Glycosyltransferase Family 138 - Revision history

Harry Brumer: /* Catalytic Residues */

2026-01-25T18:32:13Z

Catalytic Residues

Harry Brumer at 18:30, 25 January 2026

2026-01-25T18:30:49Z

Harry Brumer: Reformatted to maintain section consistency with other GT pages, also minor rephrasing.

2026-01-25T18:27:41Z

Reformatted to maintain section consistency with other GT pages, also minor rephrasing.

Harry Brumer: /* Substrate specificities */

2026-01-25T09:45:42Z

Substrate specificities

Wei Peng at 17:33, 17 December 2025

2025-12-17T17:33:19Z

Wei Peng at 20:28, 8 December 2025

2025-12-08T20:28:47Z

Wei Peng at 20:26, 8 December 2025

2025-12-08T20:26:44Z

Wei Peng at 20:25, 8 December 2025

2025-12-08T20:25:40Z

Wei Peng at 20:23, 8 December 2025

2025-12-08T20:23:59Z

Wei Peng at 20:23, 8 December 2025

2025-12-08T20:23:48Z

@@ Line 36: / Line 36: @@
 == Catalytic Residues ==
-A threonine (T166) from the protein substrate directly attacks the rhamnose moiety in the co-substrate, UDP-rhamnose (Fig. 2) <cite>Peng2024</cite>. The threonine is close to a histidine and a threonine in AvrB, which may stabilize the acceptor. UDP-rhamnose is stabilized by a few residues in the pocket (Fig. 2) <cite>Peng2024</cite>.
+A threonine (T166) from the protein substrate directly attacks the rhamnose moiety in the co-substrate, UDP-rhamnose (Fig. 1) <cite>Peng2024</cite>. The threonine is close to a histidine and a threonine in AvrB, which may stabilize the acceptor. UDP-rhamnose is stabilized by a few residues in the pocket (Fig. 1) <cite>Peng2024</cite>.
 == Three-dimensional structures ==

