Glycosyltransferase Family 37 - Revision history

Breeanna Urbanowicz at 20:47, 21 February 2024

2024-02-21T20:47:24Z

Harry Brumer: Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

2021-12-18T21:17:38Z

Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

Harry Brumer at 21:29, 22 May 2020

2020-05-22T21:29:52Z

Harry Brumer at 20:44, 18 May 2020

2020-05-18T20:44:28Z

Harry Brumer: Added PDB links

2020-05-15T22:38:02Z

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Harry Brumer: Added PDB links

2020-05-15T22:37:14Z

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2020-05-15T22:23:17Z

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2020-05-15T22:22:03Z

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Breeanna Urbanowicz at 21:36, 15 May 2020

2020-05-15T21:36:39Z

Breeanna Urbanowicz at 21:13, 15 May 2020

2020-05-15T21:13:02Z

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
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 * [[Author]]: [[User:Vivek Bharadwaj|Vivek Bharadwaj]], [[User:Hsin-Tzu Wang|Hsin-Tzu Wang]], and [[User:Breeanna Urbanowicz|Breeanna Urbanowicz]]
 * [[Responsible Curator]]:  [[User:Breeanna Urbanowicz|Breeanna Urbanowicz]]

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-* [[Author]]: ^^^Vivek Bharadwaj^^^, ^^^Hsin-Tzu Wang^^^, and ^^^Breeanna Urbanowicz^^^
+* [[Author]]: [[User:Vivek Bharadwaj|Vivek Bharadwaj]], [[User:Hsin-Tzu Wang|Hsin-Tzu Wang]], and [[User:Breeanna Urbanowicz|Breeanna Urbanowicz]]
-* [[Responsible Curator]]:  ^^^Breeanna Urbanowicz^^^
+* [[Responsible Curator]]:  [[User:Breeanna Urbanowicz|Breeanna Urbanowicz]]
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-* [[Author]]: ^^^Vivek Bharadwaj^^^, ^^^Hsin-tzu Wang^^^, and ^^^Breeanna Urbanowicz^^^
+* [[Author]]: ^^^Vivek Bharadwaj^^^, ^^^Hsin-Tzu Wang^^^, and ^^^Breeanna Urbanowicz^^^
 * [[Responsible Curator]]:  ^^^Breeanna Urbanowicz^^^
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-* [[Author]]: ^^^Vivek S. Bharadwaj^^^ ^^^Hsin-tzu Wang^^^ and ^^^Breeanna Urbanowicz^^^
+* [[Author]]: ^^^Vivek Bharadwaj^^^, ^^^Hsin-tzu Wang^^^, and ^^^Breeanna Urbanowicz^^^
 * [[Responsible Curator]]:  ^^^Breeanna Urbanowicz^^^
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 == Family Firsts ==
-;First 3-D structure: The ''At''FUT1 enzyme was the first GT-37 family to be structurally characterized using X-ray Crystallography. 5 structures of ''At''FUT1 (apo [{{PPDBlink}}5KOP PDB ID 5KOP] <cite>Rocha2016</cite>, XXLG bound [{{PPDBlink}}5KOE PDB ID 5KOE] <cite>Urbanowicz2017</cite>, GDP bound [{{PPDBlink}}5KWK PDB ID 5KWK] <cite>Urbanowicz2017</cite>, and XXLG-GDP complex [{{PPDBlink}}5KOR PDB ID 5KOR] <cite>Rocha2016</cite>) are available in PDB.
+;First 3-D structure: The ''At''FUT1 enzyme was the first GT-37 family to be structurally characterized using X-ray Crystallography. 5 structures of ''At''FUT1 (apo [{{PDBlink}}5KOP PDB ID 5KOP] <cite>Rocha2016</cite>, XXLG bound [{{PDBlink}}5KOE PDB ID 5KOE] <cite>Urbanowicz2017</cite>, GDP bound [{{PDBlink}}5KWK PDB ID 5KWK] <cite>Urbanowicz2017</cite>, and XXLG-GDP complex [{{PDBlink}}5KOR PDB ID 5KOR] <cite>Rocha2016</cite>) are available in PDB.
 == References ==
 <biblio>

