CAZypedia - User contributions [en-ca]

Glycoside Hydrolase Family 105

2019-10-27T20:39:18Z

James Stevenson:

{{CuratorApproved}}

* [[Author]]: ^^^James Stevenson^^^
* [[Responsible Curator]]: ^^^Joel Weadge^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH105'''
|-
| '''Clan'''
| none
|-
| '''Mechanism'''
| N/A
|-
| '''Active site residues'''
| known
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH105.html
|}
</div>



== Substrate specificities ==
GH105 enzymes are a class of unsaturated glucuronyl/galacturonyl hydrolases found mainly in bacteria, but a few fungal and a handful of archaeal enzymes have also been annotated <cite>Cantarel2009</cite>. Much like the [[Glycoside Hydrolase Family 88]], enzymes from GH105 perform hydrolysis via a hydration of the double bond between the C-4 and C-5 carbons of the terminal monosaccharide of their substrates <cite>Munoz-Munoz2017 Jongkees2011</cite>. Enzymes from GH105 have been organized into three subgroups: unsaturated rhamnogalacturonidases, D-4,5-unsaturated β-glucuronyl hydrolases, and D-4,5-unsaturated α-galacturonidases. The unifying feature shared between these substrates is the presence of the non-reducing monosaccharide 4-deoxy-L-threo-hex-4-enopyranuronosyl that binds at the -1 active site of the enzymes and is linked to the +1 sugar via its anomeric C-1 carbon. The 4-deoxy-L-threo-hex-4-enopyranuronosyl saccharide can be inferred as ΔGalA or ΔGlcA depending on whether it assumes an α- or β- configuration, respectively, at the anomeric C-1 carbon. In degradable substrates, the sugar present at the +1 position can be linked via its C-2, C-4, or C-6 carbon, given the substrate preference of individual enzymes <cite>Zhang2009 Munoz-Munoz2017</cite>. Some of the various carbohydrate sources targeted by GH105 enzymes include: rhamnogalacturonan-I, ulvan, and the arabinogalactan decoration on certain cell wall proteins <cite>Itoh2006 Itoh2006-1 Collen2014 Munoz-Munoz2017</cite>.

== Kinetics and Mechanism ==
GH105 enzymes do not act via a typical Koshland retaining or inverting mechanism <cite>Koshland1953</cite>, rather the current proposed mechanism of action for these enzymes is hydrolysis through syn-hydration of the double bond between the C-4 and C-5 carbons of the enopyranuronosyl residue of their substrate <cite>Itoh2006</cite>. This hydration reaction forms a hemiketal that undergoes spontaneous rearrangement to form an intermediate hemiacetyl, which undergoes further rearrangement resulting in the breakage of the bond to the neighbouring saccharide (at the +1 subsite of the enzyme) of the polymer. This mechanism was initially theorized based on the oligosaccharide and amino acid arrangement in a substrate-bound crystal structure <cite>Itoh2006-1</cite>, but has been confirmed through kinetic isotope effects and NMR analysis in the highly related unsaturated glucuronyl hydrolase family [[GH88]] <cite>Jongkees2011 Jongkees2014</cite>.

The kinetics for three enzymes from the GH105 family have been determined, two from ''Bacillus subtilis'' and one from ''Bacteriodes thetaiotaomicron''. YteR from ''B. subtilis'' was found to have a ''k''<sub>cat</sub> and ''K''<sub>M</sub> of 0.2±0.011 s<sup>-1</sup> and 100±14 μM , respectively, against the substrate ΔGalA-Rha; in contrast, YesR was found to have much higher values for both these kinetic parameters, 13.9±0.7 s<sup>-1</sup> and 719±75 μM for ''k''<sub>cat</sub> and ''K''<sub>M</sub>, respectively, with the same substrate <cite>Itoh2006-1</cite>. BT3687 from ''B. thetaiotaomicron'' was determined to have a ''k''<sub>cat</sub> of 0.59±0.057 s<sup>-1</sup> and a ''K''<sub>M</sub> of 71.87±12.51 μM against the substrate ΔGlcA-GlcNAc <cite>Munoz-Munoz2017</cite>.

Although it is atypical for a glycoside hydrolase family to contain enzymes capable of degrading both α- or β-linked substrates, this has also been observed in other families that deviate significantly from typical acid-base mechanisms (''e.g.'' [[GH3]], [[GH4]]) <cite>Rye2000</cite>.

== Catalytic Residues ==
A single aspartate residue has been proposed to be responsible for the hydration reaction based on substrate-complexed X-ray crystal structures, sequence conservation, and site-directed mutagenesis <cite>Itoh2006 Itoh2006-1</cite>. The first enzyme classified into the GH105 family (YteR; [{{PDBlink}}1NC5 PDB ID 1NC5] from ''B. subtilis'') was originally predicted to be a lyase based on 65% amino acid sequence similarity and over 60% matching secondary-structure characteristics with an ''N''-acyl-D-glucosamine 2-epimerase <cite>Zhang2009</cite>. Following sequence comparison to a GH88 hydrolase (a ''B. subtilis'' UGL enzyme), and additional functional characterization, YteR was determined to possess unsaturated galacturonyl hydrolase activity <cite>Itoh2006-1</cite>. A conserved aspartate residue (D143), was found to be the most likely candidate for initiating the hydration reaction, while a second conserved residue, histidine (H189), serves to correctly position a water molecule for deprotonation and addition to the C-5 carbon of the monosaccharide in the enzyme's -1 subsite <cite>Itoh2006-1</cite>. Based on sequence alignment and structural analysis, an arginine residue may take the place of this histidine residue in some GH105 enzymes (e.g. [{{PDBlink}}4CE7 PDB ID 4CE7] and [{{PDBlink}}5NOA PDB ID 5NOA]) <cite>Pettersen2004 Collen2014 Munoz-Munoz2017</cite>.

== Three-dimensional structures ==
A number of crystal structures of GH105 unsaturated glucuronyl hydrolases expressed in bacteria have been solved, including several structures from ''B. subtilis'' <cite>Zhang2009 Itoh2006 Itoh2006-1</cite>([{{PDBlink}}1NC5 PDB ID 1NC5]), and ''B. thetaiotaomicron'' <cite>Munoz-Munoz2017 Collen2014</cite>([{{PDBlink}}3K11 PDB ID 3K11]), as well as one each from ''Bacteriodes vulgatus'' ([{{PDBlink}}4Q88 PDB ID 4Q88]), ''Clostridium acetobutylicum'' <cite>Germane2015</cite>, ''Klebsiella pneumoniae'' ([{{PDBlink}}3PMM PDB ID 3PMM]), and ''Salmonella enterica'' ([{{PDBlink}}3QWT PDB ID 3QWT]). A single enzyme from the fungus ''Thielavia terrestris'' has also been solved ([{{PDBlink}}4XUV PDB ID 4XUV]). All of these enzymes share an (α/α)6-barrel structure (also similar to that of the related GH88 enzymes), with the main differences being seen in the structure of the loop region that determines the architecture of the binding site. At the bottom of the active site pocket is a conserved WxRxxxW motif, with the tryptophan and arginine residues forming a pocket that engages the carboxyl group on the ΔGalA/GlcA monosaccharide of the -1 subsite <cite>Itoh2006</cite>. While several residues may be conserved in sequence and position at the -1 subsite, the +1 subsite is much more variable, which likely accounts for the ability of this enzyme family to catalyze the hydrolysis of polysaccharides containing α- or β-bonds linked to the C-2, -4, or -6 carbon of the +1 saccharide <cite>Collen2014</cite>.

== Family Firsts ==
; First stereochemistry determination: Crystal structure of substrate-bound ''B. subtilis'' YteR unsaturated rhamnogalacturonan hydrolase in 2006 ([{{PDBlink}}1NC5 PDB ID 1NC5]). Functional analysis of this enzyme detected loss of a C=C bond compared to a detectable increase in α-keto acid following enzyme-substrate incubation <cite>Itoh2006-1</cite>.
; First catalytic residue identification: Crystal structure analysis of the ''B. subtilis'' YteR enzyme complexed with a ΔGlc-GalNac substrate analog suggested Asp143 is responsible for initiating the hydration reaction and kinetic assessment of a D143N mutant of YteR showed complete loss of catalytic activity <cite>Itoh2006-1</cite>.
; First evidence of hydration-based mechanism: While the mechanism of GH105 enzymes has not been fully described, the mechanism of the unsaturated glucuronyl hydrolase (UGL) from ''Clostridium perfringens'' (a closely-related GH88 protein) was determined via NMR using a methyl ketal intermediate analogue and monitoring of the reaction product during enzyme-substrate incubation in D<sub>2</sub>O <cite>Jongkees2011</cite>.
; First 3-D structure: The 1.6Å crystal structure of the ''B. subtilis'' protein YteR ([{{PDBlink}}1NC5 PDB ID 1NC5]), initially predicted to be a lyase-type enzyme, was reported in 2005 <cite>Zhang2009</cite>.

== References ==
<biblio>
#Cantarel2009 pmid=18838391
#Munoz-Munoz2017 pmid=28637865
#Jongkees2011 pmid=22047074
#Zhang2009 pmid=15906318
#Itoh2006 pmid=16870154
#Itoh2006-1 pmid=16781735
#Collen2014 pmid=24407291
#Koshland1953 Koshland, D.E. (1953) Stereochemistry and the Mechanism of Enzymatic Reactions. ''Biological Reviews'', vol. 28, no. 4., pp. 416-436. [https://doi.org/10.1111/j.1469-185X.1953.tb01386.x DOI:10.1111/j.1469-185X.1953.tb01386.x].
#Jongkees2014 pmid=24573682
#Rye2000 pmid=11006547
#Pettersen2004 pmid=15264254
#Germane2015 pmid=26249707

</biblio>

[[Category:Glycoside Hydrolase Families|GH105]]

User:James Stevenson

2019-10-11T01:03:22Z

James Stevenson:

[[File:IMG_7528.png|200px|right]]
James Stevenson received his BScH in Biochemistry & Biochemistry from Wilfrid Laurier University in 2017, where he developed an interest in protein crystallography and structural biology. James is currently a Masters candidate in the Lab of Dr. ^^^Michael Suits^^^ at WLU, where he studies the structure and function of CAZymes in ''B. thetaiotaomicron'' responsible for nutrient accession of galactose-containing polysaccharides, as well as the structure of virulence-associated proteins in the Gram-negative oral pathogen ''P. gingivalis''. His most recent work includes the structure of the ''B. thetaiotaomicron'' galactosidase BT3158 and fused spore-maturation/nucleoside transporter protein PGN1461 from ''P. gingivalis''.

----


[[Category:Contributors|Stevenson,James]]

User:James Stevenson

2019-10-11T01:02:40Z

James Stevenson:

User:James Stevenson

2019-10-11T01:02:25Z

James Stevenson:

James Stevenson received his BScH in Biochemistry & Biochemistry from Wilfrid Laurier University in 2017, where he developed an interest in protein crystallography and structural biology. James is currently a Masters candidate in the Lab of Dr. ^^^Michael Suits^^^ at WLU, where he studies the structure and function of CAZymes in ''B. thetaiotaomicron'' responsible for nutrient accession of galactose-containing polysaccharides, as well as the structure of virulence-associated proteins in the Gram-negative oral pathogen ''P. gingivalis''. His most recent work includes the structure of the ''B. thetaiotaomicron'' galactosidase BT3158 and fused spore-maturation/nucleoside transporter protein PGN1461 from ''P. gingivalis''.

[[File:IMG_7528.png|200px|right]]

----


[[Category:Contributors|Stevenson,James]]

File:IMG 7528.png

2019-10-11T01:01:55Z

James Stevenson:

User:James Stevenson

2019-10-11T00:59:53Z

James Stevenson:

[[Image:Blank_user-200px.png|200px|right]]
James Stevenson received his BScH in Biochemistry & Biochemistry from Wilfrid Laurier University in 2017, where he developed an interest in protein crystallography and structural biology. James is currently a Masters candidate in the Lab of Dr. ^^^Michael Suits^^^ at WLU, where he studies the structure and function of CAZymes in ''B. thetaiotaomicron'' responsible for nutrient accession of galactose-containing polysaccharides, as well as the structure of virulence-associated proteins in the Gram-negative oral pathogen ''P. gingivalis''. His most recent work includes the structure of the ''B. thetaiotaomicron'' galactosidase BT3158 and fused spore-maturation/nucleoside transporter protein PGN1461 from ''P. gingivalis''.

[[File:IMG_7528.png|200px|right]]

----


[[Category:Contributors|Stevenson,James]]

Glycoside Hydrolase Family 105

2019-09-04T19:13:50Z

James Stevenson:

{{CuratorApproved}}

* [[Author]]: ^^^James Stevenson^^^
* [[Responsible Curator]]: ^^^Joel Weadge^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH105'''
|-
| '''Clan'''
| none
|-
| '''Mechanism'''
| N/A
|-
| '''Active site residues'''
| known
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH105.html
|}
</div>



== Substrate specificities ==
GH105 enzymes are a class of unsaturated glucuronyl/galacturonyl hydrolases found mainly in bacteria, but a few fungal and a handful of archaeal enzymes have also been annotated <cite>Cantarel2009</cite>. Much like the [[Glycoside Hydrolase Family 88]], enzymes from GH105 perform hydrolysis via a hydration of the double bond between the C-4 and C-5 carbons of the terminal monosaccharide of their substrates <cite>Munoz-Munoz2017 Jongkees2011</cite>. Enzymes from GH105 have been organized into three subgroups: unsaturated rhamnogalacturonidases, D-4,5-unsaturated β-glucuronyl hydrolases, and D-4,5-unsaturated α-galacturonidases. The unifying feature shared between these substrates is the presence of the non-reducing monosaccharide 4-deoxy-L-threo-hex-4-enopyranuronosyl that binds at the -1 active site of the enzymes and is linked to the +1 sugar via its anomeric C-1 carbon. The 4-deoxy-L-threo-hex-4-enopyranuronosyl saccharide can be inferred as ΔGalA or ΔGlcA depending on whether it assumes an α- or β- configuration, respectively, at the anomeric C-1 carbon. In degradable substrates, the sugar present at the +1 position can be linked via its C-2, C-4, or C-6 carbon, given the substrate preference of individual enzymes <cite>Zhang2009 Munoz-Munoz2017</cite>. Some of the various carbohydrate sources targeted by GH105 enzymes include: rhamnogalacturonan-I, ulvan, and the arabinogalactan decoration on certain cell wall proteins <cite>Itoh2006 Itoh2006-1 Collen2014 Munoz-Munoz2017</cite>.

== Kinetics and Mechanism ==
GH105 enzymes do not act via a typical Koshland retaining or inverting mechanism <cite>Koshland1953</cite>, rather the current proposed mechanism of action for these enzymes is hydrolysis through syn-hydration of the double bond between the C-4 and C-5 carbons of the enopyranuronosyl residue of their substrate <cite>Itoh2006</cite>. This hydration reaction forms a hemiketal that undergoes spontaneous rearrangement to form an intermediate hemiacetyl, which undergoes further rearrangement resulting in the breakage of the bond to the neighbouring saccharide (at the +1 subsite of the enzyme) of the polymer. This mechanism was initially theorized based on the oligosaccharide and amino acid arrangement in a substrate-bound crystal structure <cite>Itoh2006-1</cite>, but has been confirmed through kinetic isotope effects and NMR analysis in the highly related unsaturated glucuronyl hydrolase family [[GH88]] <cite>Jongkees2011 Jongkees2014</cite>.

The kinetics for three enzymes from the GH105 family have been determined, two from ''Bacillus subtilis'' and one from ''Bacteriodes thetaiotaomicron''. YteR from ''B. subtilis'' was found to have a ''k''<sub>cat</sub> and ''K''<sub>M</sub> of 0.2±0.011 s<sup>-1</sup> and 100±14μM , respectively, against the substrate ΔGalA-Rha; in contrast, YesR was found to have much higher values for both these kinetic parameters, 13.9±0.7 s<sup>-1</sup> and 719±75 μM for ''k''<sub>cat</sub> and ''K''<sub>M</sub>, respectively, with the same substrate <cite>Itoh2006-1</cite>. BT3687 from ''B. thetaiotaomicron'' was determined to have a ''k''<sub>cat</sub> of 0.59±0.057 s<sup>-1</sup> and a ''K''<sub>M</sub> of 71.87±12.51 μM against the substrate ΔGlcA-GlcNAc <cite>Munoz-Munoz2017</cite>.

Although it is atypical for a glycoside hydrolase family to contain enzymes capable of degrading both α- or β-linked substrates, this has also been observed in other families that deviate significantly from typical acid-base mechanisms (''e.g.'' [[GH3]], [[GH4]]) <cite>Rye2000</cite>.

== Catalytic Residues ==
A single aspartate residue has been proposed to be responsible for the hydration reaction based on substrate-complexed X-ray crystal structures, sequence conservation, and site-directed mutagenesis <cite>Itoh2006 Itoh2006-1</cite>. The first enzyme classified into the GH105 family (YteR; [{{PDBlink}}1NC5 PDB ID 1NC5] from ''B. subtilis'') was originally predicted to be a lyase based on 65% amino acid sequence similarity and over 60% matching secondary-structure characteristics with an ''N''-acyl-D-glucosamine 2-epimerase <cite>Zhang2009</cite>. Following sequence comparison to a GH88 hydrolase (a ''B. subtilis'' UGL enzyme), and additional functional characterization, YteR was determined to possess unsaturated galacturonyl hydrolase activity <cite>Itoh2006-1</cite>. A conserved aspartate residue (D143), was found to be the most likely candidate for initiating the hydration reaction, while a second conserved residue, histidine (H189), serves to correctly position a water molecule for deprotonation and addition to the C-5 carbon of the monosaccharide in the enzyme's -1 subsite <cite>Itoh2006-1</cite>. Based on sequence alignment and structural analysis, an arginine residue may take the place of this histidine residue in some GH105 enzymes (e.g. [{{PDBlink}}4CE7 PDB ID 4CE7] and [{{PDBlink}}5NOA PDB ID 5NOA]) <cite>Pettersen2004 Collen2014 Munoz-Munoz2017</cite>.

