required for both substrate binding and catalysis.
 <!-- The figures below have been inactivated because of problems running Java applets

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 === Non-Leloir GTs ===
 Non-Leloir glycosyltransferases possess non-GT-A and -B folds. For example, the polymerizing glycosyltransferase transglycosylase, which catalyzes the condensation of oligosaccharyl polyprenolphosphate to generate the carbohydrate backbone of peptidoglycan has a bacteriophage-lysozyme-like fold <cite>Lovering2007</cite>. The ''Pyrococcus furiosius'' oligosaccharyltransferase STT3, which catalyzes the transfer of a preformed oligosaccharide from a dolichol phosphate glycosyl donor to form asparagine-linked glycoproteins, possesses a novel fold; however, this crystallized fragment is catalytically-inactive and may not represent the structure of the complete glycosyltransferase <cite>Igura2008</cite>. The same fold is also observed in the periplasmic domain of the PglB  oligosaccharyltransferase of ''Camplyobacter lari''; this latter protein was been crystallized as a full length protein incorporating a transmembrane domain that retains transferase activity <cite>Lizak2011</cite>. A structure of PglB oligosaccharyltransferase in complex with a hexapeptide substrate showed that the peptide binds to both the periplasmic domain and the transmembrane domain. These data demonstrate that the transmembrane domain of this bacterial oligosaccharyltransferase is required for both substrate binding and catalysis.
 ==== Example structures ====
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 <br style="clear: both" />
 == Role of metals ==

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 === Leloir GTs ===
 Sugar nucleotide-dependent (Leloir) glycosyltransferases have been found to possess only two different folds, termed the GT-A and GT-B folds <cite>Unligil2000</cite>. The GT-A fold is typified by the first member to have its X-ray structure determined, SpsA from''Bacillus subtilus'' <cite>Charnock1999</cite>. The GT-A fold consists of two dissimilar domains, one involved in nucleotide binding and the other binding the acceptor. The GT-B fold was exemplified by its first member, the beta-glucosyltransferase from bacteriophage T4 <cite>Vrielink1994</cite>. The GT-B fold consists of two similar Rossmann fold subdomains.
 === Non-Leloir GTs ===

← Older revision		Revision as of 04:48, 9 December 2013
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−	In the last two cases, the enzymes that catalyze the transfer of a glycosyl group from a glycosyl phosphate or pyrophosphate are more commonly referred to as [[phosphorylases]] and pyrophosphorylases. Some of these enzymes are classified into [[glycoside hydrolase]] (GH) families (eg sucrose phosphorylase, [[GH13]]) and others are classified into GT familes (eg glycogen phosphorylase).	+	In the last two cases, the enzymes that catalyze the transfer of a glycosyl group from a glycosyl phosphate or pyrophosphate are more commonly referred to as [[phosphorylases]] and pyrophosphorylases. Some of these enzymes are classified into [[glycoside hydrolase]] (GH) families (eg sucrose phosphorylase, [[GH13]]) and others are classified into GT familes (eg glycogen phosphorylase [[GT35]]).

	''For specific examples of glycosyl donor substrates, please see the [[#Common sugar donors\|Common sugar donors]] section below.''		''For specific examples of glycosyl donor substrates, please see the [[#Common sugar donors\|Common sugar donors]] section below.''

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 #Charnock1999 pmid=10350455
 #Vrielink1994 pmid=8062817
-#Uligil2000 pmid=11042447
+#Unligil2000 pmid=11042447
 #Lovering2007 pmid=17347437
 #Igura2008 pmid=18046457