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 <biblio>
 #Coutinho2003 pmid=12691742
 #Urbanowicz2017 pmid=28670741
 #Rocha2016 pmid=27637560
 #Lairson2008 pmid=18518825
 #Breton2006 pmid=22819665
 #Soto2019 Maria J. Soto, Breeanna R. Urbanowicz and Michael G. Hahn (2019) Plant Fucosyltransferases and the Emerging Biological Importance of Fucosylated Plant Structures. Critical Reviews in Plant Sciences 38, 327-338 [https://doi.org/10.1080/07352689.2019.1673968 DOI:10.1080/07352689]
 #Pena2012 pmid=23175743
+#Fry1993 Fry, S. C., York, W. S., Albersheim, P., Darvill, A., Hayashi, T., Joseleau, J.-P., Kato, Y., Lorences, E. P., Maclachlan, G. A., McNeil, M., Mort, A. J., Grant Reid, J. S., Seitz, H. U., Selvendran, R. R., Voragen, A. G. J., and White, A. R. 1993. An unambiguous nomenclature for xyloglucan-derived oligosaccharides. Physiol. Plant. 89: 1–3. [https://doi.org/10.1111/j.1399-3054.1993.tb01778.x DOI:10.1111/j.1399-3054.1993.tb01778.x]
 #Tuomivaara2015 pmid=25497333
 #Farkas1988 pmid=3134858
 #Perrin1999 pmid=10373113
 #Vanzin2002 pmid=11854459
 #Liu2015 pmid=25869654
 #Showalter2016 pmid=27379116
 #Wu2010 pmid=20194500
 #Sarria2001 pmid=11743104
 #Ruprecht2020 pmid=32396713

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 |{{Hl2}} colspan="2" align="center" |'''Glycosyltransferase Family GT37'''
 |-
-|'''Clan'''
+|'''Fold'''
-|GH-B
+|GT-B
 |-
 |'''Mechanism'''
@@ Line 40: / Line 40: @@
 == Kinetics and Mechanism ==
 GT-37 enzymes are classified as inverting GTs i.e. the anomeric configuration of the transferred sugar is inverted in the final product Coutinho2003</cite>. The recent structural characterization of ''At''FUT1 provided detailed insights into the kinetics and mechanism of one GT-37 enzyme <cite>Urbanowicz2017 Rocha2016</cite> In general, inverting GTs are considered to employ a direct displacement S<sub>N</sub>2-like reaction catalyzed by a catalytic general base at the active site to deprotonate the acceptor oxygen for nucleophilic attack <cite>Lairson2008</cite>. However, sequence, structural and biochemical analysis revealed no identifiable catalytic base residue at the active site in ''At''FUT1 <cite>Urbanowicz2017</cite>. Based on molecular dynamics simulations and quantum mechanical calculations, a water mediated semi-concerted S<sub>N</sub>1-like reaction mechanism, consistent with biochemical mutagenesis data was demonstrated for ''At''FUT1. The water facilitates catalysis as a proton shuttle that initially receives a proton from the acceptor galactose residue (O2 hydroxyl) to generate the nucleophile, which attacks the fucose residue on the donor. Simultaneously, the shuttle water donates its other proton to phosphate of the nucleotide, which acts as the base to complete the reaction mechanism <cite>Urbanowicz2017</cite>.
 == Catalytic Residues ==
@@ Line 46: / Line 48: @@
 == Three-dimensional structures ==
 GT structures have in general been classified as either belonging to GT-A or GT-B fold <cite>Breton2006</cite>. Amongst the GT-37 family of enzymes, only ''At''FUT1 has been structurally characterized <cite>Urbanowicz2017 Rocha2016</cite>. The ''At''FUT1 structure is observed to adopt a GT-B type fold, with two b/a/b Rossmann-like domains. The metal independent catalytic site is located in between the two Rossmann domains and binds the nucleotide-sugar donor. A solvent exposed substrate binding groove is created at the interface between these two domains and binds the galactose containing acceptor oligosaccharide.
 == Family Firsts ==