== Three-dimensional structures ==
A number of crystal structures of GH105 unsaturated glucuronyl hydrolases expressed in bacteria have been solved, including several structures from ''B. subtilis'' <cite>Zhang2009 Itoh2006 Itoh2006-1</cite>([{{PDBlink}}1NC5 PDB ID 1NC5]), and ''B. thetaiotaomicron'' <cite>Munoz-Munoz2017 Collen2014</cite>([{{PDBlink}}3K11 PDB ID 3K11]), as well as one each from ''Bacteriodes vulgatus'' ([{{PDBlink}}4Q88 PDB ID 4Q88]), ''Clostridium acetobutylicum'' <cite>Germane2015</cite>, ''Klebsiella pneumoniae'' ([{{PDBlink}}3PMM PDB ID 3PMM]), and ''Salmonella enterica'' ([{{PDBlink}}3QWT PDB ID 3QWT]). A single enzyme from the fungus ''Thielavia terrestris'' has also been solved ([{{PDBlink}}4XUV PDB ID 4XUV]). All of these enzymes share an (α/α)6-barrel structure (also similar to that of the related GH88 enzymes), with the main differences being seen in the structure of the loop region that determines the architecture of the binding site. At the bottom of the active site pocket is a conserved WxRxxxW motif, with the tryptophan and arginine residues forming a pocket that engages the carboxyl group on the ΔGalA/GlcA monosaccharide of the -1 subsite <cite>Itoh2006</cite>. While several residues may be conserved in sequence and position at the -1 subsite, the +1 subsite is much more variable, which likely accounts for the ability of this enzyme family to catalyze the hydrolysis of polysaccharides containing α- or β-bonds linked to the C-2, -4, or -6 carbon of the +1 saccharide <cite>Collen2014</cite>.

== Family Firsts ==
; First stereochemistry determination: Crystal structure of substrate-bound ''B. subtilis'' YteR unsaturated rhamnogalacturonan hydrolase in 2006 ([{{PDBlink}}1NC5 PDB ID 1NC5]). Functional analysis of this enzyme detected loss of a C=C bond compared to a detectable increase in α-keto acid following enzyme-substrate incubation <cite>Itoh2006-1</cite>.
; First catalytic residue identification: Crystal structure analysis of the ''B. subtilis'' YteR enzyme complexed with a ΔGlc-GalNac substrate analog suggested Asp143 is responsible for initiating the hydration reaction and kinetic assessment of a D143N mutant of YteR showed complete loss of catalytic activity <cite>Itoh2006-1</cite>.
; First evidence of hydration-based mechanism: While the mechanism of GH105 enzymes has not been fully described, the mechanism of the unsaturated glucuronyl hydrolase (UGL) from ''Clostridium perfringens'' (a closely-related GH88 protein) was determined via NMR using a methyl ketal intermediate analogue and monitoring of the reaction product during enzyme-substrate incubation in D<sub>2</sub>O <cite>Jongkees2011</cite>.
; First 3-D structure: The 1.6Å crystal structure of the ''B. subtilis'' protein YteR ([{{PDBlink}}1NC5 PDB ID 1NC5]), initially predicted to be a lyase-type enzyme, was reported in 2005 <cite>Zhang2009</cite>.

== References ==
<biblio>
#Cantarel2009 pmid=18838391
#Munoz-Munoz2017 pmid=28637865
#Jongkees2011 pmid=22047074
#Zhang2009 pmid=15906318
#Itoh2006 pmid=16870154
#Itoh2006-1 pmid=16781735
#Collen2014 pmid=24407291
#Koshland1953 Koshland, D.E. (1953) Stereochemistry and the Mechanism of Enzymatic Reactions. ''Biological Reviews'', vol. 28, no. 4., pp. 416-436. [https://doi.org/10.1111/j.1469-185X.1953.tb01386.x DOI:10.1111/j.1469-185X.1953.tb01386.x].
#Jongkees2014 pmid=24573682
#Rye2000 pmid=11006547
#Pettersen2004 pmid=15264254
#Germane2015 pmid=26249707

</biblio>

[[Category:Glycoside Hydrolase Families|GH105]]

Glycoside Hydrolase Family 105

2019-09-04T19:12:18Z

James Stevenson:

{{CuratorApproved}}

* [[Author]]: ^^^James Stevenson^^^
* [[Responsible Curator]]: ^^^Joel Weadge^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH105'''
|-
| '''Clan'''
| none
|-
| '''Mechanism'''
| N/A
|-
| '''Active site residues'''
| known
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH105.html
|}
</div>



== Substrate specificities ==
GH105 enzymes are a class of unsaturated glucuronyl/galacturonyl hydrolases found mainly in bacteria, but a few fungal and a handful of archaeal enzymes have also been annotated <cite>Cantarel2009</cite>. Much like the [[Glycoside Hydrolase Family 88]], enzymes from GH105 perform hydrolysis via a hydration of the double bond between the C-4 and C-5 carbons of the terminal monosaccharide of their substrates <cite>Munoz-Munoz2017 Jongkees2011</cite>. Enzymes from GH105 have been organized into three subgroups: unsaturated rhamnogalacturonidases, D-4,5-unsaturated β-glucuronyl hydrolases, and D-4,5-unsaturated α-galacturonidases. The unifying feature shared between these substrates is the presence of the non-reducing monosaccharide 4-deoxy-L-threo-hex-4-enopyranuronosyl that binds at the -1 active site of the enzymes and is linked to the +1 sugar via its anomeric C-1 carbon. The 4-deoxy-L-threo-hex-4-enopyranuronosyl saccharide can be inferred as ΔGalA or ΔGlcA depending on whether it assumes an α- or β- configuration, respectively, at the anomeric C-1 carbon. In degradable substrates, the sugar present at the +1 position can be linked via its C-2, C-4, or C-6 carbon, given the substrate preference of individual enzymes <cite>Zhang2009 Munoz-Munoz2017</cite>. Some of the various carbohydrate sources targeted by GH105 enzymes include: rhamnogalacturonan-I, ulvan, and the arabinogalactan decoration on certain cell wall proteins <cite>Itoh2006 Itoh2006-1 Collen2014 Munoz-Munoz2017</cite>.

== Kinetics and Mechanism ==
GH105 enzymes do not act via a typical Koshland retaining or inverting mechanism <cite>Koshland1953</cite>, rather the current proposed mechanism of action for these enzymes is hydrolysis through syn-hydration of the double bond between the C-4 and C-5 carbons of the enopyranuronosyl residue of their substrate <cite>Itoh2006</cite>. This hydration reaction forms a hemiketal that undergoes spontaneous rearrangement to form an intermediate hemiacetyl, which undergoes further rearrangement resulting in the breakage of the bond to the neighbouring saccharide (at the +1 subsite of the enzyme) of the polymer. This mechanism was initially theorized based on the oligosaccharide and amino acid arrangement in a substrate-bound crystal structure <cite>Itoh2006-1</cite>, but has been confirmed through kinetic isotope effects and NMR analysis in the highly related unsaturated glucuronyl hydrolase family [[GH88]] <cite>Jongkees2011 Jongkees2014</cite>.

The kinetics for three enzymes from the GH105 family have been determined, two from ''Bacillus subtilis'' and one from ''Bacteriodes thetaiotaomicron''. YteR from ''B. subtilis'' was found to have a ''k''<sub>cat</sub> and ''K''<sub>M</sub> of 0.2±0.011 s<sup>-1</sup> and 100±14μM , respectively, against the substrate ΔGalA-Rha; in contrast, YesR was found to have much higher values for both these kinetic parameters, 13.9±0.7 s<sup>-1</sup> and 719±75 μM for ''k''<sub>cat</sub> and ''K''<sub>M</sub>, respectively, with the same substrate <cite>Itoh2006-1</cite>. BT3687 from ''B. thetaiotaomicron'' was determined to have a ''k''<sub>cat</sub> of 0.59±0.057 s<sup>-1</sup> and a ''K''<sub>M</sub> of 71.87±12.51 μM against the substrate ΔGlcA-GlcNAc <cite>Munoz-Munoz2017</cite>.

Although it is atypical for a glycoside hydrolase family to contain enzymes capable of degrading both α- or β-linked substrates, this has also been observed in other families that deviate significantly from typical acid-base mechanisms (''e.g.'' [[GH3]], [[GH4]]) <cite>Rye2000</cite>.

== Catalytic Residues ==
A single aspartate residue has been proposed to be responsible for the hydration reaction based on substrate-complexed X-ray crystal structures, sequence conservation, and site-directed mutagenesis <cite>Itoh2006 Itoh2006-1</cite>. The first enzyme classified into the GH105 family (YteR; [{{PDBlink}}1NC5 PDB ID 1NC5] from ''B. subtilis'') was originally predicted to be a lyase based on 65% amino acid sequence similarity and over 60% matching secondary-structure characteristics with an ''N''-acyl-D-glucosamine 2-epimerase <cite>Zhang2009</cite>. Following sequence comparison to a GH88 hydrolase (a ''B. subtilis'' UGL enzyme), and additional functional characterization, YteR was determined to possess unsaturated galacturonyl hydrolase activity <cite>Itoh2006-1</cite>. A conserved aspartate residue (D143), was found to be the most likely candidate for initiating the hydration reaction, while a second conserved residue, histidine (H189), serves to correctly position a water molecule for deprotonation and addition to the C-5 carbon of the monosaccharide in the enzyme's -1 subsite <cite>Itoh2006-1</cite>. Based on sequence alignment and structural analysis, an arginine residue may take the place of this histidine residue in some GH105 enzymes (e.g. [{{PDBlink}}4CE7 PDB ID 4CE7] and [{{PDBlink}}5NOA PDB ID 5NOA]) <cite>Pettersen2004 Collen2014 Munoz-Munoz2017</cite>.

== Three-dimensional structures ==
A number of crystal structures of GH105 unsaturated glucuronyl hydrolases expressed in bacteria have been solved, including several structures from ''B. subtilis'' <cite>Zhang2009 Itoh2006 Itoh2006-1</cite>([{{PDBlink}}1NC5 PDB ID 1NC5]), and ''B. thetaiotaomicron'' <cite>Munoz-Munoz2017 Collen2014</cite>([{{PDBlink}}3K11 PDB ID 3K11]), as well as one each from ''Bacteriodes vulgatus'' ([{{PDBlink}}4Q88 PDB ID 4Q88]), ''Clostridium acetobutylicum'' <cite>Germane2015</cite>, ''Klebsiella pneumoniae'' ([{{PDBlink}}3PMM PDB ID 3PMM]), and ''Salmonella enterica'' ([{{PDBlink}}3QWT PDB ID 3QWT]). A single enzyme from the fungus ''Thielavia terrestris'' has also been solved ([{{PDBlink}}4XUV PDB ID 4XUV]). All of these enzymes share an (α/α)6-barrel structure (also similar to that of the related GH88 enzymes), with the main differences being seen in the structure of the loop region that determines the architecture of the binding site. At the bottom of the active site pocket is a conserved WxRxxGW motif, with the tryptophan and arginine residues forming a pocket that engages the carboxyl group on the ΔGalA/GlcA monosaccharide of the -1 subsite <cite>Itoh2006</cite>. While several residues may be conserved in sequence and position at the -1 subsite, the +1 subsite is much more variable, which likely accounts for the ability of this enzyme family to catalyze the hydrolysis of polysaccharides containing α- or β-bonds linked to the C-2, -4, or -6 carbon of the +1 saccharide <cite>Collen2014</cite>.

== Family Firsts ==
; First stereochemistry determination: Crystal structure of substrate-bound ''B. subtilis'' YteR unsaturated rhamnogalacturonan hydrolase in 2006 ([{{PDBlink}}1NC5 PDB ID 1NC5]). Functional analysis of this enzyme detected loss of a C=C bond compared to a detectable increase in α-keto acid following enzyme-substrate incubation <cite>Itoh2006-1</cite>.
; First catalytic residue identification: Crystal structure analysis of the ''B. subtilis'' YteR enzyme complexed with a ΔGlc-GalNac substrate analog suggested Asp143 is responsible for initiating the hydration reaction and kinetic assessment of a D143N mutant of YteR showed complete loss of catalytic activity <cite>Itoh2006-1</cite>.
; First evidence of hydration-based mechanism: While the mechanism of GH105 enzymes has not been fully described, the mechanism of the unsaturated glucuronyl hydrolase (UGL) from ''Clostridium perfringens'' (a closely-related GH88 protein) was determined via NMR using a methyl ketal intermediate analogue and monitoring of the reaction product during enzyme-substrate incubation in D<sub>2</sub>O <cite>Jongkees2011</cite>.
; First 3-D structure: The 1.6Å crystal structure of the ''B. subtilis'' protein YteR ([{{PDBlink}}1NC5 PDB ID 1NC5]), initially predicted to be a lyase-type enzyme, was reported in 2005 <cite>Zhang2009</cite>.

== References ==
<biblio>
#Cantarel2009 pmid=18838391
#Munoz-Munoz2017 pmid=28637865
#Jongkees2011 pmid=22047074
#Zhang2009 pmid=15906318
#Itoh2006 pmid=16870154
#Itoh2006-1 pmid=16781735
#Collen2014 pmid=24407291
#Koshland1953 Koshland, D.E. (1953) Stereochemistry and the Mechanism of Enzymatic Reactions. ''Biological Reviews'', vol. 28, no. 4., pp. 416-436. [https://doi.org/10.1111/j.1469-185X.1953.tb01386.x DOI:10.1111/j.1469-185X.1953.tb01386.x].
#Jongkees2014 pmid=24573682
#Rye2000 pmid=11006547
#Pettersen2004 pmid=15264254
#Germane2015 pmid=26249707

</biblio>

[[Category:Glycoside Hydrolase Families|GH105]]

User:James Stevenson

2019-07-21T22:26:13Z

James Stevenson:

[[Image:Blank_user-200px.png|200px|right]]
James Stevenson received his BScH in Biochemistry & Biochemistry from Wilfrid Laurier University in 2017, where he developed an interest in protein crystallography and structural biology. James is currently a Masters candidate in the Lab of Dr. [[Michael Suits]] at WLU, where he studies the structure and function of CAZymes in ''B. thetaiotaomicron'' responsible for nutrient accession of galactose-containing polysaccharides, as well as the structure of virulence-associated proteins in the Gram-negative oral pathogen ''P. gingivalis''. His most recent work includes the structure of the ''B. thetaiotaomicron'' galactosidase BT3158 and fused spore-maturation/nucleoside transporter protein PGN1461 from ''P. gingivalis''.

----


[[Category:Contributors|Stevenson,James]]

User:James Stevenson

2019-07-21T22:25:59Z

James Stevenson:

[[Image:Blank_user-200px.png|200px|right]]
James Stevenson received his BScH in Biochemistry & Biochemistry from Wilfrid Laurier University in 2017, where he developed an interest in protein crystallography and structural biology. James is currently a Masters candidate in the Lab of Dr. [Michael Suits] at WLU, where he studies the structure and function of CAZymes in ''B. thetaiotaomicron'' responsible for nutrient accession of galactose-containing polysaccharides, as well as the structure of virulence-associated proteins in the Gram-negative oral pathogen ''P. gingivalis''. His most recent work includes the structure of the ''B. thetaiotaomicron'' galactosidase BT3158 and fused spore-maturation/nucleoside transporter protein PGN1461 from ''P. gingivalis''.

----


[[Category:Contributors|Stevenson,James]]

User:James Stevenson

2019-07-21T21:45:48Z

James Stevenson:

[[Image:Blank_user-200px.png|200px|right]]
James Stevenson received his BScH in Biochemistry & Biochemistry from Wilfrid Laurier University in 2017, where he developed an interest in protein crystallography and structural biology. James is currently a Masters candidate in the Lab of Dr. [[User:Michael Suits]] at WLU, where he studies the structure and function of CAZymes in ''B. thetaiotaomicron'' responsible for nutrient accession of galactose-containing polysaccharides, as well as the structure of virulence-associated proteins in the Gram-negative oral pathogen ''P. gingivalis''. His most recent work includes the structure of the ''B. thetaiotaomicron'' galactosidase BT3158 and fused spore-maturation/nucleoside transporter protein PGN1461 from ''P. gingivalis''.

----


[[Category:Contributors|Stevenson,James]]

User:James Stevenson

2019-07-21T21:43:31Z

James Stevenson:

[[Image:Blank_user-200px.png|200px|right]]
James Stevenson received his BScH in Biochemistry & Biochemistry from Wilfrid Laurier University in 2017, where he developed an interest in protein crystallography and structural biology. James is currently a Masters candidate in the Lab of Dr. Michael Suits at WLU, where he studies the structure and function of CAZymes in ''B. thetaiotaomicron'' responsible for nutrient accession of galactose-containing polysaccharides, as well as the structure of virulence-associated proteins in the Gram-negative oral pathogen ''P. gingivalis''. His most recent work includes the structure of the ''B. thetaiotaomicron'' galactosidase BT3158 and fused spore-maturation/nucleoside transporter protein PGN1461 from ''P. gingivalis''.

----


[[Category:Contributors|Stevenson,James]]

User:James Stevenson

2019-07-21T19:03:49Z

James Stevenson:

[[Image:Blank_user-200px.png|200px|right]]
James Stevenson received his BScH in Biochemistry & Biochemistry from Wilfrid Laurier University in 2017, where he developed an interest in protein crystallography and structural biology. James is currently a Masters candidate in the Lab of Dr. [[Michael Suits]] at WLU, where he studies the structure and function of CAZymes in ''B. thetaiotaomicron'' responsible for nutrient accession of galactose-containing polysaccharides, as well as the structure of virulence-associated proteins in the Gram-negative oral pathogen ''P. gingivalis''. His most recent work includes the structure of the ''B. thetaiotaomicron'' galactosidase BT3158 and fused spore-maturation/nucleoside transporter protein PGN1461 from ''P. gingivalis''.

----


[[Category:Contributors|Stevenson,James]]

User:James Stevenson

2019-07-21T18:56:42Z

James Stevenson:

[[Image:Blank_user-200px.png|200px|right]]
James Stevenson received his BScH in Biochemistry & Biochemistry from Wilfrid Laurier University in 2017, where he developed an interest in protein crystallography and structural biology. James is currently a Masters candidate in the Lab of Dr. Michael Suits at WLU, where he studies the structure and function of CAZymes in ''B. thetaiotaomicron'' responsible for nutrient accession of galactose-containing polysaccharides, as well as the structure of virulence-associated proteins in the Gram-negative oral pathogen ''P. gingivalis''. His most recent work includes the structure of the ''B. thetaiotaomicron'' galactosidase BT3158 and fused spore-maturation/nucleoside transporter protein PGN1461 from ''P. gingivalis''.

----


[[Category:Contributors|Stevenson,James]]

User:James Stevenson

2019-07-21T18:56:08Z

James Stevenson:

[[Image:Blank_user-200px.png|200px|right]]
James Stevenson received his BScH in Biochemistry & Biochemistry from Wilfrid Laurier University in 2017, where he developed an interest in protein crystallography and structural biology. James is currently a Masters candidate in the Lab of Dr. Michael Suits at WLU, where he studies the structure and function of CAZymes in ''B. thetaiotaomicron'' responsible for nutrient accession of galactose-containing polysaccharides, as well as the structure of virulence-associated proteins in the Gram-negative pathogen ''P. gingivalis''. His most recent work includes the structure of the ''B. thetaiotaomicron'' galactosidase BT3158 and fused spore-maturation/nucleoside transporter protein PGN1461 from ''P. gingivalis''.