@@ Line 29: / Line 29: @@
 == Substrate specificities ==
-The GT138 family of glycosyltransferase is exemplified by AvrB <cite>Peng2024</cite>.  As a bacterial effector from the plant pathogen ''Pseudomonas syringae'', AvrB utilizes host UDP-rhamnose (or dTDP-rhamnose ''in vitro'') as a co-substrate to rhamnosylate the host protein RIN4, and causes the programmed cell death (i.e. the hypersensitive response) <cite>Peng2024, Mackey2002</cite>.  AvrB contains a "Fido" domain <cite>Lee2004, Kinch2009</cite>, different from other known glycosyltransferases (see below). Interestingly, Fido proteins can also have  AMPylation <cite>Yarbrough2009</cite>, phosphorylation <cite>Castro-Roa2013</cite>, UMPylation <cite>Feng2012</cite>, and phosphocholination <cite>Mukherjee2011, Campanacci2013</cite> activities. Hence, AvrB is a unique Fido protein that functions as a glycosyltransferase.
+The GT138 family of [[glycosyltransferases]] is exemplified by AvrB <cite>Peng2024</cite>.  As a bacterial effector from the plant pathogen ''Pseudomonas syringae'', AvrB utilizes host UDP-rhamnose (or dTDP-rhamnose ''in vitro'') as a co-substrate to rhamnosylate the host protein RIN4, and causes the programmed cell death (i.e. the hypersensitive response) <cite>Peng2024, Mackey2002</cite>.  AvrB contains a "Fido" domain <cite>Lee2004, Kinch2009</cite>, different from other known glycosyltransferases (see below). Interestingly, Fido proteins can also have  AMPylation <cite>Yarbrough2009</cite>, phosphorylation <cite>Castro-Roa2013</cite>, UMPylation <cite>Feng2012</cite>, and phosphocholination <cite>Mukherjee2011, Campanacci2013</cite> activities. Hence, AvrB is a unique Fido protein that functions as a glycosyltransferase.
 == Kinetics and Mechanism ==
 In the reaction, rhamnose is directly transferred to the side chain of a threonine of RIN4, T166 (Fig. 1) <cite>Peng2024</cite>. The rhamnosylation reaction catalyzed by AvrB does not require divalent cations (e.g., Mg<sup>2+</sup>) <cite>Peng2024</cite>.
@@ Line 38: / Line 39: @@
 == Three-dimensional structures ==
-AvrB represents the prototype for [[glycosyltransferases]] comprised of a Fido fold (Fig. 2A) <cite>Peng2024</cite>.  Most [[glycosyltransferases]] contain GT-A, GT-B, GT-C, lysozyme-type, GT101, or GT108 folds (Fig. 2B) <cite>Varki2022, Lairson2008, Zhang2014, Sernee2019</cite>.  AvrB contains a large internal domain between helix α2 and helix α3 (Fig. 2A) <cite>Lee2004, Desveaux2007, Kinch2009, Peng2024</cite>. AvrB shares similar structural features with other Fido proteins despite substantial primary sequence divergence <cite>Kinch2009</cite>.
+AvrB represents the prototype for [[glycosyltransferases]] comprised of a Fido fold (Fig. 2A) <cite>Peng2024</cite>.  Most [[glycosyltransferases]] contain GT-A, GT-B, GT-C, lysozyme-type, [[GT101]], or [[GT108]] folds (Fig. 2B) <cite>Varki2022, Lairson2008, Zhang2014, Sernee2019</cite>.  AvrB contains a large internal domain between helix α2 and helix α3 (Fig. 2A) <cite>Lee2004, Desveaux2007, Kinch2009, Peng2024</cite>. AvrB shares similar structural features with other Fido proteins despite substantial primary sequence divergence <cite>Kinch2009</cite>.
 [[File:GT138-Fig1-V3.png|thumb|1250px|center|'''Figure 1. Glycosyltransferase folds.''' ('''A''') Fido fold (left, image from <cite>Kinch2009</cite>) is found in diverse enzymes including AvrB (right), which is a distinct glycosyltransferase. ('''B''') Other known glycosyltransferases contain folds of GT-A, GT-B, GT-C, lysozyme-type, GT101, and GT108. PDB codes are provided for representative structures.]]
 == Family Firsts ==
 The first member of GT138 family shown to be a glycosyltransferase is AvrB <cite>Peng2024</cite>.
-The first structure of GT138 family is AvrB (Fig. 1A) <cite>Lee2004</cite>. A few AvrB structures are available to reveal the catalysis mechanisms <cite>Lee2004, Desveaux2007, Peng2024</cite>
+The first structure of GT138 family is AvrB (Fig. 2A) <cite>Lee2004</cite>. A few AvrB structures are available to reveal the catalysis mechanisms <cite>Lee2004, Desveaux2007, Peng2024</cite>
 == References ==