@@ Line 30: / Line 30: @@
 == Substrate specificities ==
-The enzymes belonging to the GT37 family are Golgi localized, plant-specific fucosyltransferases (FUTs) that utilize guanidine 5’-diphosphate-β-L-Fucose (GDP-Fuc) as a donor substrate, and catalyze the transfer of fucose to saccharide acceptor substrates. There are 10 members of this family in the model plant species ''Arabidopsis thaliana'' (''At''FUT1-10), seven members in ''Populus trichocarpa'' (''Pt''FUT1-7). The known acceptor substrates for GT37 FUTs are cell wall glycans, including xyloglucans (XyGs) and arabinogalactan proteins (AGPs). It is hypothesized that members of this family may also be involved in the synthesis of the pectic polysaccharides rhamnogalacturonan I (RG-I) and rhamnogalacturonan II (RG-II). All biochemically characterized GT37 FUTs to date are α-(1-2)-fucosyltransferases (Soto et al., 2019).
+The enzymes belonging to the GT37 family are Golgi localized, plant-specific fucosyltransferases (FUTs) that utilize guanidine 5’-diphosphate-β-L-Fucose (GDP-Fuc) as a donor substrate, and catalyze the transfer of fucose to saccharide acceptor substrates. There are 10 members of this family in the model plant species ''Arabidopsis thaliana'' (''At''FUT1-10), seven members in ''Populus trichocarpa'' (''Pt''FUT1-7). The known acceptor substrates for GT37 FUTs are cell wall glycans, including xyloglucans (XyGs) and arabinogalactan proteins (AGPs). It is hypothesized that members of this family may also be involved in the synthesis of the pectic polysaccharides rhamnogalacturonan I (RG-I) and rhamnogalacturonan II (RG-II). All biochemically characterized GT37 FUTs to date are α-(1-2)-fucosyltransferases <cite>Soto2019</cite>.
-XyGs are hemicellulosic polysaccharides composed of a β-(1,4)-linked glucosyl backbone with a variety of sidechains initiated with an α-D-xylose (Xyl) at ''O''-6 position. The xylosyl residue on the sidechain can be further substituted with β-D-galactose (Gal), β-D-galacturonic acid (GalA), α-L- Arabinofuranose (Ara''f''), or α-L-Arabinopyranose (Ara''p'')depending on the species and tissue (Peña et al., 2012). Gal, GalA, and Ara''p'' be further substituted by an α-L-fucose (Fuc) through an α-(1-2) linkage (Fry et al., 1993; Tuomivaara et al., 2015). So far, there are three FUTs that have been identified and characterized to be specifically involved in fucosylating the Gal or GalA in XyGs, including ''Ps''FUT1 (Farkas and Maclachlan, 1988), ''At''FUT1 (Perrin et al., 1999) and ''Os''MUR2 (Vanzin et al., 2002; Liu et al., 2015).
+XyGs are hemicellulosic polysaccharides composed of a β-(1,4)-linked glucosyl backbone with a variety of sidechains initiated with an α-D-xylose (Xyl) at ''O''-6 position. The xylosyl residue on the sidechain can be further substituted with β-D-galactose (Gal), β-D-galacturonic acid (GalA), α-L- Arabinofuranose (Ara''f''), or α-L-Arabinopyranose (Ara''p'')depending on the species and tissue <cite>Pena2012</cite>. Gal, GalA, and Ara''p'' be further substituted by an α-L-fucose (Fuc) through an α-(1-2) linkage <cite>Fry1993 Tuomivaara2015</cite>. So far, there are three FUTs that have been identified and characterized to be specifically involved in fucosylating the Gal or GalA in XyGs, including ''Ps''FUT1 <cite>Farkas1988</cite>, ''At''FUT1 <cite>Perrin1999</cite> and ''Os''MUR2 <cite>Vanzin2002 Liu2015</cite>.
-FUTs are also involved in AGPs synthesis. AGPs are a diverse family of cell wall glycoproteins with large arabinogalactan polysaccharide chains attached to non-contiguous hydroxyproline residues. The backbone of the O-glycan chains on AGPs is composed of β-1,3-linked galactosyl residues that are branched by β-1,6-linked galactosyl sidechains which are further substituted by α-L-Araf and β-D-(methyl)glucuronic acid (GlcA). Araf and GlcA on the sidechains can then be decorated by α-L-Fuc and α-L-Rhamnose (Rha), respectively, as well as other sugars such as α-D-Xyl ( Ref). Three of the family members in GT37, ''At''FUT4, ''At''FUT6 and ''At''FUT7 from'' A. thaliana'', are involved in fucosylating AGPs (Ruprecht et al., 2020; Wu et al., 2010). A previous study done using tobacco Bright Yellow-2 (BY-2) suspension cells indicated that the ''AtFUT4''- and ''AtFUT6''-overexpressed BY-2 cells produced AGPs with Fuc attached to the ''O''-2 position of α-L-Ara (Wu et al., 2010). Recently, a glycan array-based assay using recombinant ''At''FUT4, ''At''FUT6 and ''At''FUT7 showed that all three enzymes have a broad substrate specificity and are able to fucosylate oligosaccharides  containing Ara''f'' residues α-1,3-linked to Gal, structures representative of AGPs,  as well as β-1,4-xylotertrose appended with an α-1,3-linked Ara''f''  at the non-reducing end (Ruprecht et al., 2020).