----


[[Category:Contributors|Stevenson,James]]

Glycoside Hydrolase Family 105

2019-07-21T18:53:22Z

James Stevenson:

{{CuratorApproved}}

* [[Author]]: ^^^James Stevenson^^^
* [[Responsible Curator]]: ^^^Joel Weadge^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH105'''
|-
| '''Clan'''
| none
|-
| '''Mechanism'''
| N/A
|-
| '''Active site residues'''
| known
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH105.html
|}
</div>



== Substrate specificities ==
GH105 enzymes are a class of unsaturated glucuronyl/galacturonyl hydrolases found mainly in bacteria, but a few fungal and a handful of archaeal enzymes have also been annotated <cite>Cantarel2009</cite>. Much like the [[Glycoside Hydrolase Family 88]], enzymes from GH105 perform hydrolysis via a hydration of the double bond between the C-4 and C-5 carbons of the terminal monosaccharide of their substrates <cite>Munoz-Munoz2017 Jongkees2011</cite>. Enzymes from GH105 have been organized into three subgroups: unsaturated rhamnogalacturonidases, D-4,5-unsaturated β-glucuronyl hydrolases, and d-4,5-unsaturated α-galacturonidases. The unifying feature shared between these substrates is the presence of the non-reducing monosaccharide 4-deoxy-L-threo-hex-4-enopyranuronosyl that binds at the -1 active site of the enzymes and is linked to the +1 sugar via its anomeric C-1 carbon. The 4-deoxy-L-threo-hex-4-enopyranuronosyl saccharide is defined as ΔGal or ΔGlc depending on whether it assumes an α- or β- configuration at the anomeric C-1 carbon, respectively. In degradable substrates, the sugar present at the +1 position can be linked via its C-2, C-4, or C-6 carbon, given the substrate preference of individual enzymes <cite>Zhang2009 Munoz-Munoz2017</cite>. Some of the various carbohydrate sources targeted by GH105 enzymes include: rhamnogalacturonan-I, ulvan, and the arabinogalactan decoration on certain cell wall proteins <cite>Itoh2006 Itoh2006-1 Collen2014 Munoz-Munoz2017</cite>.

== Kinetics and Mechanism ==
GH105 enzymes do not act via a typical Koshland retaining or inverting mechanism <cite>Koshland1953</cite>, rather the current proposed mechanism of action for these enzymes is hydrolysis through syn-hydration of the double bond between the C-4 and C-5 carbons of the enopyranuronosyl residue of their substrate <cite>Itoh2006</cite>. This hydration reaction forms a hemiketal that undergoes spontaneous rearrangement to form an intermediate hemiacetyl, which undergoes further rearrangement resulting in the breakage of the bond to the neighbouring saccharide (at the +1 subsite of the enzyme) of the polymer. This mechanism was initially theorized based on the oligosaccharide and amino acid arrangement in a substrate-bound crystal structure <cite>Itoh2006-1</cite>, but has been confirmed through kinetic isotope effects and NMR analysis in the highly related unsaturated glucuronyl hydrolase family [[GH88]] <cite>Jongkees2011 Jongkees2014</cite>.

The kinetics for three enzymes from the GH105 family have been determined, two from ''Bacillus subtilis'' and one from ''Bacteriodes thetaiotaomicron''. YteR from ''B. subtilis'' was found to have a ''k''<sub>cat</sub> and ''K''<sub>M</sub> of 0.2±0.011 s<sup>-1</sup> and 100±14μM , respectively, against the substrate ΔGal-Rha; in contrast, YesR was found to have much higher values for both these kinetic parameters, 13.9±0.7 s<sup>-1</sup> and 719±75 μM for ''k''<sub>cat</sub> and ''K''<sub>M</sub>, respectively, with the same substrate <cite>Itoh2006-1</cite>. BT3687 from ''B. thetaiotaomicron'' was determined to have a ''k''<sub>cat</sub> of 0.59±0.057 s<sup>-1</sup> and a ''K''<sub>M</sub> of 71.87±12.51 μM against the substrate ΔGlc-GlcNAc <cite>Munoz-Munoz2017</cite>.

Although it is atypical for a glycoside hydrolase family to contain enzymes capable of degrading both α- or β-linked substrates, this has also been observed in other families that deviate significantly from typical acid-base mechanisms (''e.g.'' [[GH3]], [[GH4]]) <cite>Rye2000</cite>.

== Catalytic Residues ==
A single aspartate residue has been proposed to be responsible for the hydration reaction based on substrate-complexed X-ray crystal structures, sequence conservation, and site-directed mutagenesis <cite>Itoh2006 Itoh2006-1</cite>. The first enzyme classified into the GH105 family ([{{PDBlink}}1NC5 PDB ID 1NC5] from ''B. subtilis'') was originally predicted to be a lyase based on 65% amino acid sequence similarity and over 60% matching secondary-structure characteristics with an N-acyl-D-glucosamine 2-epimerase <cite>Zhang2009</cite>. Following sequence comparison to a GH88 hydrolase (a ''B. subtilis'' UGL enzyme), and additional functional characterization, 1NC5 was determined to possess unsaturated galacturonyl hydrolase activity <cite>Itoh2006-1</cite>. A conserved aspartate residue (D143), was found to be the most likely candidate for initiating the hydration reaction, while a second conserved residue, histidine (H189), serves to correctly position a water molecule for deprotonation and addition to the C-5 carbon of the monosaccharide in the enzyme's -1 subsite <cite>Itoh2006-1</cite>. Based on sequence alignment and structural analysis, an arginine residue may take the place of this histidine residue in some GH105 enzymes (e.g. [{{PDBlink}}4CE7 PDB ID 4CE7] and [{{PDBlink}}5NOA PDB ID 5NOA]) <cite>Pettersen2004 Collen2014 Munoz-Munoz2017</cite>.

== Three-dimensional structures ==
A number of crystal structures of GH105 unsaturated glucuronyl hydrolases expressed in bacteria have been solved, including several structures from ''B. subtilis'' <cite>Zhang2009 Itoh2006 Itoh2006-1</cite>([{{PDBlink}}1NC5 PDB ID 1NC5]), and ''B. thetaiotaomicron'' <cite>Munoz-Munoz2017 Collen2014</cite>([{{PDBlink}}3K11 PDB ID 3K11]), as well as one each from ''Bacteriodes vulgatus'' ([{{PDBlink}}4Q88 PDB ID 4Q88]), ''Clostridium acetobutylicum'' <cite>Germane2015</cite>, ''Klebsiella pneumoniae'' ([{{PDBlink}}3PMM PDB ID 3PMM]), and ''Salmonella enterica'' ([{{PDBlink}}3QWT PDB ID 3QWT]). A single enzyme from the fungus ''Thielavia terrestris'' has also been solved ([{{PDBlink}}4XUV PDB ID 4XUV]). All of these enzymes share an (α/α)6-barrel structure (also similar to that of the related GH88 enzymes), with the main differences being seen in the structure of the loop region that determines the architecture of the binding site. At the bottom of the active site pocket is a conserved WxRxxGW motif, with the tryptophan and arginine residues forming a pocket that engages the carboxyl group on the ΔGal/Glc monosaccharide of the -1 subsite <cite>Itoh2006</cite>. While several residues may be conserved in sequence and position at the -1 subsite, the +1 subsite is much more variable, which likely accounts for the ability of this enzyme family to catalyze the hydrolysis of polysaccharides containing α- or β-bonds linked to the C-2, -4, or -6 carbon of the +1 saccharide <cite>Collen2014</cite>.

== Family Firsts ==
; First stereochemistry determination: Crystal structure of substrate-bound ''B. subtilis'' YteR unsaturated rhamnogalacturonan hydrolase in 2006 ([{{PDBlink}}1NC5 PDB ID 1NC5]). Functional analysis of this enzyme detected loss of a C=C bond compared to a detectable increase in α-keto acid following enzyme-substrate incubation <cite>Itoh2006-1</cite>.
; First catalytic residue identification: Crystal structure analysis of the ''B. subtilis'' YteR enzyme complexed with a ΔGlc-GalNac substrate analog suggested Asp143 is responsible for initiating the hydration reaction and kinetic assessment of a D143N mutant of YteR showed complete loss of catalytic activity <cite>Itoh2006-1</cite>.
; First evidence of hydration-based mechanism: While the mechanism of GH105 enzymes has not been fully described, the mechanism of the unsaturated glucuronyl hydrolase (UGL) from ''Clostridium perfringens'' (a closely-related GH88 protein) was determined via NMR using a methyl ketal intermediate analogue and monitoring of the reaction product during enzyme-substrate incubation in D<sub>2</sub>O <cite>Jongkees2011</cite>.
; First 3-D structure: The 1.6Å crystal structure of the ''B. subtilis'' protein YteR, initially predicted to be a lyase-type enzyme, was reported in 2005 <cite>Zhang2009</cite>.

== References ==
<biblio>
#Cantarel2009 pmid=18838391
#Munoz-Munoz2017 pmid=28637865
#Jongkees2011 pmid=22047074
#Zhang2009 pmid=15906318
#Itoh2006 pmid=16870154
#Itoh2006-1 pmid=16781735
#Collen2014 pmid=24407291
#Koshland1953 Koshland, D.E. (1953) Stereochemistry and the Mechanism of Enzymatic Reactions. ''Biological Reviews'', vol. 28, no. 4., pp. 416-436. [https://doi.org/10.1111/j.1469-185X.1953.tb01386.x DOI:10.1111/j.1469-185X.1953.tb01386.x].
#Jongkees2014 pmid=24573682
#Rye2000 pmid=11006547
#Pettersen2004 pmid=15264254
#Germane2015 pmid=26249707

</biblio>

[[Category:Glycoside Hydrolase Families|GH105]]

User:James Stevenson

2019-07-21T18:43:14Z

James Stevenson:

[[Image:Blank_user-200px.png|200px|right]]
James Stevenson received his BScH in Biochemistry & Biochemistry from Wilfrid Laurier University in 2017, where he developed an interest in protein crystallography and structural biology. James is currently a Masters candidate in the Lab of Dr. Michael Suits at WLU, where he studies the structure and function of CAZymes in ''B. thetaiotaomicron'' responsible for nutrient accession of galactose-containing polysaccharides, as well as the structure of virulence-associated proteins in the Gram-negative pathogen ''P. gingivalis''. His most recent work includes the structure of the ''B. thetaiotaomicron'' galactosidase BT3158 and fused spore-maturation/nucleoside transporter PGN1461 from ''P. gingivalis''.

----


[[Category:Contributors|Stevenson,James]]

User:James Stevenson

2019-07-21T18:43:01Z

James Stevenson:

[[Image:Blank_user-200px.png|200px|right]]
James Stevenson received his BScH in Biochemistry & Biochemistry from Wilfrid Laurier University in 2017, where he developed an interest in protein crystallography and structural biology. James is currently a Masters candidate in the Lab of Dr. Michael Suits at WLU, where he studies the structure and function of CAZymes in ''B. thetaiotaomicron'' responsible for nutrient accession of galactose-containing polysaccharides, as well as the structure of virulence-associated proteins in the Gram-negative pathogen ''P. gingivalis''. His most recent work includes the structure of the ''B. thetaiotaomicron'' galactosidase BT3158 and fused spore-maturation/nucleoside transporter PGN1461 from ''P. gingivalis''.

----

<biblio>

</biblio>


[[Category:Contributors|Stevenson,James]]

Glycoside Hydrolase Family 105

2019-07-19T14:11:26Z

James Stevenson:

{{UnderConstruction}}

* [[Author]]: ^^^James Stevenson^^^
* [[Responsible Curator]]: ^^^Joel Weadge^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH105'''
|-
| '''Clan'''
| none
|-
| '''Mechanism'''
| N/A
|-
| '''Active site residues'''
| known
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH105.html
|}
</div>



== Substrate specificities ==

GH105 enzymes are a class of unsaturated glucuronyl/galacturonyl hydrolases found mainly in bacteria, but a few fungial and a handful of archaeal enzymes have also been annotated <cite>Cantarel2009</cite>. Much like the glycoside hydrolase family 88, enzymes from GH105 perform hydrolysis via a hydration of the double bond between the C-4 and C-5 carbons of the terminal monosaccharide of their substrates <cite>Munoz-Munoz2017 Jongkees2011</cite>. Enzymes from GH105 have been organized into three subgroups: unsaturated rhamnogalacturonidases, d-4,5-unsaturated β-glucuronyl hydrolases, and d-4,5-unsaturated α-galacturonidases. The unifying feature shared between these substrates is the presence of the non-reducing monosaccharide 4-deoxy-L-threo-hex-4-enopyranuronosyl that binds at the -1 active site of the enzymes, and is linked to the +1 sugar via its anomeric C-1 carbon. The 4-deoxy-L-threo-hex-4-enopyranuronosyl saccharide is defined as ΔGal or ΔGlc depending on whether it assumes an α- or β- configuration, respectively. In degradable substrates, the sugar present at the +1 position can be linked via its C-2, C-4, or C-6 carbon, given the substrate preference of individual enzymes <cite>Zhang2009 Munoz-Munoz2017</cite>. Some of the various carbohydrate sources targeted by GH105 enzymes include: rhamnogalacturonan-I, ulvan, and the arabinogalactan decoration on certain cell wall proteins <cite>Itoh2006 Itoh2006-1 Collen2014 Munoz-Munoz2017</cite>.

== Kinetics and Mechanism ==

GH105 enzymes do not act via a typical Koshland retaining or inverting mechanism <cite>Koshland1953</cite>, rather the current proposed mechanism of action for these enzymes is hydrolysis through syn-hydration of the double bond between the C-4 and C-5 carbons of the enopyranuronosyl residue of their substrate <cite>Itoh2006</cite>. This hydration reaction forms a hemiketal that undergoes spontaneous rearrangement to form an intermediate hemiacetyl, which undergoes another rearrangement resulting in the breakage of the bond to the neighbouring saccharide(at the +1 subsite of the enzyme) of the polymer. This mechanism was initially theorized based on the oligosaccharide and amino acid arrangement in a substrate-bound crystal structure <cite>Itoh2006-1</cite>, but has been confirmed through kinetic isotope effects and NMR analysis in the highly related unsaturated glucuronyl hydrolase GH88 family <cite>Jongkees2011 Jongkees2014</cite>.

The kinetics for three enzymes from this family have been determined, two from ''B. subtilis'' and one from ''B. thetaiotaomicron''. YteR from ''B. subtilis'' was found to have a ''k''<sub>cat</sub> and ''K''<sub>M</sub> of 0.2±0.011s<sup>-1</sup> and 100±14μM, respectively, against the substrate ΔGal-Rha; in contrast, YesR was found to have much higher values for both these kinetic parameters, 13.9±0.7s<sup>-1</sup> and 719±75μM for ''k''<sub>cat</sub> and ''K''<sub>M</sub>, respectively, with the same substrate <cite>Itoh2006-1</cite>. BT3687 from ''B. thetaiotaomicron'' was determined to have a ''k''<sub>cat</sub> of 0.59±0.057s<sup>-1</sup> and a ''K''<sub>M</sub> of 71.87±12.51μM against the substrate ΔGlc-GlcNAc <cite>Munoz-Munoz2017</cite>.

Although it is atypical for a glycoside hydrolase family to contain enzymes capable of degrading both α- or β-linked substrates, this has also been observed in other families that deviate significantly from typical acid-base mechanisms(eg. GH3, GH4) <cite>Rye2000</cite>.

== Catalytic Residues ==

A single aspartate residue has been proposed to be responsible for the hydration reaction based on substrate-complexed X-ray crystals structures, sequence conservation, and site-directed mutagenesis <cite>Itoh2006 Itoh2006-1</cite>. The first enzyme classified into the GH105 family (PDB ID: 1NC5 from ''B. subtilis'') was originally predicted to be a lyase based on 65% amino acid sequence similarity and over 60% matching secondary-structure characteristics with an N-acyl-D-glucosamine 2-epimerase <cite>Zhang2009</cite>. Following sequence comparison to a GH88 hydrolase (a ''B. subtilis'' UGL enzyme), and additional functional characterization, 1NC5 was determined to possess unsaturated galacturonyl hydrolase activity <cite>Itoh2006-1</cite>. A conserved aspartate residue (D143), was found to be the most likely candidate for initiating the hydration reaction, while a second conserved residue, histidine (H189), serves to correctly position a water molecule for deprotonation and addition to the C-5 carbon of the monosaccharide in the enzymes -1 subsite <cite>Itoh2006-1</cite>. Based on sequence alignment and structural analysis, an arginine residue may take the place of this histidine residue in some GH105 enzymes (ie. in PDB ID enzymes: 4CE7 and 5NOA) <cite>Pettersen2004 Collen2014 Munoz-Munoz2017</cite>.

== Three-dimensional structures ==

A number of crystal structures of GH105 unsaturated glucuronyl hydrolases expressed in bacteria have been solved, including several structures from ''B. subtilis'' <cite>Zhang2009 Itoh2006 Itoh2006-1</cite>, and ''B. thetaiotaomicron'' <cite>Munoz-Munoz2017 Collen2014 JCSG2009</cite>, as well as one each from ''B. vulgatus'' <cite>Osipiuk2014</cite>, ''C. acetobutylicum'' <cite>Germane2015</cite>, ''K. pneumoniae'' <cite>Tan2010</cite>, and ''S. enterica'' <cite>Tan2011</cite>. A single enzyme from the fungus ''T. terrestris'' has also been solved <cite>Stogios2015</cite>. All of these enzymes share an (α/α)6-barrel structure (also similar to that of the related GH88 enzymes), with the main differences being seen in the structure of the loop region that determines the architecture of the binding site. At the bottom of the active site pocket is a conserved WxRxxGW motif, with the tryptophan and arginine residues forming a pocket that engages the carboxyl group on the ΔGal/Glc monosaccharide of the -1 subsite <cite>Itoh2006</cite>. While several residues may be conserved in sequence and position at the -1 subsite, the +1 subsite is much more variable, which likely accounts for the ability of this enzyme family to catalyze the hydrolysis of polysaccharides containing α- or β-bonds linked to the C-2, -4, or -6 carbon of the +1 saccharide <cite>Collen2014</cite>.

== Family Firsts ==

; First stereochemistry determination: Crystal structure of substrate-bound ''Bacillus subtilis'' YteR unsaturated rhamnogalacturonan hydrolase in 2006. Functional analysis of this enzyme detected loss of a C=C bond compared to a detectable increase in α-keto acid following enzyme-substrate incubation <cite>Itoh2006-1</cite>.
; First catalytic residue identification: Crystal structure analysis of YteR (the ''Bacillus subtilis'' unsaturated rhamnogalacturonal hydrolase) complexed with a ΔGlc-GalNac substrate analog suggested Asp143 is responsible for initiating the hydration reaction, and kinetic assessment of a D143N mutant of YteR showed complete loss of catalytic activity <cite>Itoh2006-1</cite>.
; First evidence of hydration-based mechanism: While the mechanism of GH105 enzymes has not been fully described, the mechanism of the unsaturated glucuronyl hydrolase (UGL) from ''Clostridium perfringens'' (a closely-related GH88 protein) was determined via NMR using a methyl ketal intermediate analogue and monitoring of the reaction product during enzyme-substrate incubation in D<sub>2</sub>O <cite>Jongkees2011</cite>.
; First 3-D structure: The 1.6Å crystal structure of the ''Bacillus subtilis'' protein YteR, initially predicted to be a lyase-type enzyme, was reported in 2005 <cite>Zhang2009</cite>.