@@ Line 27: / Line 27: @@
 <!-- This is the end of the table -->
 == Substrate specificities ==
-As a bacterial effector from the plant pathogen ''Pseudomonas syringae'', AvrB utilizes host UDP-rhamnose (or dTDP-rhamnose ''in vitro'') as a co-substrate to rhamnosylate the host protein RIN4, and causes the programmed cell death (namely hypersensitive response) <cite>Peng2024, Mackey2002</cite>.
+The GT138 family of glycosyltransferase is exemplified by AvrB <cite>Peng2024</cite>.  As a bacterial effector from the plant pathogen ''Pseudomonas syringae'', AvrB utilizes host UDP-rhamnose (or dTDP-rhamnose ''in vitro'') as a co-substrate to rhamnosylate the host protein RIN4, and causes the programmed cell death (i.e. the hypersensitive response) <cite>Peng2024, Mackey2002</cite>.  AvrB contains a "Fido" domain <cite>Lee2004, Kinch2009</cite>, different from other known glycosyltransferases (see below). Interestingly, Fido proteins can also have  AMPylation <cite>Yarbrough2009</cite>, phosphorylation <cite>Castro-Roa2013</cite>, UMPylation <cite>Feng2012</cite>, and phosphocholination <cite>Mukherjee2011, Campanacci2013</cite> activities. Hence, AvrB is a unique Fido protein that functions as a glycosyltransferase.
 == Kinetics and Mechanism ==
-In the reaction, rhamnose is directly transferred to the side chain of a threonine of RIN4, T166 (Fig. 2) <cite>Peng2024</cite>. The rhamnosylation reaction catalyzed by AvrB does not require divalent cations (e.g., Mg<sup>2+</sup>) <cite>Peng2024</cite>.
+In the reaction, rhamnose is directly transferred to the side chain of a threonine of RIN4, T166 (Fig. 1) <cite>Peng2024</cite>. The rhamnosylation reaction catalyzed by AvrB does not require divalent cations (e.g., Mg<sup>2+</sup>) <cite>Peng2024</cite>.
-[[File:GT138-figure-2.png|thumb|900px|center|'''Figure 2. Catalysis mechanisms for RIN4 rhamnosylation by AvrB supported by crystal structures (image from''' <cite>Peng2024</cite>''').''' ('''A''') AvrB bound with RIN4. ('''B''') UDP-rhamnose bound with AvrB and RIN4. ('''C''') Rhamnose transferred to T166 of RIN4. ('''D''') Release of rhamnosylated RIN4.]]
+[[File:GT138-figure-2.png|thumb|900px|center|'''Figure 1. Catalysis mechanisms for RIN4 rhamnosylation by AvrB supported by crystal structures (image from''' <cite>Peng2024</cite>''').''' ('''A''') AvrB bound with RIN4. ('''B''') UDP-rhamnose bound with AvrB and RIN4. ('''C''') Rhamnose transferred to T166 of RIN4. ('''D''') Release of rhamnosylated RIN4.]]
 == Catalytic Residues ==
@@ Line 45: / Line 38: @@
 == Three-dimensional structures ==
-AvrB represents the prototype for glycosyltransferases of Fido fold (Fig. 1A) <cite>Peng2024</cite>. AvrB contains a large internal domain between helix α2 and helix α3 (Fig. 1A) <cite>Lee2004, Desveaux2007, Kinch2009, Peng2024</cite>. AvrB shares similar structural features with other Fido proteins despite the primary sequences are divergent <cite>Kinch2009</cite>.
+AvrB represents the prototype for [[glycosyltransferases]] comprised of a Fido fold (Fig. 2A) <cite>Peng2024</cite>.  Most [[glycosyltransferases]] contain GT-A, GT-B, GT-C, lysozyme-type, GT101, or GT108 folds (Fig. 2B) <cite>Varki2022, Lairson2008, Zhang2014, Sernee2019</cite>.  AvrB contains a large internal domain between helix α2 and helix α3 (Fig. 2A) <cite>Lee2004, Desveaux2007, Kinch2009, Peng2024</cite>. AvrB shares similar structural features with other Fido proteins despite substantial primary sequence divergence <cite>Kinch2009</cite>.
 == Family members ==
 AvrB is the only well-studied member so far in the GT138 family <cite>Peng2024</cite>.

@@ Line 35: / Line 35: @@
 == Substrate specificities ==
-As a bacterial effector from the plant pathogen ''Pseudomonas syringae'', '''AvrB utilizes host UDP-rhamnose''' '''(or dTDP-rhamnose ''in vitro'')''' '''as a co-substrate to rhamnosylate the host protein RIN4''' and causes the programmed cell death (namely hypersensitive response) <cite>Peng2024, Mackey2002</cite>.
+As a bacterial effector from the plant pathogen ''Pseudomonas syringae'', AvrB utilizes host UDP-rhamnose (or dTDP-rhamnose ''in vitro'') as a co-substrate to rhamnosylate the host protein RIN4, and causes the programmed cell death (namely hypersensitive response) <cite>Peng2024, Mackey2002</cite>.
 == Kinetics and Mechanism ==