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 Further, crystal structures of retaining glycosyltransferases are mostly ambiguous with respect to identifying possible candidate nucleophiles, with some lacking any suitable nucleophile situated close enough to the glycosyl donor to be able to form a covalent intermediate. In other cases structural analysis has identified possible candidate nucleophiles, which mutagenesis studies have supported. In some cases mutagenesis of the candidate residue to a non-nucleophilic amino acid has not resulted in the expected, dramatic loss in catalytic activity (of the order of 10<sup>6</sup>), as seen for retaining glycoside hydrolases.
-The most common alternative mechanism that is invoked is one that involves an S<sub>N</sub>i process, also termed 'internal return'. In this process, the leaving group on the donor departs, and the nucleophile attacks from the same face, with the other face of the donor being blocked by the enzyme. An open question is whether this process is concerted (''i.e.'' involving a single [[transition state]] in which bonds are formed and broken at similar times) or stepwise (''i.e.'' involving two [[transition states]], and therefore an oxocarbenium ion intermediate). A detailed kinetic study of the retaining glycosyltransferase OtsA (which catalyzes the synthesis of trehalose-6-phosphate from UDP-glucose and glucose-6-phosphate) yielded data that was consistent with a frontside, S<sub>N</sub>i-type reaction <cite>Lee2011</cite>.
+The most common alternative mechanism that is invoked is one that involves an S<sub>N</sub>i process, also termed 'internal return'. In this process, the leaving group on the donor departs, and the nucleophile attacks from the same face, with the other face of the donor being blocked by the enzyme. An open question is whether this process is concerted (''i.e.'' involving a single [[transition state]] in which bonds are formed and broken at similar times) or stepwise (''i.e.'' involving two [[transition state]]s, and therefore an oxocarbenium ion intermediate). A detailed kinetic study of the retaining glycosyltransferase OtsA (which catalyzes the synthesis of trehalose-6-phosphate from UDP-glucose and glucose-6-phosphate) yielded data that was consistent with a frontside, S<sub>N</sub>i-type reaction <cite>Lee2011</cite>.
 [[Image:Retaining glycosyltransferase mechanism.png|center|700px]]

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 The most common alternative mechanism that is invoked is one that involves an S<sub>N</sub>i process, also termed 'internal return'. In this process, the leaving group on the donor departs, and the nucleophile attacks from the same face, with the other face of the donor being blocked by the enzyme. An open question is whether this process is concerted (''i.e.'' involving a single [[transition state]] in which bonds are formed and broken at similar times) or stepwise (''i.e.'' involving two [[transition states]], and therefore an oxocarbenium ion intermediate). A detailed kinetic study of the retaining glycosyltransferase OtsA (which catalyzes the synthesis of trehalose-6-phosphate from UDP-glucose and glucose-6-phosphate) yielded data that was consistent with a frontside, S<sub>N</sub>i-type reaction <cite>Lee2011</cite>.
-[[Image:Retaining glycosyltransferase mechanism.png|center|500px]]
+[[Image:Retaining glycosyltransferase mechanism.png|center|700px]]
 == Classification ==

← Older revision		Revision as of 03:56, 27 June 2013
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	The most common alternative mechanism that is invoked is one that involves an S<sub>N</sub>i process, also termed 'internal return'. In this process, the leaving group on the donor departs, and the nucleophile attacks from the same face, with the other face of the donor being blocked by the enzyme. An open question is whether this process is concerted (''i.e.'' involving a single [[transition state]] in which bonds are formed and broken at similar times) or stepwise (''i.e.'' involving two [[transition states]], and therefore an oxocarbenium ion intermediate). A detailed kinetic study of the retaining glycosyltransferase OtsA (which catalyzes the synthesis of trehalose-6-phosphate from UDP-glucose and glucose-6-phosphate) yielded data that was consistent with a frontside, S<sub>N</sub>i-type reaction <cite>Lee2011</cite>.		The most common alternative mechanism that is invoked is one that involves an S<sub>N</sub>i process, also termed 'internal return'. In this process, the leaving group on the donor departs, and the nucleophile attacks from the same face, with the other face of the donor being blocked by the enzyme. An open question is whether this process is concerted (''i.e.'' involving a single [[transition state]] in which bonds are formed and broken at similar times) or stepwise (''i.e.'' involving two [[transition states]], and therefore an oxocarbenium ion intermediate). A detailed kinetic study of the retaining glycosyltransferase OtsA (which catalyzes the synthesis of trehalose-6-phosphate from UDP-glucose and glucose-6-phosphate) yielded data that was consistent with a frontside, S<sub>N</sub>i-type reaction <cite>Lee2011</cite>.
		+
		+	[[Image:Retaining glycosyltransferase mechanism.png\|center\|500px]]

	== Classification ==		== Classification ==