== References ==

<biblio>
#Cantarel2009 pmid=18838391
#Munoz-Munoz2017 pmid=28637865
#Jongkees2011 pmid=22047074
#Zhang2009 pmid=15906318
#Itoh2006 pmid=16870154
#Itoh2006-1 pmid=16781735
#Collen2014 pmid=24407291
#Koshland1953 Koshland, D.E. (1953) Stereochemistry and the Mechanism of Enzymatic Reactions. ''Biological Reviews'', vol. 28, no. 4., pp. 416-436. [https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-185X.1953.tb01386.x].
#Jongkees2014 pmid=24573682
#Rye2000 pmid=11006547
#Pettersen2004 pmid=15264254
#JCSG2009 Joint Center for Structural Genomics(JCSG) (2009) Crystal structure of Putative glycosyl hydrolase (NP_813087.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.80 A resolution. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3K11].
#Osipiuk2014 Osipiuk, J., Li, H., Endres, M., Joachimiak, A. (2014) Glycosyl hydrolase family 88 from Bacteroides vulgatus. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/4Q88].
#Germane2015 pmid=26249707
#Tan2010 Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A. (2010) The crystal structure of a possible member of GH105 family from Klebsiella pneumoniae subsp. pneumoniae MGH 78578. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3pmm].
#Tan2011 Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A. (2011) The crystal structure of a possible member of GH105 family from Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3qwt].
#Stogios2015 Stogios, P.J., Xu, X., Cui, H., Yim, V., Savchenko, A. (2015) Crystal structure of a glycoside hydrolase family 105 (GH105) enzyme from Thielavia terrestris. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/4XUV].
</biblio>

[[Category:Glycoside Hydrolase Families|GH105]]

Glycoside Hydrolase Family 105

2019-07-18T23:27:19Z

James Stevenson:

{{UnderConstruction}}

* [[Author]]: ^^^James Stevenson^^^
* [[Responsible Curator]]: ^^^Joel Weadge^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH105'''
|-
| '''Clan'''
| none
|-
| '''Mechanism'''
| N/A
|-
| '''Active site residues'''
| known
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH105.html
|}
</div>



== Substrate specificities ==

GH105 enzymes are a class of unsaturated glucuronyl/galacturonyl hydrolases found mainly in bacteria, but a few fungial and a handful of archaeal enzymes have also been annotated <cite>Cantarel2009</cite>. Much like the glycoside hydrolase family 88, enzymes from GH105 perform hydrolysis via a hydration of the double bond between the C-4 and C-5 carbons of the terminal monosaccharide of their substrates <cite>Munoz-Munoz2017 Jongkees2011</cite>. Enzymes from GH105 have been organized into three subgroups: unsaturated rhamnogalacturonidases, d-4,5-unsaturated β-glucuronyl hydrolases, and d-4,5-unsaturated α-galacturonidases. The unifying feature shared between these substrates is the presence of the non-reducing monosaccharide 4-deoxy-L-threo-hex-4-enopyranuronosyl that binds at the -1 active site of the enzymes, and is linked to the +1 sugar via its anomeric C-1 carbon. The 4-deoxy-L-threo-hex-4-enopyranuronosyl saccharide is defined as ΔGal or ΔGlc depending on whether it assumes an α- or β- configuration, respectively. In degradable substrates, the sugar present at the +1 position can be linked via its C-2, C-4, or C-6 carbon, given the substrate preference of individual enzymes <cite>Zhang2009 Munoz-Munoz2017</cite>. Some of the various carbohydrate sources targeted by GH105 enzymes include: rhamnogalacturonan-I, ulvan, and the arabinogalactan decoration on certain cell wall proteins <cite>Itoh2006 Itoh2006-1 Collen2014 Munoz-Munoz2017</cite>.

== Kinetics and Mechanism ==

GH105 enzymes do not act via a typical Koshland retaining or inverting mechanism <cite>Koshland1953</cite>, rather the current proposed mechanism of action for these enzymes is hydrolysis through syn-hydration of the double bond between the C-4 and C-5 carbons of the enopyranuronosyl residue of their substrate <cite>Itoh2006</cite>. This hydration reaction forms a hemiketal that undergoes spontaneous rearrangement to form an intermediate hemiacetyl, which undergoes another rearrangement resulting in the breakage of the bond to the neighbouring saccharide(at the +1 subsite of the enzyme) of the polymer. This mechanism was initially theorized based on the oligosaccharide and amino acid arrangement in a substrate-bound crystal structure <cite>Itoh2006-1</cite>, but has been confirmed through kinetic isotope effects and NMR analysis in the highly related unsaturated glucuronyl hydrolase GH88 family <cite>Jongkees2011 Jongkees2014</cite>.

The kinetics for three enzymes from this family have been determined, two from ''B. subtilis'' and one from ''B. thetaiotaomicron''. YteR from ''B. subtilis'' was found to have a kcat and KM of 0.2±0.011s<sup>-1</sup> and 100±14μM, respectively, against the substrate ΔGal-Rha; in contrast, YesR was found to have much higher values for both these kinetic parameters, 13.9±0.7s<sup>-1</sup> and 719±75μM for kcat and KM, respectively, with the same substrate <cite>Itoh2006-1</cite>. BT3687 from ''B. thetaiotaomicron'' was determined to have a kcat of 0.59±0.057s<sup>-1</sup> and a KM of 71.87±12.51μM against the substrate ΔGlc-GlcNAc <cite>Munoz-Munoz2017</cite>.

Although it is atypical for a glycoside hydrolase family to contain enzymes capable of degrading both α- or β-linked substrates, this has also been observed in other families that deviate significantly from typical acid-base mechanisms(eg. GH3, GH4) <cite>Rye2000</cite>.

== Catalytic Residues ==

A single aspartate residue has been proposed to be responsible for the hydration reaction based on substrate-complexed X-ray crystals structures, sequence conservation, and site-directed mutagenesis <cite>Itoh2006 Itoh2006-1</cite>. The first enzyme classified into the GH105 family (PDB ID: 1NC5 from ''B. subtilis'') was originally predicted to be a lyase based on 65% amino acid sequence similarity and over 60% matching secondary-structure characteristics with an N-acyl-D-glucosamine 2-epimerase <cite>Zhang2009</cite>. Following sequence comparison to a GH88 hydrolase (a ''B. subtilis'' UGL enzyme), and additional functional characterization, 1NC5 was determined to possess unsaturated galacturonyl hydrolase activity <cite>Itoh2006-1</cite>. A conserved aspartate residue (D143), was found to be the most likely candidate for initiating the hydration reaction, while a second conserved residue, histidine (H189), serves to correctly position a water molecule for deprotonation and addition to the C-5 carbon of the monosaccharide in the enzymes -1 subsite <cite>Itoh2006-1</cite>. Based on sequence alignment and structural analysis, an arginine residue may take the place of this histidine residue in some GH105 enzymes (ie. in PDB ID enzymes: 4CE7 and 5NOA) <cite>Pettersen2004 Collen2014 Munoz-Munoz2017</cite>.

== Three-dimensional structures ==

A number of crystal structures of GH105 unsaturated glucuronyl hydrolases expressed in bacteria have been solved, including several structures from ''B. subtilis'' <cite>Zhang2009 Itoh2006 Itoh2006-1</cite>, and ''B. thetaiotaomicron'' <cite>Munoz-Munoz2017 Collen2014 JCSG2009</cite>, as well as one each from ''B. vulgatus'' <cite>Osipiuk2014</cite>, ''C. acetobutylicum'' <cite>Germane2015</cite>, ''K. pneumoniae'' <cite>Tan2010</cite>, and ''S. enterica'' <cite>Tan2011</cite>. A single enzyme from the fungus ''T. terrestris'' has also been solved <cite>Stogios2015</cite>. All of these enzymes share an (α/α)6-barrel structure (also similar to that of the related GH88 enzymes), with the main differences being seen in the structure of the loop region that determines the architecture of the binding site. At the bottom of the active site pocket is a conserved WxRxxGW motif, with the tryptophan and arginine residues forming a pocket that engages the carboxyl group on the ΔGal/Glc monosaccharide of the -1 subsite <cite>Itoh2006</cite>. While several residues may be conserved in sequence and position at the -1 subsite, the +1 subsite is much more variable, which likely accounts for the ability of this enzyme family to catalyze the hydrolysis of polysaccharides containing α- or β-bonds linked to the C-2, -4, or -6 carbon of the +1 saccharide <cite>Collen2014</cite>.

== Family Firsts ==

; First stereochemistry determination: Crystal structure of substrate-bound ''Bacillus subtilis'' YteR unsaturated rhamnogalacturonan hydrolase in 2006. Functional analysis of this enzyme detected loss of a C=C bond compared to a detectable increase in α-keto acid following enzyme-substrate incubation <cite>Itoh2006-1</cite>.
; First catalytic residue identification: Crystal structure analysis of YteR (the ''Bacillus subtilis'' unsaturated rhamnogalacturonal hydrolase) complexed with a ΔGlc-GalNac substrate analog suggested Asp143 is responsible for initiating the hydration reaction, and kinetic assessment of a D143N mutant of YteR showed complete loss of catalytic activity <cite>Itoh2006-1</cite>.
; First evidence of hydration-based mechanism: While the mechanism of GH105 enzymes has not been fully described, the mechanism of the unsaturated glucuronyl hydrolase (UGL) from ''Clostridium perfringens'' (a closely-related GH88 protein) was determined via NMR using a methyl ketal intermediate analogue and monitoring of the reaction product during enzyme-substrate incubation in D<sub>2</sub>O <cite>Jongkees2011</cite>.
; First 3-D structure: The 1.6Å crystal structure of the ''Bacillus subtilis'' protein YteR, initially predicted to be a lyase-type enzyme, was reported in 2005 <cite>Zhang2009</cite>.

== References ==

<biblio>
#Cantarel2009 pmid=18838391
#Munoz-Munoz2017 pmid=28637865
#Jongkees2011 pmid=22047074
#Zhang2009 pmid=15906318
#Itoh2006 pmid=16870154
#Itoh2006-1 pmid=16781735
#Collen2014 pmid=24407291
#Koshland1953 Koshland, D.E. (1953) Stereochemistry and the Mechanism of Enzymatic Reactions. ''Biological Reviews'', vol. 28, no. 4., pp. 416-436. [https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-185X.1953.tb01386.x].
#Jongkees2014 pmid=24573682
#Rye2000 pmid=11006547
#Pettersen2004 pmid=15264254
#JCSG2009 Joint Center for Structural Genomics(JCSG) (2009) Crystal structure of Putative glycosyl hydrolase (NP_813087.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.80 A resolution. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3K11].
#Osipiuk2014 Osipiuk, J., Li, H., Endres, M., Joachimiak, A. (2014) Glycosyl hydrolase family 88 from Bacteroides vulgatus. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/4Q88].
#Germane2015 pmid=26249707
#Tan2010 Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A. (2010) The crystal structure of a possible member of GH105 family from Klebsiella pneumoniae subsp. pneumoniae MGH 78578. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3pmm].
#Tan2011 Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A. (2011) The crystal structure of a possible member of GH105 family from Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3qwt].
#Stogios2015 Stogios, P.J., Xu, X., Cui, H., Yim, V., Savchenko, A. (2015) Crystal structure of a glycoside hydrolase family 105 (GH105) enzyme from Thielavia terrestris. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/4XUV].
</biblio>

[[Category:Glycoside Hydrolase Families|GH105]]

Glycoside Hydrolase Family 105

2019-07-18T23:25:20Z

James Stevenson:

{{UnderConstruction}}

* [[Author]]: ^^^James Stevenson^^^
* [[Responsible Curator]]: ^^^Joel Weadge^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH105'''
|-
| '''Clan'''
| none
|-
| '''Mechanism'''
| N/A
|-
| '''Active site residues'''
| known
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH105.html
|}
</div>



== Substrate specificities ==

GH105 enzymes are a class of unsaturated glucuronyl/galacturonyl hydrolases found mainly in bacteria, but a few fungial and a handful of archaeal enzymes have also been annotated <cite>Cantarel2009</cite>. Much like the glycoside hydrolase family 88, enzymes from GH105 perform hydrolysis via a hydration of the double bond between the C-4 and C-5 carbons of the terminal monosaccharide of their substrates <cite>Munoz-Munoz2017 Jongkees2011</cite>. Enzymes from GH105 have been organized into three subgroups: unsaturated rhamnogalacturonidases, d-4,5-unsaturated β-glucuronyl hydrolases, and d-4,5-unsaturated α-galacturonidases. The unifying feature shared between these substrates is the presence of the non-reducing monosaccharide 4-deoxy-L-threo-hex-4-enopyranuronosyl that binds at the -1 active site of the enzymes, and is linked to the +1 sugar via its anomeric C-1 carbon. The 4-deoxy-L-threo-hex-4-enopyranuronosyl saccharide is defined as ΔGal or ΔGlc depending on whether it assumes an α- or β- configuration, respectively. In degradable substrates, the sugar present at the +1 position can be linked via its C-2, C-4, or C-6 carbon, given the substrate preference of individual enzymes <cite>Zhang2009 Munoz-Munoz2017</cite>. Some of the various carbohydrate sources targeted by GH105 enzymes include: rhamnogalacturonan-I, ulvan, and the arabinogalactan decoration on certain cell wall proteins <cite>Itoh2006 Itoh2006-1 Collen2014 Munoz-Munoz2017</cite>.

== Kinetics and Mechanism ==

GH105 enzymes do not act via a typical Koshland retaining or inverting mechanism <cite>Koshland1953</cite>, rather the current proposed mechanism of action for these enzymes is hydrolysis through syn-hydration of the double bond between the C-4 and C-5 carbons of the enopyranuronosyl residue of their substrate <cite>Itoh2006</cite>. This hydration reaction forms a hemiketal that undergoes spontaneous rearrangement to form an intermediate hemiacetyl, which undergoes another rearrangement resulting in the breakage of the bond to the neighbouring saccharide(at the +1 subsite of the enzyme) of the polymer. This mechanism was initially theorized based on the oligosaccharide and amino acid arrangement in a substrate-bound crystal structure <cite>Itoh2006-1</cite>, but has been confirmed through kinetic isotope effects and NMR analysis in the highly related unsaturated glucuronyl hydrolase GH88 family <cite>Jongkees2011 Jongkees2014</cite>.

The kinetics for three enzymes from this family have been determined, two from ''B. subtilis'' and one from ''B. thetaiotaomicron''. YteR from ''B. subtilis'' was found to have a kcat and KM of 0.2±0.011s<sup>-1</sup> and 100±14μM, respectively, against the substrate ΔGal-Rha; in contrast, YesR was found to have much higher values for both these kinetic parameters, 13.9±0.7s<sup>-1</sup> and 719±75μM for kcat and KM, respectively, with the same substrate <cite>Itoh2006-1</cite>. BT3687 from ''B. thetaiotaomicron'' was determined to have a kcat of 0.59±0.057s<sup>-1</sup> and a KM of 71.87±12.51μM against the substrate ΔGlc-GlcNAc <cite>Munoz-Munoz2017</cite>.

Although it is atypical for a glycoside hydrolase family to contain enzymes capable of degrading both α- or β-linked substrates, this has also been observed in other families that deviate significantly from typical acid-base mechanisms(eg. GH3, GH4) <cite>Rye2000</cite>.

== Catalytic Residues ==

A single aspartate residue has been proposed to be responsible for the hydration reaction based on substrate-complexed X-ray crystals structures, sequence conservation, and site-directed mutagenesis <cite>Itoh2006 Itoh2006-1</cite>. The first enzyme classified into the GH105 family (PDB ID: 1NC5 from ''B. subtilis'') was originally predicted to be a lyase based on 65% amino acid sequence similarity and over 60% matching secondary-structure characteristics with an N-acyl-D-glucosamine 2-epimerase <cite>Zhang2009</cite>. Following sequence comparison to a GH88 hydrolase (a ''B. subtilis'' UGL enzyme), and additional functional characterization, 1NC5 was determined to possess unsaturated galacturonyl hydrolase activity <cite>Itoh2006-1</cite>. A conserved aspartate residue (D143), was found to be the most likely candidate for initiating the hydration reaction, while a second conserved residue, histidine (H189), serves to correctly position a water molecule for deprotonation and addition to the C-5 carbon of the monosaccharide in the enzymes -1 subsite <cite>Itoh2006-1</cite>. Based on sequence alignment and structural analysis, an arginine residue may take the place of this histidine residue in some GH105 enzymes (ie. in PDB ID enzymes: 4CE7 and 5NOA) <cite>Pettersen2004 Collen2014 Munoz-Munoz2017</cite>.

== Three-dimensional structures ==

A number of crystal structures of GH105 unsaturated glucuronyl hydrolases expressed in bacteria have been solved, including several structures from ''B. subtilis'' <cite>Zhang2009 Itoh2006 Itoh2006-1</cite>, and ''B. thetaiotaomicron'' <cite>Munoz-Munoz2017 Collen2014 JCSG2009</cite>, as well as one each from ''B. vulgatus'' <cite>Osipiuk2014</cite>, ''C. acetobutylicum'' <cite>Germane2015</cite>, ''K. pneumoniae'' <cite>Tan2010</cite>, and ''S. enterica'' <cite>Tan2011</cite>. A single enzyme from the fungus ''T. terrestris'' has also been solved <cite>Stogios2015</cite>. All of these enzymes share an (α/α)6-barrel structure (also similar to that of the related GH88 enzymes), with the main differences being seen in the structure of the loop region that determines the architecture of the binding site. At the bottom of the active site pocket is a conserved WxRxxGW motif, with the tryptophan and arginine residues forming a pocket that engages the carboxyl group on the ΔGal/Glc monosaccharide of the -1 subsite <cite>Itoh2006</cite>. While several residues may be conserved in sequence and position at the -1 subsite, the +1 subsite is much more variable, which likely accounts for the ability of this enzyme family to catalyze the hydrolysis of polysaccharides containing α- or β-bonds linked to the C-2, -4, or -6 carbon of the +1 saccharide <cite>Collen2014</cite>.

== Family Firsts ==

; First stereochemistry determination: Crystal structure of substrate-bound ''Bacillus subtilis'' YteR unsaturated rhamnogalacturonan hydrolase in 2006. Functional analysis of this enzyme detected loss of a C=C bond compared to a detectable increase in α-keto acid following enzyme-substrate incubation <cite>Itoh2006-1</cite>.
; First catalytic nucleophile identification: Crystal structure analysis of YteR (the ''Bacillus subtilis'' unsaturated rhamnogalacturonal hydrolase) complexed with a ΔGlc-GalNac substrate analog suggested Asp143 is responsible for initiating the hydration reaction, and kinetic assessment of a D143N mutant of YteR showed complete loss of catalytic activity <cite>Itoh2006-1</cite>.
; First general acid/base residue identification: While the mechanism of GH105 enzymes has not been fully described, the mechanism of the unsaturated glucuronyl hydrolase (UGL) from ''Clostridium perfringens'' (a closely-related GH88 protein) was determined via NMR using a methyl ketal intermediate analogue and monitoring of the reaction product during enzyme-substrate incubation in D<sub>2</sub>O <cite>Jongkees2011</cite>.
; First 3-D structure: The 1.6Å crystal structure of the ''Bacillus subtilis'' protein YteR, initially predicted to be a lyase-type enzyme, was reported in 2005 <cite>Zhang2009</cite>.