@@ Line 45: / Line 45: @@
 == Three-dimensional structures ==
-AvrB represents the prototype for glycosyltransferases of Fido fold <cite>Peng2024</cite>. AvrB contains a large internal domain between helix α2 and helix α3 (Fig. 1A) <cite>Lee2004, Desveaux2007, Kinch2009, Peng2024</cite>. AvrB shares similar structural features with other Fido proteins despite the primary sequences are divergent <cite>Kinch2009</cite>.
+AvrB represents the prototype for glycosyltransferases of Fido fold (Fig. 1A) <cite>Peng2024</cite>. AvrB contains a large internal domain between helix α2 and helix α3 (Fig. 1A) <cite>Lee2004, Desveaux2007, Kinch2009, Peng2024</cite>. AvrB shares similar structural features with other Fido proteins despite the primary sequences are divergent <cite>Kinch2009</cite>.
 == Family members ==
@@ Line 53: / Line 53: @@
 The first member of GT138 family shown to be a glycosyltransferase is AvrB <cite>Peng2024</cite>.
-The first structure of GT138 family is AvrB <cite>Lee2004</cite>. A few AvrB structures are available to reveal the catalysis mechanisms <cite>Lee2004, Desveaux2007, Peng2024</cite>
+The first structure of GT138 family is AvrB (Fig. 1A) <cite>Lee2004</cite>. A few AvrB structures are available to reveal the catalysis mechanisms <cite>Lee2004, Desveaux2007, Peng2024</cite>
 == References ==

@@ Line 32: / Line 32: @@
 Interestingly, Fido proteins can also be enzymes with activities of AMPylation <cite>Yarbrough2009</cite>, phosphorylation <cite>Castro-Roa2013</cite>, UMPylation <cite>Feng2012</cite>, and phosphocholination <cite>Mukherjee2011, Campanacci2013</cite>. Hence, AvrB is a unique Fido protein that functions as a glycosyltransferase.
-[[File:GT138-Fig1-V3.png|thumb|1250px|center|'''Figure 1. Glycosyltransferase folds.''' ('''A''') Fido fold (left <cite>Kinch2009</cite>) is found in diverse enzymes including AvrB (right), which is a distinct glycosyltransferase. ('''B''') Other known glycosyltransferases contain folds of GT-A, GT-B, GT-C, lysozyme-type, GT101, and GT108. PDB codes are provided for representative structures.]]
+[[File:GT138-Fig1-V3.png|thumb|1250px|center|'''Figure 1. Glycosyltransferase folds.''' ('''A''') Fido fold (left, image from <cite>Kinch2009</cite>) is found in diverse enzymes including AvrB (right), which is a distinct glycosyltransferase. ('''B''') Other known glycosyltransferases contain folds of GT-A, GT-B, GT-C, lysozyme-type, GT101, and GT108. PDB codes are provided for representative structures.]]
 == Substrate specificities ==
@@ Line 39: / Line 39: @@
 == Kinetics and Mechanism ==
 In the reaction, rhamnose is directly transferred to the side chain of a threonine of RIN4, T166 (Fig. 2) <cite>Peng2024</cite>. The rhamnosylation reaction catalyzed by AvrB does not require divalent cations (e.g., Mg<sup>2+</sup>) <cite>Peng2024</cite>.
-[[File:GT138-figure-2.png|thumb|900px|center|'''Figure 2. Catalysis mechanisms for RIN4 rhamnosylation by AvrB supported by crystal structures <cite>Peng2024</cite>.''' ('''A''') AvrB bound with RIN4. ('''B''') UDP-rhamnose bound with AvrB and RIN4. ('''C''') Rhamnose transferred to T166 of RIN4. ('''D''') Release of rhamnosylated RIN4.]]
+[[File:GT138-figure-2.png|thumb|900px|center|'''Figure 2. Catalysis mechanisms for RIN4 rhamnosylation by AvrB supported by crystal structures (image from <cite>Peng2024</cite>''')'''.''' ('''A''') AvrB bound with RIN4. ('''B''') UDP-rhamnose bound with AvrB and RIN4. ('''C''') Rhamnose transferred to T166 of RIN4. ('''D''') Release of rhamnosylated RIN4.]]
 == Catalytic Residues ==