+FUTs are also involved in AGPs synthesis. AGPs are a diverse family of cell wall glycoproteins with large arabinogalactan polysaccharide chains attached to non-contiguous hydroxyproline residues. The backbone of the O-glycan chains on AGPs is composed of β-1,3-linked galactosyl residues that are branched by β-1,6-linked galactosyl sidechains which are further substituted by α-L-Araf and β-D-(methyl)glucuronic acid (GlcA). Araf and GlcA on the sidechains can then be decorated by α-L-Fuc and α-L-Rhamnose (Rha), respectively, as well as other sugars such as α-D-Xyl <cite>Showalter2016</cite>. Three of the family members in GT37, ''At''FUT4, ''At''FUT6 and ''At''FUT7 from'' A. thaliana'', are involved in fucosylating AGPs <cite>Ruprecht2020 Wu2010</cite>. A previous study done using tobacco Bright Yellow-2 (BY-2) suspension cells indicated that the ''AtFUT4''- and ''AtFUT6''-overexpressed BY-2 cells produced AGPs with Fuc attached to the ''O''-2 position of α-L-Ara <cite>Wu2010</cite>. Recently, a glycan array-based assay using recombinant ''At''FUT4, ''At''FUT6 and ''At''FUT7 showed that all three enzymes have a broad substrate specificity and are able to fucosylate oligosaccharides  containing Ara''f'' residues α-1,3-linked to Gal, structures representative of AGPs,  as well as β-1,4-xylotertrose appended with an α-1,3-linked Ara''f''  at the non-reducing end <cite>Ruprecht2020</cite>.
-There is an α-L-Fuc α-(1-2)-linked to β-D-Gal on in RG-I, and a 2-''O''-Me-α-L-Fuc that is attached to β-D-Gal via an α-(1-2)-linkage on sidechain B of RG-II, it is hypothesized that the uncharacterized members of the GT37 family are involved in the synthesis of these structures (Sarria et al., 2001, Soto et al., 2019).
+There is an α-L-Fuc α-(1-2)-linked to β-D-Gal on in RG-I, and a 2-''O''-Me-α-L-Fuc that is attached to β-D-Gal via an α-(1-2)-linkage on sidechain B of RG-II, it is hypothesized that the uncharacterized members of the GT37 family are involved in the synthesis of these structures <cite>Sarria2001 Soto2019</cite>.
 == Kinetics and Mechanism ==
-GT-37 enzymes are classified as inverting GTs i.e. the anomeric configuration of the transferred sugar is inverted in the final product.(1) The recent structural characterization of ''At''FUT1 provided detailed insights into the kinetics and mechanism of one GT-37 enzyme.(2,3) In general, inverting GTs are considered to employ a direct displacement S<sub>N</sub>2-like reaction catalyzed by a catalytic general base at the active site to deprotonate the acceptor oxygen for nucleophilic attack.(4) However, sequence, structural and biochemical analysis revealed no identifiable catalytic base residue at the active site in ''At''FUT1.(2) Based on molecular dynamics simulations and quantum mechanical calculations, a water mediated semi-concerted S<sub>N</sub>1-like reaction mechanism, consistent with biochemical mutagenesis data was demonstrated for ''At''FUT1. The water facilitates catalysis as a proton shuttle that initially receives a proton from the acceptor galactose residue (O2 hydroxyl) to generate the nucleophile, which attacks the fucose residue on the donor. Simultaneously, the shuttle water donates its other proton to phosphate of the nucleotide, which acts as the base to complete the reaction mechanism.(2)