== References ==

<biblio>
#Cantarel2009 pmid=18838391
#Munoz-Munoz2017 pmid=28637865
#Jongkees2011 pmid=22047074
#Zhang2009 pmid=15906318
#Itoh2006 pmid=16870154
#Itoh2006-1 pmid=16781735
#Collen2014 pmid=24407291
#Koshland1953 Koshland, D.E. (1953) Stereochemistry and the Mechanism of Enzymatic Reactions. ''Biological Reviews'', vol. 28, no. 4., pp. 416-436. [https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-185X.1953.tb01386.x].
#Jongkees2014 pmid=24573682
#Rye2000 pmid=11006547
#Pettersen2004 pmid=15264254
#JCSG2009 Joint Center for Structural Genomics(JCSG) (2009) Crystal structure of Putative glycosyl hydrolase (NP_813087.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.80 A resolution. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3K11].
#Osipiuk2014 Osipiuk, J., Li, H., Endres, M., Joachimiak, A. (2014) Glycosyl hydrolase family 88 from Bacteroides vulgatus. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/4Q88].
#Germane2015 pmid=26249707
#Tan2010 Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A. (2010) The crystal structure of a possible member of GH105 family from Klebsiella pneumoniae subsp. pneumoniae MGH 78578. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3pmm].
#Tan2011 Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A. (2011) The crystal structure of a possible member of GH105 family from Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3qwt].
#Stogios2015 Stogios, P.J., Xu, X., Cui, H., Yim, V., Savchenko, A. (2015) Crystal structure of a glycoside hydrolase family 105 (GH105) enzyme from Thielavia terrestris. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/4XUV].
</biblio>

[[Category:Glycoside Hydrolase Families|GH105]]

Glycoside Hydrolase Family 105

2019-07-18T22:30:56Z

James Stevenson:

{{UnderConstruction}}

* [[Author]]: ^^^James Stevenson^^^
* [[Responsible Curator]]: ^^^Joel Weadge^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH105'''
|-
| '''Clan'''
| GH-x
|-
| '''Mechanism'''
| retaining/inverting
|-
| '''Active site residues'''
| known/not known
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH105.html
|}
</div>



== Substrate specificities ==

GH105 enzymes are a class of unsaturated glucuronyl/galacturonyl hydrolases found mainly in bacteria, but a few fungial and a handful of archaeal enzymes have also been annotated <cite>Cantarel2009</cite>. Much like the glycoside hydrolase family 88, enzymes from GH105 perform hydrolysis via a hydration of the double bond between the C-4 and C-5 carbons of the terminal monosaccharide of their substrates <cite>Munoz-Munoz2017 Jongkees2011</cite>. Enzymes from GH105 have been organized into three subgroups: unsaturated rhamnogalacturonidases, d-4,5-unsaturated β-glucuronyl hydrolases, and d-4,5-unsaturated α-galacturonidases. The unifying feature shared between these substrates is the presence of the non-reducing monosaccharide 4-deoxy-L-threo-hex-4-enopyranuronosyl that binds at the -1 active site of the enzymes, and is linked to the +1 sugar via its anomeric C-1 carbon. The 4-deoxy-L-threo-hex-4-enopyranuronosyl saccharide is defined as ΔGal or ΔGlc depending on whether it assumes an α- or β- configuration, respectively. In degradable substrates, the sugar present at the +1 position can be linked via its C-2, C-4, or C-6 carbon, given the substrate preference of individual enzymes <cite>Zhang2009 Munoz-Munoz2017</cite>. Some of the various carbohydrate sources targeted by GH105 enzymes include: rhamnogalacturonan-I, ulvan, and the arabinogalactan decoration on certain cell wall proteins <cite>Itoh2006 Itoh2006-1 Collen2014 Munoz-Munoz2017</cite>.

== Kinetics and Mechanism ==

GH105 enzymes do not act via a typical Koshland retaining or inverting mechanism <cite>Koshland1953</cite>, rather the current proposed mechanism of action for these enzymes is hydrolysis through syn-hydration of the double bond between the C-4 and C-5 carbons of the enopyranuronosyl residue of their substrate <cite>Itoh2006</cite>. This hydration reaction forms a hemiketal that undergoes spontaneous rearrangement to form an intermediate hemiacetyl, which undergoes another rearrangement resulting in the breakage of the bond to the neighbouring saccharide(at the +1 subsite of the enzyme) of the polymer. This mechanism was initially theorized based on the oligosaccharide and amino acid arrangement in a substrate-bound crystal structure <cite>Itoh2006-1</cite>, but has been confirmed through kinetic isotope effects and NMR analysis in the highly related unsaturated glucuronyl hydrolase GH88 family <cite>Jongkees2011 Jongkees2014</cite>.

The kinetics for three enzymes from this family have been determined, two from ''B. subtilis'' and one from ''B. thetaiotaomicron''. YteR from ''B. subtilis'' was found to have a kcat and KM of 0.2±0.011s<sup>-1</sup> and 100±14μM, respectively, against the substrate ΔGal-Rha; in contrast, YesR was found to have much higher values for both these kinetic parameters, 13.9±0.7s<sup>-1</sup> and 719±75μM for kcat and KM, respectively, with the same substrate <cite>Itoh2006-1</cite>. BT3687 from ''B. thetaiotaomicron'' was determined to have a kcat of 0.59±0.057s<sup>-1</sup> and a KM of 71.87±12.51μM against the substrate ΔGlc-GlcNAc <cite>Munoz-Munoz2017</cite>.

Although it is atypical for a glycoside hydrolase family to contain enzymes capable of degrading both α- or β-linked substrates, this has also been observed in other families that deviate significantly from typical acid-base mechanisms(eg. GH3, GH4) <cite>Rye2000</cite>.

== Catalytic Residues ==

A single aspartate residue has been proposed to be responsible for the hydration reaction based on substrate-complexed X-ray crystals structures, sequence conservation, and site-directed mutagenesis <cite>Itoh2006 Itoh2006-1</cite>. The first enzyme classified into the GH105 family (PDB ID: 1NC5 from ''B. subtilis'') was originally predicted to be a lyase based on 65% amino acid sequence similarity and over 60% matching secondary-structure characteristics with an N-acyl-D-glucosamine 2-epimerase <cite>Zhang2009</cite>. Following sequence comparison to a GH88 hydrolase (a ''B. subtilis'' UGL enzyme), and additional functional characterization, 1NC5 was determined to possess unsaturated galacturonyl hydrolase activity <cite>Itoh2006-1</cite>. A conserved aspartate residue (D143), was found to be the most likely candidate for initiating the hydration reaction, while a second conserved residue, histidine (H189), serves to correctly position a water molecule for deprotonation and addition to the C-5 carbon of the monosaccharide in the enzymes -1 subsite <cite>Itoh2006-1</cite>. Based on sequence alignment and structural analysis, an arginine residue may take the place of this histidine residue in some GH105 enzymes (ie. in PDB ID enzymes: 4CE7 and 5NOA) <cite>Pettersen2004 Collen2014 Munoz-Munoz2017</cite>.

== Three-dimensional structures ==

A number of crystal structures of GH105 unsaturated glucuronyl hydrolases expressed in bacteria have been solved, including several structures from ''B. subtilis'' <cite>Zhang2009 Itoh2006 Itoh2006-1</cite>, and ''B. thetaiotaomicron'' <cite>Munoz-Munoz2017 Collen2014 JCSG2009</cite>, as well as one each from ''B. vulgatus'' <cite>Osipiuk2014</cite>, ''C. acetobutylicum'' <cite>Germane2015</cite>, ''K. pneumoniae'' <cite>Tan2010</cite>, and ''S. enterica'' <cite>Tan2011</cite>. A single enzyme from the fungus ''T. terrestris'' has also been solved <cite>Stogios2015</cite>. All of these enzymes share an (α/α)6-barrel structure (also similar to that of the related GH88 enzymes), with the main differences being seen in the structure of the loop region that determines the architecture of the binding site. At the bottom of the active site pocket is a conserved WxRxxGW motif, with the tryptophan and arginine residues forming a pocket that engages the carboxyl group on the ΔGal/Glc monosaccharide of the -1 subsite <cite>Itoh2006</cite>. While several residues may be conserved in sequence and position at the -1 subsite, the +1 subsite is much more variable, which likely accounts for the ability of this enzyme family to catalyze the hydrolysis of polysaccharides containing α- or β-bonds linked to the C-2, -4, or -6 carbon of the +1 saccharide <cite>Collen2014</cite>.

== Family Firsts ==

; First stereochemistry determination: Crystal structure of substrate-bound ''Bacillus subtilis'' YteR unsaturated rhamnogalacturonan hydrolase in 2006. Functional analysis of this enzyme detected loss of a C=C bond compared to a detectable increase in α-keto acid following enzyme-substrate incubation <cite>Itoh2006-1</cite>.
; First catalytic nucleophile identification: Crystal structure analysis of YteR (the ''Bacillus subtilis'' unsaturated rhamnogalacturonal hydrolase) complexed with a ΔGlc-GalNac substrate analog suggested Asp143 is responsible for initiating the hydration reaction, and kinetic assessment of a D143N mutant of YteR showed complete loss of catalytic activity <cite>Itoh2006-1</cite>.
; First general acid/base residue identification: While the mechanism of GH105 enzymes has not been fully described, the mechanism of the unsaturated glucuronyl hydrolase (UGL) from ''Clostridium perfringens'' (a closely-related GH88 protein) was determined via NMR using a methyl ketal intermediate analogue and monitoring of the reaction product during enzyme-substrate incubation in D<sub>2</sub>O <cite>Jongkees2011</cite>.
; First 3-D structure: The 1.6Å crystal structure of the ''Bacillus subtilis'' protein YteR, initially predicted to be a lyase-type enzyme, was reported in 2005 <cite>Zhang2009</cite>.

== References ==

<biblio>
#Cantarel2009 pmid=18838391
#Munoz-Munoz2017 pmid=28637865
#Jongkees2011 pmid=22047074
#Zhang2009 pmid=15906318
#Itoh2006 pmid=16870154
#Itoh2006-1 pmid=16781735
#Collen2014 pmid=24407291
#Koshland1953 Koshland, D.E. (1953) Stereochemistry and the Mechanism of Enzymatic Reactions. ''Biological Reviews'', vol. 28, no. 4., pp. 416-436. [https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-185X.1953.tb01386.x].
#Jongkees2014 pmid=24573682
#Rye2000 pmid=11006547
#Pettersen2004 pmid=15264254
#JCSG2009 Joint Center for Structural Genomics(JCSG) (2009) Crystal structure of Putative glycosyl hydrolase (NP_813087.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.80 A resolution. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3K11].
#Osipiuk2014 Osipiuk, J., Li, H., Endres, M., Joachimiak, A. (2014) Glycosyl hydrolase family 88 from Bacteroides vulgatus. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/4Q88].
#Germane2015 pmid=26249707
#Tan2010 Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A. (2010) The crystal structure of a possible member of GH105 family from Klebsiella pneumoniae subsp. pneumoniae MGH 78578. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3pmm].
#Tan2011 Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A. (2011) The crystal structure of a possible member of GH105 family from Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3qwt].
#Stogios2015 Stogios, P.J., Xu, X., Cui, H., Yim, V., Savchenko, A. (2015) Crystal structure of a glycoside hydrolase family 105 (GH105) enzyme from Thielavia terrestris. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/4XUV].
</biblio>

[[Category:Glycoside Hydrolase Families|GH105]]

Glycoside Hydrolase Family 105

2019-07-18T22:30:06Z

James Stevenson:

{{UnderConstruction}}

* [[Author]]: ^^^James Stevenson^^^
* [[Responsible Curator]]: ^^^Joel Weadge^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH105'''
|-
| '''Clan'''
| GH-x
|-
| '''Mechanism'''
| retaining/inverting
|-
| '''Active site residues'''
| known/not known
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH105.html
|}
</div>



== Substrate specificities ==

GH105 enzymes are a class of unsaturated glucuronyl/galacturonyl hydrolases found mainly in bacteria, but a few fungial and a handful of archaeal enzymes have also been annotated <cite>Cantarel2009</cite>. Much like the glycoside hydrolase family 88, enzymes from GH105 perform hydrolysis via a hydration of the double bond between the C-4 and C-5 carbons of the terminal monosaccharide of their substrates <cite>Munoz-Munoz2017 Jongkees2011</cite>. Enzymes from GH105 have been organized into three subgroups: unsaturated rhamnogalacturonidases, d-4,5-unsaturated β-glucuronyl hydrolases, and d-4,5-unsaturated α-galacturonidases. The unifying feature shared between these substrates is the presence of the non-reducing monosaccharide 4-deoxy-L-threo-hex-4-enopyranuronosyl that binds at the -1 active site of the enzymes, and is linked to the +1 sugar via its anomeric C-1 carbon. The 4-deoxy-L-threo-hex-4-enopyranuronosyl saccharide is defined as ΔGal or ΔGlc depending on whether it assumes an α- or β- configuration, respectively. In degradable substrates, the sugar present at the +1 position can be linked via its C-2, C-4, or C-6 carbon, given the substrate preference of individual enzymes <cite>Zhang2009 Munoz-Munoz2017</cite>. Some of the various carbohydrate sources targeted by GH105 enzymes include: rhamnogalacturonan-I, ulvan, and the arabinogalactan decoration on certain cell wall proteins <cite>Itoh2006 Itoh2006-1 Collen2014 Munoz-Munoz2017</cite>.

== Kinetics and Mechanism ==

GH105 enzymes do not act via a typical Koshland retaining or inverting mechanism <cite>Koshland1953</cite>, rather the current proposed mechanism of action for these enzymes is hydrolysis through syn-hydration of the double bond between the C-4 and C-5 carbons of the enopyranuronosyl residue of their substrate <cite>Itoh2006</cite>. This hydration reaction forms a hemiketal that undergoes spontaneous rearrangement to form an intermediate hemiacetyl, which undergoes another rearrangement resulting in the breakage of the bond to the neighbouring saccharide(at the +1 subsite of the enzyme) of the polymer. This mechanism was initially theorized based on the oligosaccharide and amino acid arrangement in a substrate-bound crystal structure <cite>Itoh2006-1</cite>, but has been confirmed through kinetic isotope effects and NMR analysis in the highly related unsaturated glucuronyl hydrolase GH88 family <cite>Jongkees2011 Jongkees2014</cite>.

The kinetics for three enzymes from this family have been determined, two from ''B. subtilis'' and one from ''B. thetaiotaomicron''. YteR from ''B. subtilis'' was found to have a kcat and KM of 0.2±0.011s<sup>-1</sup> and 100±14μM, respectively, against the substrate ΔGal-Rha; in contrast, YesR was found to have much higher values for both these kinetic parameters, 13.9±0.7s<sup>-1</sup> and 719±75μM for kcat and KM, respectively, with the same substrate <cite>Itoh2006-1</cite>. BT3687 from ''B. thetaiotaomicron'' was determined to have a kcat of 0.59±0.057s<sup>-1</sup> and a KM of 71.87±12.51μM against the substrate ΔGlc-GlcNAc <cite>Munoz-Munoz2017</cite>.

Although it is atypical for a glycoside hydrolase family to contain enzymes capable of degrading both α- or β-linked substrates, this has also been observed in other families that deviate significantly from typical acid-base mechanisms(eg. GH3, GH4) <cite>Rye2000</cite>.

== Catalytic Residues ==

A single aspartate residue has been proposed to be responsible for the hydration reaction based on substrate-complexed X-ray crystals structures, sequence conservation, and site-directed mutagenesis <cite>Itoh2006 Itoh2006-1</cite>. The first enzyme classified into the GH105 family (PDB ID: 1NC5 from ''B. subtilis'') was originally predicted to be a lyase based on 65% amino acid sequence similarity and over 60% matching secondary-structure characteristics with an N-acyl-D-glucosamine 2-epimerase <cite>Zhang2009</cite>. Following sequence comparison to a GH88 hydrolase (a ''B. subtilis'' UGL enzyme), and additional functional characterization, 1NC5 was determined to possess unsaturated galacturonyl hydrolase activity <cite>Itoh2006-1</cite>. A conserved aspartate residue (D143), was found to be the most likely candidate for initiating the hydration reaction, while a second conserved residue, histidine (H189), serves to correctly position a water molecule for deprotonation and addition to the C-5 carbon of the monosaccharide in the enzymes -1 subsite <cite>Itoh2006-1</cite>. Based on sequence alignment and structural analysis, an arginine residue may take the place of this histidine residue in some GH105 enzymes (ie. in PDB ID enzymes: 4CE7 and 5NOA) <cite>Pettersen2004 Collen2014 Munoz-Munoz2017</cite>.

== Three-dimensional structures ==

A number of crystal structures of GH105 unsaturated glucuronyl hydrolases expressed in bacteria have been solved, including several structures from ''B. subtilis'' <cite>Zhang2009 Itoh2006 Itoh2006-1</cite>, and ''B. thetaiotaomicron'' <cite>Munoz-Munoz2017 Collen2014 JCSG2009</cite>, as well as one each from ''B. vulgatus'' <cite>Osipiuk2014</cite>, ''C. acetobutylicum'' <cite>Germane2015</cite>, ''K. pneumoniae'' <cite>Tan2010</cite>, and ''S. enterica'' <cite>Tan2011</cite>. A single enzyme from the fungus ''T. terrestris'' has also been solved <cite>Stogios2015</cite>. All of these enzymes share an (α/α)6-barrel structure (also similar to that of the related GH88 enzymes), with the main differences being seen in the structure of the loop region that determines the architecture of the binding site. At the bottom of the active site pocket is a conserved WxRxxGW motif, with the tryptophan and arginine residues forming a pocket that engages the carboxyl group on the ΔGal/Glc monosaccharide of the -1 subsite <cite>Itoh2006</cite>. While several residues may be conserved in sequence and position at the -1 subsite, the +1 subsite is much more variable, which likely accounts for the ability of this enzyme family to catalyze the hydrolysis of polysaccharides containing α- or β-bonds linked to the C-2, -4, or -6 carbon of the +1 saccharide <cite>Collen2014</cite>.

== Family Firsts ==

; First stereochemistry determination: Crystal structure of substrate-bound ''Bacillus subtilis'' YteR unsaturated rhamnogalacturonan hydrolase in 2006. Functional analysis of this enzyme detected loss of a C=C bond compared to a detectable increase in α-keto acid following enzyme-substrate incubation <cite>Itoh2006-1</cite>.
; First catalytic nucleophile identification: Crystal structure analysis of YteR (the ''Bacillus subtilis'' unsaturated rhamnogalacturonal hydrolase) complexed with a ΔGlc-GalNac substrate analog suggested Asp143 is responsible for initiating the hydration reaction, and kinetic assessment of a D143N mutant of YteR showed complete loss of catalytic activity <cite>Itoh2006-1</cite>.
; First general acid/base residue identification: While the mechanism of GH105 enzymes has not been fully described, the mechanism of the unsaturated glucuronyl hydrolase (UGL) from ''Clostridium perfringens'' (a closely-related GH88 protein) was determined via NMR using a methyl ketal intermediate analogue and monitoring of the reaction product during enzyme-substrate incubation in D<sub>2</sub>O <cite>Jongkees2011</cite>.
; First 3-D structure: The 1.6Å crystal structure of the ''Bacillus subtilis'' protein YteR, initially predicted to be a lyase-type enzyme, was reported in 2005 <cite>Zhang2009</cite>.

== References ==

<biblio>
#Cantarel2009 pmid=18838391
#Munoz-Munoz2017 pmid=28637865
#Jongkees2011 pmid=22047074
#Zhang2009 pmid=15906318
#Itoh2006 pmid=16870154
#Itoh2006-1 pmid=16781735
#Collen2014 pmid=24407291
#Koshland1953 Koshland, D.E. (1953) Stereochemistry and the Mechanism of Enzymatic Reactions. ''Biological Reviews'', vol. 28, no. 4., pp. 416-436. [https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-185X.1953.tb01386.x].
#Jongkees2014 pmid=24573682
#Rye2000 pmid=11006547
#Pettersen2004 pmid=15264254
#JCSG2009 JointCenterforStructuralGenomics(JCSG) (2009) Crystal structure of Putative glycosyl hydrolase (NP_813087.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.80 A resolution. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3K11].
#Osipiuk2014 Osipiuk, J., Li, H., Endres, M., Joachimiak, A. (2014) Glycosyl hydrolase family 88 from Bacteroides vulgatus. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/4Q88].
#Germane2015 pmid=26249707
#Tan2010 Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A. (2010) The crystal structure of a possible member of GH105 family from Klebsiella pneumoniae subsp. pneumoniae MGH 78578. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3pmm].
#Tan2011 Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A. (2011) The crystal structure of a possible member of GH105 family from Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3qwt].
#Stogios2015 Stogios, P.J., Xu, X., Cui, H., Yim, V., Savchenko, A. (2015) Crystal structure of a glycoside hydrolase family 105 (GH105) enzyme from Thielavia terrestris. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/4XUV].
</biblio>

[[Category:Glycoside Hydrolase Families|GH105]]

Glycoside Hydrolase Family 105

2019-07-18T22:26:08Z

James Stevenson:

{{UnderConstruction}}

* [[Author]]: ^^^James Stevenson^^^
* [[Responsible Curator]]: ^^^Joel Weadge^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH105'''
|-
| '''Clan'''
| GH-x
|-
| '''Mechanism'''
| retaining/inverting
|-
| '''Active site residues'''
| known/not known
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH105.html
|}
</div>



== Substrate specificities ==

GH105 enzymes are a class of unsaturated glucuronyl/galacturonyl hydrolases found mainly in bacteria, but a few fungial and a handful of archaeal enzymes have also been annotated <cite>Cantarel2009</cite>. Much like the glycoside hydrolase family 88, enzymes from GH105 perform hydrolysis via a hydration of the double bond between the C-4 and C-5 carbons of the terminal monosaccharide of their substrates <cite>Munoz-Munoz2017 Jongkees2011</cite>. Enzymes from GH105 have been organized into three subgroups: unsaturated rhamnogalacturonidases, d-4,5-unsaturated β-glucuronyl hydrolases, and d-4,5-unsaturated α-galacturonidases. The unifying feature shared between these substrates is the presence of the non-reducing monosaccharide 4-deoxy-L-threo-hex-4-enopyranuronosyl that binds at the -1 active site of the enzymes, and is linked to the +1 sugar via its anomeric C-1 carbon. The 4-deoxy-L-threo-hex-4-enopyranuronosyl saccharide is defined as ΔGal or ΔGlc depending on whether it assumes an α- or β- configuration, respectively. In degradable substrates, the sugar present at the +1 position can be linked via its C-2, C-4, or C-6 carbon, given the substrate preference of individual enzymes <cite>Zhang2009 Munoz-Munoz2017</cite>. Some of the various carbohydrate sources targeted by GH105 enzymes include: rhamnogalacturonan-I, ulvan, and the arabinogalactan decoration on certain cell wall proteins <cite>Itoh2006 Itoh2006-1 Collen2014 Munoz-Munoz2017</cite>.

== Kinetics and Mechanism ==

GH105 enzymes do not act via a typical Koshland retaining or inverting mechanism <cite>Koshland1953</cite>, rather the current proposed mechanism of action for these enzymes is hydrolysis through syn-hydration of the double bond between the C-4 and C-5 carbons of the enopyranuronosyl residue of their substrate <cite>Itoh2006</cite>. This hydration reaction forms a hemiketal that undergoes spontaneous rearrangement to form an intermediate hemiacetyl, which undergoes another rearrangement resulting in the breakage of the bond to the neighbouring saccharide(at the +1 subsite of the enzyme) of the polymer. This mechanism was initially theorized based on the oligosaccharide and amino acid arrangement in a substrate-bound crystal structure <cite>Itoh2006-1</cite>, but has been confirmed through kinetic isotope effects and NMR analysis in the highly related unsaturated glucuronyl hydrolase GH88 family <cite>Jongkees2011 Jongkees2014</cite>.

The kinetics for three enzymes from this family have been determined, two from B. subtilis and one from B. thetaiotaomicron. YteR from B. subtilis was found to have a kcat and KM of 0.2±0.011s<sup>-1</sup> and 100±14μM, respectively, against the substrate ΔGal-Rha; in contrast, YesR was found to have much higher values for both these kinetic parameters, 13.9±0.7s<sup>-1</sup> and 719±75μM for kcat and KM, respectively, with the same substrate <cite>Itoh2006-1</cite>. BT3687 from B. thetaiotaomicron was determined to have a kcat of 0.59±0.057s<sup>-1</sup> and a KM of 71.87±12.51μM against the substrate ΔGlc-GlcNAc <cite>Munoz-Munoz2017</cite>.

Although it is atypical for a glycoside hydrolase family to contain enzymes capable of degrading both α- or β-linked substrates, this has also been observed in other families that deviate significantly from typical acid-base mechanisms(eg. GH3, GH4) <cite>Rye2000</cite>.

== Catalytic Residues ==

A single aspartate residue has been proposed to be responsible for the hydration reaction based on substrate-complexed X-ray crystals structures, sequence conservation, and site-directed mutagenesis <cite>Itoh2006 Itoh2006-1</cite>. The first enzyme classified into the GH105 family (PDB ID: 1NC5 from B. subtilis) was originally predicted to be a lyase based on 65% amino acid sequence similarity and over 60% matching secondary-structure characteristics with an N-acyl-D-glucosamine 2-epimerase <cite>Zhang2009</cite>. Following sequence comparison to a GH88 hydrolase (a B. subtilis UGL enzyme), and additional functional characterization, 1NC5 was determined to possess unsaturated galacturonyl hydrolase activity <cite>Itoh2006-1</cite>. A conserved aspartate residue (D143), was found to be the most likely candidate for initiating the hydration reaction, while a second conserved residue, histidine (H189), serves to correctly position a water molecule for deprotonation and addition to the C-5 carbon of the monosaccharide in the enzymes -1 subsite <cite>Itoh2006-1</cite>. Based on sequence alignment and structural analysis, an arginine residue may take the place of this histidine residue in some GH105 enzymes (ie. in PDB ID enzymes: 4CE7 and 5NOA) <cite>Pettersen2004 Collen2014 Munoz-Munoz2017</cite>.

== Three-dimensional structures ==

A number of crystal structures of GH105 unsaturated glucuronyl hydrolases expressed in bacteria have been solved, including several structures from B. subtilis <cite>Zhang2009 Itoh2006 Itoh2006-1</cite>, and B. thetaiotaomicron <cite>Munoz-Munoz2017 Collen2014 JCSG2009</cite>, as well as one each from B. vulgatus <cite>Osipiuk2014</cite>, C. acetobutylicum <cite>Germane2015</cite>, K. pneumoniae <cite>Tan2010</cite>, and S. enterica <cite>Tan2011</cite>. A single enzyme from the fungus T. terrestris has also been solved <cite>Stogios2015</cite>. All of these enzymes share an (α/α)6-barrel structure (also similar to that of the related GH88 enzymes), with the main differences being seen in the structure of the loop region that determines the architecture of the binding site. At the bottom of the active site pocket is a conserved WxRxxGW motif, with the tryptophan and arginine residues forming a pocket that engages the carboxyl group on the ΔGal/Glc monosaccharide of the -1 subsite <cite>Itoh2006</cite>. While several residues may be conserved in sequence and position at the -1 subsite, the +1 subsite is much more variable, which likely accounts for the ability of this enzyme family to catalyze the hydrolysis of polysaccharides containing α- or β-bonds linked to the C-2, -4, or -6 carbon of the +1 saccharide <cite>Collen2014</cite>.

== Family Firsts ==

; First stereochemistry determination: Crystal structure of substrate-bound Bacillus subtilis YteR unsaturated rhamnogalacturonan hydrolase in 2006. Functional analysis of this enzyme detected loss of a C=C bond compared to a detectable increase in α-keto acid following enzyme-substrate incubation <cite>Itoh2006-1</cite>.
; First catalytic nucleophile identification: Crystal structure analysis of YteR (the Bacillus subtilis unsaturated rhamnogalacturonal hydrolase) complexed with a ΔGlc-GalNac substrate analog suggested Asp143 is responsible for initiating the hydration reaction, and kinetic assessment of a D143N mutant of YteR showed complete loss of catalytic activity <cite>Itoh2006-1</cite>.
; First general acid/base residue identification: While the mechanism of GH105 enzymes has not been fully described, the mechanism of the unsaturated glucuronyl hydrolase (UGL) from Clostridium perfringens (a closely-related GH88 protein) was determined via NMR using a methyl ketal intermediate analogue and monitoring of the reaction product during enzyme-substrate incubation in D<sub>2</sub>O <cite>Jongkees2011</cite>.
; First 3-D structure: The 1.6Å crystal structure of the Bacillus subtilis protein YteR, initially predicted to be a lyase-type enzyme, was reported in 2005 <cite>Zhang2009</cite>.

== References ==

<biblio>
#Cantarel2009 pmid=18838391
#Munoz-Munoz2017 pmid=28637865
#Jongkees2011 pmid=22047074
#Zhang2009 pmid=15906318
#Itoh2006 pmid=16870154
#Itoh2006-1 pmid=16781735
#Collen2014 pmid=24407291
#Koshland1953 Koshland, D.E. (1953) Stereochemistry and the Mechanism of Enzymatic Reactions. ''Biological Reviews'', vol. 28, no. 4., pp. 416-436. [https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-185X.1953.tb01386.x].
#Jongkees2014 pmid=24573682
#Rye2000 pmid=11006547
#Pettersen2004 pmid=15264254
#JCSG2009 JointCenterforStructuralGenomics(JCSG) (2009) Crystal structure of Putative glycosyl hydrolase (NP_813087.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.80 A resolution. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3K11].
#Osipiuk2014 Osipiuk, J., Li, H., Endres, M., Joachimiak, A. (2014) Glycosyl hydrolase family 88 from Bacteroides vulgatus. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/4Q88].
#Germane2015 pmid=26249707
#Tan2010 Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A. (2010) The crystal structure of a possible member of GH105 family from Klebsiella pneumoniae subsp. pneumoniae MGH 78578. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3pmm].
#Tan2011 Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A. (2011) The crystal structure of a possible member of GH105 family from Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3qwt].
#Stogios2015 Stogios, P.J., Xu, X., Cui, H., Yim, V., Savchenko, A. (2015) Crystal structure of a glycoside hydrolase family 105 (GH105) enzyme from Thielavia terrestris. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/4XUV].
</biblio>

[[Category:Glycoside Hydrolase Families|GH105]]

Glycoside Hydrolase Family 105

2019-07-18T22:23:59Z

James Stevenson:

{{UnderConstruction}}

* [[Author]]: ^^^James Stevenson^^^
* [[Responsible Curator]]: ^^^Joel Weadge^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH105'''
|-
| '''Clan'''
| GH-x
|-
| '''Mechanism'''
| retaining/inverting
|-
| '''Active site residues'''
| known/not known
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH105.html
|}
</div>



== Substrate specificities ==

GH105 enzymes are a class of unsaturated glucuronyl/galacturonyl hydrolases found mainly in bacteria, but a few fungial and a handful of archaeal enzymes have also been annotated <cite>Cantarel2009</cite>. Much like the glycoside hydrolase family 88, enzymes from GH105 perform hydrolysis via a hydration of the double bond between the C-4 and C-5 carbons of the terminal monosaccharide of their substrates <cite>Munoz-Munoz2017 Jongkees2011</cite>. Enzymes from GH105 have been organized into three subgroups: unsaturated rhamnogalacturonidases, d-4,5-unsaturated β-glucuronyl hydrolases, and d-4,5-unsaturated α-galacturonidases. The unifying feature shared between these substrates is the presence of the non-reducing monosaccharide 4-deoxy-L-threo-hex-4-enopyranuronosyl that binds at the -1 active site of the enzymes, and is linked to the +1 sugar via its anomeric C-1 carbon. The 4-deoxy-L-threo-hex-4-enopyranuronosyl saccharide is defined as ΔGal or ΔGlc depending on whether it assumes an α- or β- configuration, respectively. In degradable substrates, the sugar present at the +1 position can be linked via its C-2, C-4, or C-6 carbon, given the substrate preference of individual enzymes <cite>Zhang2009 Munoz-Munoz2017</cite>. Some of the various carbohydrate sources targeted by GH105 enzymes include: rhamnogalacturonan-I, ulvan, and the arabinogalactan decoration on certain cell wall proteins <cite>Itoh2006 Itoh2006-1 Collen2014 Munoz-Munoz2017</cite>.

== Kinetics and Mechanism ==

GH105 enzymes do not act via a typical Koshland retaining or inverting mechanism <cite>Koshland1953</cite>, rather the current proposed mechanism of action for these enzymes is hydrolysis through syn-hydration of the double bond between the C-4 and C-5 carbons of the enopyranuronosyl residue of their substrate <cite>Itoh2006</cite>. This hydration reaction forms a hemiketal that undergoes spontaneous rearrangement to form an intermediate hemiacetyl, which undergoes another rearrangement resulting in the breakage of the bond to the neighbouring saccharide(at the +1 subsite of the enzyme) of the polymer. This mechanism was initially theorized based on the oligosaccharide and amino acid arrangement in a substrate-bound crystal structure <cite>Itoh2006-1</cite>, but has been confirmed through kinetic isotope effects and NMR analysis in the highly related unsaturated glucuronyl hydrolase GH88 family <cite>Jongkees2011 Jongkees2014</cite>.

The kinetics for three enzymes from this family have been determined, two from B. subtilis and one from B. thetaiotaomicron. YteR from B. subtilis was found to have a kcat and KM of 0.2±0.011s-1 and 100±14μM, respectively, against the substrate ΔGal-Rha; in contrast, YesR was found to have much higher values for both these kinetic parameters, 13.9±0.7s-1 and 719±75μM for kcat and KM, respectively, with the same substrate <cite>Itoh2006-1</cite>. BT3687 from B. thetaiotaomicron was determined to have a kcat of 0.59±0.057s-1 and a KM of 71.87±12.51μM against the substrate ΔGlc-GlcNAc <cite>Munoz-Munoz2017</cite>.

Although it is atypical for a glycoside hydrolase family to contain enzymes capable of degrading both α- or β-linked substrates, this has also been observed in other families that deviate significantly from typical acid-base mechanisms(eg. GH3, GH4) <cite>Rye2000</cite>.

== Catalytic Residues ==

A single aspartate residue has been proposed to be responsible for the hydration reaction based on substrate-complexed X-ray crystals structures, sequence conservation, and site-directed mutagenesis <cite>Itoh2006 Itoh2006-1</cite>. The first enzyme classified into the GH105 family (PDB ID: 1NC5 from B. subtilis) was originally predicted to be a lyase based on 65% amino acid sequence similarity and over 60% matching secondary-structure characteristics with an N-acyl-D-glucosamine 2-epimerase <cite>Zhang2009</cite>. Following sequence comparison to a GH88 hydrolase (a B. subtilis UGL enzyme), and additional functional characterization, 1NC5 was determined to possess unsaturated galacturonyl hydrolase activity <cite>Itoh2006-1</cite>. A conserved aspartate residue (D143), was found to be the most likely candidate for initiating the hydration reaction, while a second conserved residue, histidine (H189), serves to correctly position a water molecule for deprotonation and addition to the C-5 carbon of the monosaccharide in the enzymes -1 subsite <cite>Itoh2006-1</cite>. Based on sequence alignment and structural analysis, an arginine residue may take the place of this histidine residue in some GH105 enzymes (ie. in PDB ID enzymes: 4CE7 and 5NOA) <cite>Pettersen2004 Collen2014 Munoz-Munoz2017</cite>.

== Three-dimensional structures ==

A number of crystal structures of GH105 unsaturated glucuronyl hydrolases expressed in bacteria have been solved, including several structures from B. subtilis <cite>Zhang2009 Itoh2006 Itoh2006-1</cite>, and B. thetaiotaomicron <cite>Munoz-Munoz2017 Collen2014 JCSG2009</cite>, as well as one each from B. vulgatus <cite>Osipiuk2014</cite>, C. acetobutylicum <cite>Germane2015</cite>, K. pneumoniae <cite>Tan2010</cite>, and S. enterica <cite>Tan2011</cite>. A single enzyme from the fungus T. terrestris has also been solved <cite>Stogios2015</cite>. All of these enzymes share an (α/α)6-barrel structure (also similar to that of the related GH88 enzymes), with the main differences being seen in the structure of the loop region that determines the architecture of the binding site. At the bottom of the active site pocket is a conserved WxRxxGW motif, with the tryptophan and arginine residues forming a pocket that engages the carboxyl group on the ΔGal/Glc monosaccharide of the -1 subsite <cite>Itoh2006</cite>. While several residues may be conserved in sequence and position at the -1 subsite, the +1 subsite is much more variable, which likely accounts for the ability of this enzyme family to catalyze the hydrolysis of polysaccharides containing α- or β-bonds linked to the C-2, -4, or -6 carbon of the +1 saccharide <cite>Collen2014</cite>.