+GT-37 enzymes are classified as inverting GTs i.e. the anomeric configuration of the transferred sugar is inverted in the final product Coutinho2003</cite>. The recent structural characterization of ''At''FUT1 provided detailed insights into the kinetics and mechanism of one GT-37 enzyme <cite>Urbanowicz2017 Rocha2016</cite> In general, inverting GTs are considered to employ a direct displacement S<sub>N</sub>2-like reaction catalyzed by a catalytic general base at the active site to deprotonate the acceptor oxygen for nucleophilic attack <cite>Lairson2008</cite>. However, sequence, structural and biochemical analysis revealed no identifiable catalytic base residue at the active site in ''At''FUT1 <cite>Urbanowicz2017</cite>. Based on molecular dynamics simulations and quantum mechanical calculations, a water mediated semi-concerted S<sub>N</sub>1-like reaction mechanism, consistent with biochemical mutagenesis data was demonstrated for ''At''FUT1. The water facilitates catalysis as a proton shuttle that initially receives a proton from the acceptor galactose residue (O2 hydroxyl) to generate the nucleophile, which attacks the fucose residue on the donor. Simultaneously, the shuttle water donates its other proton to phosphate of the nucleotide, which acts as the base to complete the reaction mechanism <cite>Urbanowicz2017</cite>.
 == Catalytic Residues ==
-An arginine residue (Arg366 in ''At''FUT1) is established to be indispensable for catalysis, as it binds the nucleotide-sugar at the active site and stabilizes the oxygen atoms on the phosphate group.(2) In the reaction mechanism, this arginine residue facilitates the release of the fucose group by stabilizing the developing negative charge on the phosphate oxygens, consistent with its indispensable role in catalysis. In light of the absence of a single proximal catalytic general base in ''At''FUT1, mutagenic and computational studies reveal that multiple residues are observed to play a critical role in ''At''FUT1 catalysis. A H-bonding network involving Asp550, Tyr486 and His523 is proposed to be crucial for activating the shuttle water molecule to initiate catalysis and stabilizing the transition state.(2)
+An arginine residue (Arg366 in ''At''FUT1) is established to be indispensable for catalysis, as it binds the nucleotide-sugar at the active site and stabilizes the oxygen atoms on the phosphate group <cite>Urbanowicz2017</cite>. In the reaction mechanism, this arginine residue facilitates the release of the fucose group by stabilizing the developing negative charge on the phosphate oxygens, consistent with its indispensable role in catalysis. In light of the absence of a single proximal catalytic general base in ''At''FUT1, mutagenic and computational studies reveal that multiple residues are observed to play a critical role in ''At''FUT1 catalysis. A H-bonding network involving Asp550, Tyr486 and His523 is proposed to be crucial for activating the shuttle water molecule to initiate catalysis and stabilizing the transition state <cite>Urbanowicz2017</cite>.
 == Three-dimensional structures ==
-GT structures have in general been classified as either belonging to GT-A or GT-B fold.(5) Amongst the GT-37 family of enzymes, only ''At''FUT1 has been structurally characterized.(2,3) The ''At''FUT1 structure is observed to adopt a GT-B type fold, with two b/a/b Rossmann-like domains. The metal independent catalytic site is located in between the two Rossmann domains and binds the nucleotide-sugar donor. A solvent exposed substrate binding groove is created at the interface between these two domains and binds the galactose containing acceptor oligosaccharide.
+GT structures have in general been classified as either belonging to GT-A or GT-B fold <cite>Breton2006</cite>. Amongst the GT-37 family of enzymes, only ''At''FUT1 has been structurally characterized <cite>Urbanowicz2017 Rocha2016</cite>. The ''At''FUT1 structure is observed to adopt a GT-B type fold, with two b/a/b Rossmann-like domains. The metal independent catalytic site is located in between the two Rossmann domains and binds the nucleotide-sugar donor. A solvent exposed substrate binding groove is created at the interface between these two domains and binds the galactose containing acceptor oligosaccharide.
 == Family Firsts ==
-;First stereochemistry determination: Content is to be added here.
+;First 3-D structure: The ''At''FUT1 enzyme was the first GT-37 family to be structurally characterized using X-ray Crystallography. 5 structures of ''At''FUT1 (apo [PDB-5KOP] <cite>Rocha2016</cite>, XXLG bound [PDB-5KOE] <cite>Urbanowicz2017</cite>, GDP bound [PDB-5KWK] <cite>Urbanowicz2017</cite>, and XXLG-GDP complex [PDB-5KOR] <cite>Rocha2016</cite>) are currently available in PDB.
 == References ==
 <biblio>