== Family Firsts ==

; First stereochemistry determination: Crystal structure of substrate-bound Bacillus subtilis YteR unsaturated rhamnogalacturonan hydrolase in 2006. Functional analysis of this enzyme detected loss of a C=C bond compared to a detectable increase in α-keto acid following enzyme-substrate incubation <cite>Itoh2006-1</cite>.
; First catalytic nucleophile identification: Crystal structure analysis of YteR (the Bacillus subtilis unsaturated rhamnogalacturonal hydrolase) complexed with a ΔGlc-GalNac substrate analog suggested Asp143 is responsible for initiating the hydration reaction, and kinetic assessment of a D143N mutant of YteR showed complete loss of catalytic activity <cite>Itoh2006-1</cite>.
; First general acid/base residue identification: While the mechanism of GH105 enzymes has not been fully described, the mechanism of the unsaturated glucuronyl hydrolase (UGL) from Clostridium perfringens (a closely-related GH88 protein) was determined via NMR using a methyl ketal intermediate analogue and monitoring of the reaction product during enzyme-substrate incubation in D<sub>2</sub>O <cite>Jongkees2011</cite>.
; First 3-D structure: The 1.6Å crystal structure of the Bacillus subtilis protein YteR, initially predicted to be a lyase-type enzyme, was reported in 2005 <cite>Zhang2009</cite>.

== References ==

<biblio>
#Cantarel2009 pmid=18838391
#Munoz-Munoz2017 pmid=28637865
#Jongkees2011 pmid=22047074
#Zhang2009 pmid=15906318
#Itoh2006 pmid=16870154
#Itoh2006-1 pmid=16781735
#Collen2014 pmid=24407291
#Koshland1953 Koshland, D.E. (1953) Stereochemistry and the Mechanism of Enzymatic Reactions. ''Biological Reviews'', vol. 28, no. 4., pp. 416-436. [https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-185X.1953.tb01386.x].
#Jongkees2014 pmid=24573682
#Rye2000 pmid=11006547
#Pettersen2004 pmid=15264254
#JCSG2009 JointCenterforStructuralGenomics(JCSG) (2009) Crystal structure of Putative glycosyl hydrolase (NP_813087.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.80 A resolution. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3K11].
#Osipiuk2014 Osipiuk, J., Li, H., Endres, M., Joachimiak, A. (2014) Glycosyl hydrolase family 88 from Bacteroides vulgatus. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/4Q88].
#Germane2015 pmid=26249707
#Tan2010 Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A. (2010) The crystal structure of a possible member of GH105 family from Klebsiella pneumoniae subsp. pneumoniae MGH 78578. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3pmm].
#Tan2011 Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A. (2011) The crystal structure of a possible member of GH105 family from Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3qwt].
#Stogios2015 Stogios, P.J., Xu, X., Cui, H., Yim, V., Savchenko, A. (2015) Crystal structure of a glycoside hydrolase family 105 (GH105) enzyme from Thielavia terrestris. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/4XUV].
</biblio>

[[Category:Glycoside Hydrolase Families|GH105]]

Glycoside Hydrolase Family 105

2019-07-18T22:23:33Z

James Stevenson:

{{UnderConstruction}}

* [[Author]]: ^^^James Stevenson^^^
* [[Responsible Curator]]: ^^^Joel Weadge^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH105'''
|-
| '''Clan'''
| GH-x
|-
| '''Mechanism'''
| retaining/inverting
|-
| '''Active site residues'''
| known/not known
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH105.html
|}
</div>



== Substrate specificities ==

GH105 enzymes are a class of unsaturated glucuronyl/galacturonyl hydrolases found mainly in bacteria, but a few fungial and a handful of archaeal enzymes have also been annotated <cite>Cantarel2009</cite>. Much like the glycoside hydrolase family 88, enzymes from GH105 perform hydrolysis via a hydration of the double bond between the C-4 and C-5 carbons of the terminal monosaccharide of their substrates <cite>Munoz-Munoz2017 Jongkees2011</cite>. Enzymes from GH105 have been organized into three subgroups: unsaturated rhamnogalacturonidases, d-4,5-unsaturated β-glucuronyl hydrolases, and d-4,5-unsaturated α-galacturonidases. The unifying feature shared between these substrates is the presence of the non-reducing monosaccharide 4-deoxy-L-threo-hex-4-enopyranuronosyl that binds at the -1 active site of the enzymes, and is linked to the +1 sugar via its anomeric C-1 carbon. The 4-deoxy-L-threo-hex-4-enopyranuronosyl saccharide is defined as ΔGal or ΔGlc depending on whether it assumes an α- or β- configuration, respectively. In degradable substrates, the sugar present at the +1 position can be linked via its C-2, C-4, or C-6 carbon, given the substrate preference of individual enzymes <cite>Zhang2009 Munoz-Munoz2017</cite>. Some of the various carbohydrate sources targeted by GH105 enzymes include: rhamnogalacturonan-I, ulvan, and the arabinogalactan decoration on certain cell wall proteins <cite>Itoh2006 Itoh2006-1 Collen2014 Munoz-Munoz2017</cite>.

== Kinetics and Mechanism ==

GH105 enzymes do not act via a typical Koshland retaining or inverting mechanism <cite>Koshland1953</cite>, rather the current proposed mechanism of action for these enzymes is hydrolysis through syn-hydration of the double bond between the C-4 and C-5 carbons of the enopyranuronosyl residue of their substrate <cite>Itoh2006</cite>. This hydration reaction forms a hemiketal that undergoes spontaneous rearrangement to form an intermediate hemiacetyl, which undergoes another rearrangement resulting in the breakage of the bond to the neighbouring saccharide(at the +1 subsite of the enzyme) of the polymer. This mechanism was initially theorized based on the oligosaccharide and amino acid arrangement in a substrate-bound crystal structure <cite>Itoh2006-1</cite>, but has been confirmed through kinetic isotope effects and NMR analysis in the highly related unsaturated glucuronyl hydrolase GH88 family <cite>Jongkees2011 Jongkees2014</cite>.

The kinetics for three enzymes from this family have been determined, two from B. subtilis and one from B. thetaiotaomicron. YteR from B. subtilis was found to have a kcat and KM of 0.2±0.011s-1 and 100±14μM, respectively, against the substrate ΔGal-Rha; in contrast, YesR was found to have much higher values for both these kinetic parameters, 13.9±0.7s-1 and 719±75μM for kcat and KM, respectively, with the same substrate <cite>Itoh2006-1</cite>. BT3687 from B. thetaiotaomicron was determined to have a kcat of 0.59±0.057s-1 and a KM of 71.87±12.51μM against the substrate ΔGlc-GlcNAc <cite>Munoz-Munoz2017</cite>.

Although it is atypical for a glycoside hydrolase family to contain enzymes capable of degrading both α- or β-linked substrates, this has also been observed in other families that deviate significantly from typical acid-base mechanisms(eg. GH3, GH4) <cite>Rye2000</cite>.

== Catalytic Residues ==

A single aspartate residue has been proposed to be responsible for the hydration reaction based on substrate-complexed X-ray crystals structures, sequence conservation, and site-directed mutagenesis <cite>Itoh2006 Itoh2006-1</cite>. The first enzyme classified into the GH105 family (PDB ID: 1NC5 from B. subtilis) was originally predicted to be a lyase based on 65% amino acid sequence similarity and over 60% matching secondary-structure characteristics with an N-acyl-D-glucosamine 2-epimerase <cite>Zhang2009</cite>. Following sequence comparison to a GH88 hydrolase (a B. subtilis UGL enzyme), and additional functional characterization, 1NC5 was determined to possess unsaturated galacturonyl hydrolase activity <cite>Itoh2006-1</cite>. A conserved aspartate residue (D143), was found to be the most likely candidate for initiating the hydration reaction, while a second conserved residue, histidine (H189), serves to correctly position a water molecule for deprotonation and addition to the C-5 carbon of the monosaccharide in the enzymes -1 subsite <cite>Itoh2006-1</cite>. Based on sequence alignment and structural analysis, an arginine residue may take the place of this histidine residue in some GH105 enzymes (ie. in PDB ID enzymes: 4CE7 and 5NOA) <cite>Pettersen2004 Collen2014 Munoz-Munoz2017</cite>.

== Three-dimensional structures ==

A number of crystal structures of GH105 unsaturated glucuronyl hydrolases expressed in bacteria have been solved, including several structures from B. subtilis <cite>Zhang2009 Itoh2006 Itoh2006-1</cite>, and B. thetaiotaomicron <cite>Munoz-Munoz2017 Collen2014 JCSG2009</cite>, as well as one each from B. vulgatus <cite>Osipiuk2014</cite>, C. acetobutylicum <cite>Germane2015</cite>, K. pneumoniae <cite>Tan2010</cite>, and S. enterica <cite>Tan2011</cite>. A single enzyme from the fungus T. terrestris has also been solved <cite>Stogios2015</cite>. All of these enzymes share an (α/α)6-barrel structure (also similar to that of the related GH88 enzymes), with the main differences being seen in the structure of the loop region that determines the architecture of the binding site. At the bottom of the active site pocket is a conserved WxRxxGW motif, with the tryptophan and arginine residues forming a pocket that engages the carboxyl group on the ΔGal/Glc monosaccharide of the -1 subsite <cite>Itoh2006</cite>. While several residues may be conserved in sequence and position at the -1 subsite, the +1 subsite is much more variable, which likely accounts for the ability of this enzyme family to catalyze the hydrolysis of polysaccharides containing α- or β-bonds linked to the C-2, -4, or -6 carbon of the +1 saccharide <cite>Collen2014</cite>.

== Family Firsts ==

; First stereochemistry determination: Crystal structure of substrate-bound Bacillus subtilis YteR unsaturated rhamnogalacturonan hydrolase in 2006. Functional analysis of this enzyme detected loss of a C=C bond compared to a detectable increase in α-keto acid following enzyme-substrate incubation <cite>Itoh2006-1</cite>.
; First catalytic nucleophile identification: Crystal structure analysis of YteR (the Bacillus subtilis unsaturated rhamnogalacturonal hydrolase) complexed with a ΔGlc-GalNac substrate analog suggested Asp143 is responsible for initiating the hydration reaction, and kinetic assessment of a D143N mutant of YteR showed complete loss of catalytic activity <cite>Itoh2006-1</cite>.
; First general acid/base residue identification: While the mechanism of GH105 enzymes has not been fully described, the mechanism of the unsaturated glucuronyl hydrolase (UGL) from Clostridium perfringens (a closely-related GH88 protein) was determined via NMR using a methyl ketal intermediate analogue and monitoring of the reaction product during enzyme-substrate incubation in D<sub>2</sub>O <cite>Jongkees2011</cite>.
; First 3-D structure: The 1.6Å crystal structure of the Bacillus subtilis protein YteR, initially predicted to be a lyase-type enzyme, was reported in 2005 <cite>Zhang</cite>.

== References ==

<biblio>
#Cantarel2009 pmid=18838391
#Munoz-Munoz2017 pmid=28637865
#Jongkees2011 pmid=22047074
#Zhang2009 pmid=15906318
#Itoh2006 pmid=16870154
#Itoh2006-1 pmid=16781735
#Collen2014 pmid=24407291
#Koshland1953 Koshland, D.E. (1953) Stereochemistry and the Mechanism of Enzymatic Reactions. ''Biological Reviews'', vol. 28, no. 4., pp. 416-436. [https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-185X.1953.tb01386.x].
#Jongkees2014 pmid=24573682
#Rye2000 pmid=11006547
#Pettersen2004 pmid=15264254
#JCSG2009 JointCenterforStructuralGenomics(JCSG) (2009) Crystal structure of Putative glycosyl hydrolase (NP_813087.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.80 A resolution. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3K11].
#Osipiuk2014 Osipiuk, J., Li, H., Endres, M., Joachimiak, A. (2014) Glycosyl hydrolase family 88 from Bacteroides vulgatus. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/4Q88].
#Germane2015 pmid=26249707
#Tan2010 Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A. (2010) The crystal structure of a possible member of GH105 family from Klebsiella pneumoniae subsp. pneumoniae MGH 78578. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3pmm].
#Tan2011 Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A. (2011) The crystal structure of a possible member of GH105 family from Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3qwt].
#Stogios2015 Stogios, P.J., Xu, X., Cui, H., Yim, V., Savchenko, A. (2015) Crystal structure of a glycoside hydrolase family 105 (GH105) enzyme from Thielavia terrestris. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/4XUV].
</biblio>

[[Category:Glycoside Hydrolase Families|GH105]]

Glycoside Hydrolase Family 105

2019-07-18T22:19:27Z

James Stevenson:

{{UnderConstruction}}

* [[Author]]: ^^^James Stevenson^^^
* [[Responsible Curator]]: ^^^Joel Weadge^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH105'''
|-
| '''Clan'''
| GH-x
|-
| '''Mechanism'''
| retaining/inverting
|-
| '''Active site residues'''
| known/not known
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH105.html
|}
</div>



== Substrate specificities ==

GH105 enzymes are a class of unsaturated glucuronyl/galacturonyl hydrolases found mainly in bacteria, but a few fungial and a handful of archaeal enzymes have also been annotated <cite>Cantarel2009</cite>. Much like the glycoside hydrolase family 88, enzymes from GH105 perform hydrolysis via a hydration of the double bond between the C-4 and C-5 carbons of the terminal monosaccharide of their substrates <cite>Munoz-Munoz2017 Jongkees2011</cite>. Enzymes from GH105 have been organized into three subgroups: unsaturated rhamnogalacturonidases, d-4,5-unsaturated β-glucuronyl hydrolases, and d-4,5-unsaturated α-galacturonidases. The unifying feature shared between these substrates is the presence of the non-reducing monosaccharide 4-deoxy-L-threo-hex-4-enopyranuronosyl that binds at the -1 active site of the enzymes, and is linked to the +1 sugar via its anomeric C-1 carbon. The 4-deoxy-L-threo-hex-4-enopyranuronosyl saccharide is defined as ΔGal or ΔGlc depending on whether it assumes an α- or β- configuration, respectively. In degradable substrates, the sugar present at the +1 position can be linked via its C-2, C-4, or C-6 carbon, given the substrate preference of individual enzymes <cite>Zhang2009 Munoz-Munoz2017</cite>. Some of the various carbohydrate sources targeted by GH105 enzymes include: rhamnogalacturonan-I, ulvan, and the arabinogalactan decoration on certain cell wall proteins <cite>Itoh2006 Itoh2006-1 Collen2014 Munoz-Munoz2017</cite>.

== Kinetics and Mechanism ==

GH105 enzymes do not act via a typical Koshland retaining or inverting mechanism <cite>Koshland1953</cite>, rather the current proposed mechanism of action for these enzymes is hydrolysis through syn-hydration of the double bond between the C-4 and C-5 carbons of the enopyranuronosyl residue of their substrate <cite>Itoh2006</cite>. This hydration reaction forms a hemiketal that undergoes spontaneous rearrangement to form an intermediate hemiacetyl, which undergoes another rearrangement resulting in the breakage of the bond to the neighbouring saccharide(at the +1 subsite of the enzyme) of the polymer. This mechanism was initially theorized based on the oligosaccharide and amino acid arrangement in a substrate-bound crystal structure <cite>Itoh2006-1</cite>, but has been confirmed through kinetic isotope effects and NMR analysis in the highly related unsaturated glucuronyl hydrolase GH88 family <cite>Jongkees2011 Jongkees2014</cite>.

The kinetics for three enzymes from this family have been determined, two from B. subtilis and one from B. thetaiotaomicron. YteR from B. subtilis was found to have a kcat and KM of 0.2±0.011s-1 and 100±14μM, respectively, against the substrate ΔGal-Rha; in contrast, YesR was found to have much higher values for both these kinetic parameters, 13.9±0.7s-1 and 719±75μM for kcat and KM, respectively, with the same substrate <cite>Itoh2006-1</cite>. BT3687 from B. thetaiotaomicron was determined to have a kcat of 0.59±0.057s-1 and a KM of 71.87±12.51μM against the substrate ΔGlc-GlcNAc <cite>Munoz-Munoz2017</cite>.

Although it is atypical for a glycoside hydrolase family to contain enzymes capable of degrading both α- or β-linked substrates, this has also been observed in other families that deviate significantly from typical acid-base mechanisms(eg. GH3, GH4) <cite>Rye2000</cite>.

== Catalytic Residues ==

A single aspartate residue has been proposed to be responsible for the hydration reaction based on substrate-complexed X-ray crystals structures, sequence conservation, and site-directed mutagenesis <cite>Itoh2006 Itoh2006-1</cite>. The first enzyme classified into the GH105 family (PDB ID: 1NC5 from B. subtilis) was originally predicted to be a lyase based on 65% amino acid sequence similarity and over 60% matching secondary-structure characteristics with an N-acyl-D-glucosamine 2-epimerase <cite>Zhang2009</cite>. Following sequence comparison to a GH88 hydrolase (a B. subtilis UGL enzyme), and additional functional characterization, 1NC5 was determined to possess unsaturated galacturonyl hydrolase activity <cite>Itoh2006-1</cite>. A conserved aspartate residue (D143), was found to be the most likely candidate for initiating the hydration reaction, while a second conserved residue, histidine (H189), serves to correctly position a water molecule for deprotonation and addition to the C-5 carbon of the monosaccharide in the enzymes -1 subsite <cite>Itoh2006-1</cite>. Based on sequence alignment and structural analysis, an arginine residue may take the place of this histidine residue in some GH105 enzymes (ie. in PDB ID enzymes: 4CE7 and 5NOA) <cite>Pettersen2004 Collen2014 Munoz-Munoz2017</cite>.

== Three-dimensional structures ==

A number of crystal structures of GH105 unsaturated glucuronyl hydrolases expressed in bacteria have been solved, including several structures from B. subtilis <cite>Zhang2009 Itoh2006 Itoh2006-1</cite>, and B. thetaiotaomicron <cite>Munoz-Munoz2017 Collen2014 JCSG2009</cite>, as well as one each from B. vulgatus <cite>Osipiuk2014</cite>, C. acetobutylicum <cite>Germane2015</cite>, K. pneumoniae <cite>Tan2010</cite>, and S. enterica <cite>Tan2011</cite>. A single enzyme from the fungus T. terrestris has also been solved <cite>Stogios2015</cite>. All of these enzymes share an (α/α)6-barrel structure (also similar to that of the related GH88 enzymes), with the main differences being seen in the structure of the loop region that determines the architecture of the binding site. At the bottom of the active site pocket is a conserved WxRxxGW motif, with the tryptophan and arginine residues forming a pocket that engages the carboxyl group on the ΔGal/Glc monosaccharide of the -1 subsite <cite>Itoh2006</cite>. While several residues may be conserved in sequence and position at the -1 subsite, the +1 subsite is much more variable, which likely accounts for the ability of this enzyme family to catalyze the hydrolysis of polysaccharides containing α- or β-bonds linked to the C-2, -4, or -6 carbon of the +1 saccharide <cite>Collen2014</cite>.

== Family Firsts ==

; First stereochemistry determination: Content is to be added here.
; First catalytic nucleophile identification: Content is to be added here.
; First general acid/base residue identification: Content is to be added here.
; First 3-D structure: Content is to be added here.

== References ==

<biblio>
#Cantarel2009 pmid=18838391
#Munoz-Munoz2017 pmid=28637865
#Jongkees2011 pmid=22047074
#Zhang2009 pmid=15906318
#Itoh2006 pmid=16870154
#Itoh2006-1 pmid=16781735
#Collen2014 pmid=24407291
#Koshland1953 Koshland, D.E. (1953) Stereochemistry and the Mechanism of Enzymatic Reactions. ''Biological Reviews'', vol. 28, no. 4., pp. 416-436. [https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-185X.1953.tb01386.x].
#Jongkees2014 pmid=24573682
#Rye2000 pmid=11006547
#Pettersen2004 pmid=15264254
#JCSG2009 JointCenterforStructuralGenomics(JCSG) (2009) Crystal structure of Putative glycosyl hydrolase (NP_813087.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.80 A resolution. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3K11].
#Osipiuk2014 Osipiuk, J., Li, H., Endres, M., Joachimiak, A. (2014) Glycosyl hydrolase family 88 from Bacteroides vulgatus. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/4Q88].
#Germane2015 pmid=26249707
#Tan2010 Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A. (2010) The crystal structure of a possible member of GH105 family from Klebsiella pneumoniae subsp. pneumoniae MGH 78578. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3pmm].
#Tan2011 Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A. (2011) The crystal structure of a possible member of GH105 family from Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3qwt].
#Stogios2015 Stogios, P.J., Xu, X., Cui, H., Yim, V., Savchenko, A. (2015) Crystal structure of a glycoside hydrolase family 105 (GH105) enzyme from Thielavia terrestris. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/4XUV].
</biblio>

[[Category:Glycoside Hydrolase Families|GH105]]

Glycoside Hydrolase Family 105

2019-07-18T22:18:45Z

James Stevenson:

{{UnderConstruction}}

* [[Author]]: ^^^James Stevenson^^^
* [[Responsible Curator]]: ^^^Joel Weadge^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH105'''
|-
| '''Clan'''
| GH-x
|-
| '''Mechanism'''
| retaining/inverting
|-
| '''Active site residues'''
| known/not known
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH105.html
|}
</div>



== Substrate specificities ==

GH105 enzymes are a class of unsaturated glucuronyl/galacturonyl hydrolases found mainly in bacteria, but a few fungial and a handful of archaeal enzymes have also been annotated <cite>Cantarel2009</cite>. Much like the glycoside hydrolase family 88, enzymes from GH105 perform hydrolysis via a hydration of the double bond between the C-4 and C-5 carbons of the terminal monosaccharide of their substrates <cite>Munoz-Munoz2017 Jongkees2011</cite>. Enzymes from GH105 have been organized into three subgroups: unsaturated rhamnogalacturonidases, d-4,5-unsaturated β-glucuronyl hydrolases, and d-4,5-unsaturated α-galacturonidases. The unifying feature shared between these substrates is the presence of the non-reducing monosaccharide 4-deoxy-L-threo-hex-4-enopyranuronosyl that binds at the -1 active site of the enzymes, and is linked to the +1 sugar via its anomeric C-1 carbon. The 4-deoxy-L-threo-hex-4-enopyranuronosyl saccharide is defined as ΔGal or ΔGlc depending on whether it assumes an α- or β- configuration, respectively. In degradable substrates, the sugar present at the +1 position can be linked via its C-2, C-4, or C-6 carbon, given the substrate preference of individual enzymes <cite>Zhang2009 Munoz-Munoz2017</cite>. Some of the various carbohydrate sources targeted by GH105 enzymes include: rhamnogalacturonan-I, ulvan, and the arabinogalactan decoration on certain cell wall proteins <cite>Itoh2006 Itoh2006-1 Collen2014 Munoz-Munoz2017</cite>.

== Kinetics and Mechanism ==

GH105 enzymes do not act via a typical Koshland retaining or inverting mechanism <cite>Koshland1953</cite>, rather the current proposed mechanism of action for these enzymes is hydrolysis through syn-hydration of the double bond between the C-4 and C-5 carbons of the enopyranuronosyl residue of their substrate <cite>Itoh2006</cite>. This hydration reaction forms a hemiketal that undergoes spontaneous rearrangement to form an intermediate hemiacetyl, which undergoes another rearrangement resulting in the breakage of the bond to the neighbouring saccharide(at the +1 subsite of the enzyme) of the polymer. This mechanism was initially theorized based on the oligosaccharide and amino acid arrangement in a substrate-bound crystal structure <cite>Itoh2006-1</cite>, but has been confirmed through kinetic isotope effects and NMR analysis in the highly related unsaturated glucuronyl hydrolase GH88 family <cite>Jongkees2011 Jongkees2014</cite>.

The kinetics for three enzymes from this family have been determined, two from B. subtilis and one from B. thetaiotaomicron. YteR from B. subtilis was found to have a kcat and KM of 0.2±0.011s-1 and 100±14μM, respectively, against the substrate ΔGal-Rha; in contrast, YesR was found to have much higher values for both these kinetic parameters, 13.9±0.7s-1 and 719±75μM for kcat and KM, respectively, with the same substrate <cite>Itoh2006-1</cite>. BT3687 from B. thetaiotaomicron was determined to have a kcat of 0.59±0.057s-1 and a KM of 71.87±12.51μM against the substrate ΔGlc-GlcNAc <cite>Munoz-Munoz2017</cite>.

Although it is atypical for a glycoside hydrolase family to contain enzymes capable of degrading both α- or β-linked substrates, this has also been observed in other families that deviate significantly from typical acid-base mechanisms(eg. GH3, GH4) <cite>Rye2000</cite>.

== Catalytic Residues ==

A single aspartate residue has been proposed to be responsible for the hydration reaction based on substrate-complexed X-ray crystals structures, sequence conservation, and site-directed mutagenesis <cite>Itoh2006 Itoh2006-1</cite>. The first enzyme classified into the GH105 family (PDB ID: 1NC5 from B. subtilis) was originally predicted to be a lyase based on 65% amino acid sequence similarity and over 60% matching secondary-structure characteristics with an N-acyl-D-glucosamine 2-epimerase <cite>Zhang2009</cite>. Following sequence comparison to a GH88 hydrolase (a B. subtilis UGL enzyme), and additional functional characterization, 1NC5 was determined to possess unsaturated galacturonyl hydrolase activity <cite>Itoh2006-1</cite>. A conserved aspartate residue (D143), was found to be the most likely candidate for initiating the hydration reaction, while a second conserved residue, histidine (H189), serves to correctly position a water molecule for deprotonation and addition to the C-5 carbon of the monosaccharide in the enzymes -1 subsite <cite>Itoh2006-1</cite>. Based on sequence alignment and structural analysis, an arginine residue may take the place of this histidine residue in some GH105 enzymes (ie. in PDB ID enzymes: 4CE7 and 5NOA) <cite>Pettersen2004 Collen2014 Munoz-Munoz2017</cite>.

== Three-dimensional structures ==

A number of crystal structures of GH105 unsaturated glucuronyl hydrolases expressed in bacteria have been solved, including several structures from B. subtilis <cite>Zhang2009 Itoh2006 Itoh2006-1</cite>, and B. thetaiotaomicron <cite>Munoz-Munoz2017 Collen2014 JCSG2009</cite>, as well as one each from B. vulgatus <cite>Osipiuk2014</cite>, C. acetobutylicum <cite>Germane2015</cite>, K. pneumoniae <cite>Tan2010</cite>, and S. enterica <cite>Tan2011</cite>. A single enzyme from the fungus T. terrestris has also been solved <cite>Stogios2015</cite>. All of these enzymes share an (α/α)6-barrel structure (also similar to that of the related GH88 enzymes), with the main differences being seen in the structure of the loop region that determines the architecture of the binding site. At the bottom of the active site pocket is a conserved WxRxxGW motif, with the tryptophan and arginine residues forming a pocket that engages the carboxyl group on the ΔGal/Glc monosaccharide of the -1 subsite <cite>Itoh2006</cite>. While several residues may be conserved in sequence and position at the -1 subsite, the +1 subsite is much more variable, which likely accounts for the ability of this enzyme family to catalyze the hydrolysis of polysaccharides containing α- or β-bonds linked to the C-2, -4, or -6 carbon of the +1 saccharide <cite>Collen2014</cite>.

== Family Firsts ==

; First stereochemistry determination: Content is to be added here.
; First catalytic nucleophile identification: Content is to be added here.
; First general acid/base residue identification: Content is to be added here.
; First 3-D structure: Content is to be added here.

== References ==

<biblio>
#Cantarel2009 pmid=18838391
#Munoz-Munoz2017 pmid=28637865
#Jongkees2011 pmid=22047074
#Zhang2009 pmid=15906318
#Itoh2006 pmid=16870154
#Itoh2006-1 pmid=16781735
#Collen2014 pmid=24407291
#Koshland1953 Koshland, D.E. (1953) Stereochemistry and the Mechanism of Enzymatic Reactions. ''Biological Reviews'', vol. 28, no. 4., pp. 416-436. [https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-185X.1953.tb01386.x].
#Jongkees2014 pmid=24573682
#Rye2000 pmid=11006547
#Pettersen2004 pmid=15264254
#JCSG2009 JointCenterforStructuralGenomics(JCSG) (2009) Crystal structure of Putative glycosyl hydrolase (NP_813087.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.80 A resolution. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3K11].
#Osipiuk2014 Osipiuk, J., Li, H., Endres, M., Joachimiak, A. (2014) Glycosyl hydrolase family 88 from Bacteroides vulgatus. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/4Q88].
#Germane2015 pmid=26249707
#Tan2010 Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A. (2010) The crystal structure of a possible member of GH105 family from Klebsiella pneumoniae subsp. pneumoniae MGH 78578. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3pmm].
#Tan2011 Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A. (2011) The crystal structure of a possible member of GH105 family from Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3qwt].
#Stogios2015 Stogios, P.J., Xu, X., Cui, H., Yim, V., Savchenko, A. (2015) Crystal structure of a glycoside hydrolase family 105 (GH105) enzyme from Thielavia terrestris. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/4XUV].
</biblio>

[[Category:Glycoside Hydrolase Families|GH105]]

Glycoside Hydrolase Family 105

2019-07-18T22:08:59Z

James Stevenson:

{{UnderConstruction}}

* [[Author]]: ^^^James Stevenson^^^
* [[Responsible Curator]]: ^^^Joel Weadge^^^

----


<div style="float: right">
{| {{Prettytable}}
|-
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH105'''
|-
| '''Clan'''
| GH-x
|-
| '''Mechanism'''
| retaining/inverting
|-
| '''Active site residues'''
| known/not known
|-
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH105.html
|}
</div>



== Substrate specificities ==

GH105 enzymes are a class of unsaturated glucuronyl/galacturonyl hydrolases found mainly in bacteria, but a few fungial and a handful of archaeal enzymes have also been annotated <cite>Cantarel2009</cite>. Much like the glycoside hydrolase family 88, enzymes from GH105 perform hydrolysis via a hydration of the double bond between the C-4 and C-5 carbons of the terminal monosaccharide of their substrates <cite>Munoz-Munoz2017 Jongkees2011</cite>. Enzymes from GH105 have been organized into three subgroups: unsaturated rhamnogalacturonidases, d-4,5-unsaturated β-glucuronyl hydrolases, and d-4,5-unsaturated α-galacturonidases. The unifying feature shared between these substrates is the presence of the non-reducing monosaccharide 4-deoxy-L-threo-hex-4-enopyranuronosyl that binds at the -1 active site of the enzymes, and is linked to the +1 sugar via its anomeric C-1 carbon. The 4-deoxy-L-threo-hex-4-enopyranuronosyl saccharide is defined as ΔGal or ΔGlc depending on whether it assumes an α- or β- configuration, respectively. In degradable substrates, the sugar present at the +1 position can be linked via its C-2, C-4, or C-6 carbon, given the substrate preference of individual enzymes <cite>Zhang2009 Munoz-Munoz2017</cite>. Some of the various carbohydrate sources targeted by GH105 enzymes include: rhamnogalacturonan-I, ulvan, and the arabinogalactan decoration on certain cell wall proteins <cite>Itoh2006 Itoh2006-1 Collen2014 Munoz-Munoz2017</cite>.

== Kinetics and Mechanism ==

GH105 enzymes do not act via a typical Koshland retaining or inverting mechanism <cite>Koshland1953</cite>, rather the current proposed mechanism of action for these enzymes is hydrolysis through syn-hydration of the double bond between the C-4 and C-5 carbons of the enopyranuronosyl residue of their substrate <cite>Itoh2006</cite>. This hydration reaction forms a hemiketal that undergoes spontaneous rearrangement to form an intermediate hemiacetyl, which undergoes another rearrangement resulting in the breakage of the bond to the neighbouring saccharide(at the +1 subsite of the enzyme) of the polymer. This mechanism was initially theorized based on the oligosaccharide and amino acid arrangement in a substrate-bound crystal structure <cite>Itoh2006-1</cite>, but has been confirmed through kinetic isotope effects and NMR analysis in the highly related unsaturated glucuronyl hydrolase GH88 family <cite>Jongkees2011 Jongkees2014</cite>.

The kinetics for three enzymes from this family have been determined, two from B. subtilis and one from B. thetaiotaomicron. YteR from B. subtilis was found to have a kcat and KM of 0.2±0.011s-1 and 100±14μM, respectively, against the substrate ΔGal-Rha; in contrast, YesR was found to have much higher values for both these kinetic parameters, 13.9±0.7s-1 and 719±75μM for kcat and KM, respectively, with the same substrate <cite>Itoh2006-1</cite>. BT3687 from B. thetaiotaomicron was determined to have a kcat of 0.59±0.057s-1 and a KM of 71.87±12.51μM against the substrate ΔGlc-GlcNAc <cite>Munoz-Munoz2017</cite>.

Although it is atypical for a glycoside hydrolase family to contain enzymes capable of degrading both α- or β-linked substrates, this has also been observed in other families that deviate significantly from typical acid-base mechanisms(eg. GH3, GH4) <cite>Rye2000</cite>.

== Catalytic Residues ==

A single aspartate residue has been proposed to be responsible for the hydration reaction based on substrate-complexed X-ray crystals structures, sequence conservation, and site-directed mutagenesis <cite>Itoh2006 Itoh2006-1</cite>. The first enzyme classified into the GH105 family (PDB ID: 1NC5 from B. subtilis) was originally predicted to be a lyase based on 65% amino acid sequence similarity and over 60% matching secondary-structure characteristics with an N-acyl-D-glucosamine 2-epimerase <cite>Zhang2009</cite>. Following sequence comparison to a GH88 hydrolase (a B. subtilis UGL enzyme), and additional functional characterization, 1NC5 was determined to possess unsaturated galacturonyl hydrolase activity <cite>Itoh2006-1</cite>. A conserved aspartate residue (D143), was found to be the most likely candidate for initiating the hydration reaction, while a second conserved residue, histidine (H189), serves to correctly position a water molecule for deprotonation and addition to the C-5 carbon of the monosaccharide in the enzymes -1 subsite <cite>Itoh2006-1</cite>. Based on sequence alignment and structural analysis, an arginine residue may take the place of this histidine residue in some GH105 enzymes (ie. in PDB ID enzymes: 4CE7 and 5NOA) <cite>Pettersen2004 Collen2014 Munoz-Munoz2017</cite>.

== Three-dimensional structures ==

Content is to be added here.

== Family Firsts ==

; First stereochemistry determination: Content is to be added here.
; First catalytic nucleophile identification: Content is to be added here.
; First general acid/base residue identification: Content is to be added here.
; First 3-D structure: Content is to be added here.

== References ==

<biblio>
#Cantarel2009 pmid=18838391
#Munoz-Munoz2017 pmid=28637865
#Jongkees2011 pmid=22047074
#Zhang2009 pmid=15906318
#Itoh2006 pmid=16870154
#Itoh2006-1 pmid=16781735
#Collen2014 pmid=24407291
#Koshland1953 Koshland, D.E. (1953) Stereochemistry and the Mechanism of Enzymatic Reactions. ''Biological Reviews'', vol. 28, no. 4., pp. 416-436. [https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-185X.1953.tb01386.x].
#Jongkees2014 pmid=24573682
#Rye2000 pmid=11006547
#Pettersen2004 pmid=15264254
#JCSG2009 JointCenterforStructuralGenomics(JCSG) (2009) Crystal structure of Putative glycosyl hydrolase (NP_813087.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.80 A resolution. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3K11].
#Osipiuk2014 Osipiuk, J., Li, H., Endres, M., Joachimiak, A. (2014) Glycosyl hydrolase family 88 from Bacteroides vulgatus. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/4Q88].
#Germane2015 pmid=26249707
#Tan2010 Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A. (2010) The crystal structure of a possible member of GH105 family from Klebsiella pneumoniae subsp. pneumoniae MGH 78578. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3pmm].
#Tan2011 Tan, K., Hatzos-Skintges, C., Bearden, J., Joachimiak, A. (2011) The crystal structure of a possible member of GH105 family from Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/3qwt].
#Stogios2015 Stogios, P.J., Xu, X., Cui, H., Yim, V., Savchenko, A. (2015) Crystal structure of a glycoside hydrolase family 105 (GH105) enzyme from Thielavia terrestris. ''RCSB Protein Data Bank''. [https://www.rcsb.org/structure/4XUV].
</biblio>

[[Category:Glycoside Hydrolase Families|GH105]]

Glycoside Hydrolase Family 105

2019-07-18T22:04:29Z

James Stevenson:

Glycoside Hydrolase Family 105

2019-07-18T22:04:13Z

James Stevenson:

Glycoside Hydrolase Family 105

2019-07-18T22:01:12Z

James Stevenson:

Glycoside Hydrolase Family 105

2019-07-18T21:58:57Z

James Stevenson:

Glycoside Hydrolase Family 105

2019-07-18T21:57:32Z

James Stevenson:

Glycoside Hydrolase Family 105

2019-07-18T21:53:13Z

James Stevenson:

Glycoside Hydrolase Family 105

2019-07-18T21:50:03Z

James Stevenson:

Glycoside Hydrolase Family 105

2019-07-18T21:49:36Z

James Stevenson:

Glycoside Hydrolase Family 105

2019-07-18T21:48:33Z

James Stevenson:

Glycoside Hydrolase Family 105

2019-07-18T21:47:27Z

James Stevenson:

Glycoside Hydrolase Family 105

2019-07-18T21:44:48Z

James Stevenson:

Glycoside Hydrolase Family 105

2019-07-18T21:44:10Z

James Stevenson:

Glycoside Hydrolase Family 105

2019-07-18T21:43:51Z

James Stevenson:

Glycoside Hydrolase Family 105

2019-07-18T21:43:14Z

James Stevenson:

Glycoside Hydrolase Family 105

2019-07-18T21:35:36Z

James Stevenson:

Glycoside Hydrolase Family 105

2019-07-18T21:24:44Z

James Stevenson: