https://www.cazypedia.org/api.php?action=feedcontributions&user=Cecelia+Garcia&feedformat=atomCAZypedia - User contributions [en-ca]2024-03-29T06:28:59ZUser contributionsMediaWiki 1.35.10https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_37&diff=16283Glycoside Hydrolase Family 372021-09-13T20:24:16Z<p>Cecelia Garcia: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Tracey Gloster^^^, ^^^Cecelia Garcia^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH37'''<br />
|-<br />
|'''Clan''' <br />
|GH-G<br />
|-<br />
|'''Mechanism'''<br />
|Inverting<br />
|-<br />
|'''Active site residues'''<br />
|Known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH37.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
To date, GH37 [[glycoside hydrolases]] have been shown to hydrolyze the α-1,1 bound trehalose (α-D-glucopyranosyl-(1→1)-α-D-glucopyranoside) into two molecules of D-glucose (EC [{{EClink}}3.2.1.28 3.2.1.28]). GH37 enzymes are further classified by their optimal pH; neutral or acidic, and also by their cellular localization; soluble or membrane bound <cite>DEnfert1999</cite>. There is some evidence that organisms possessing multiple GH37 trehalases will utilize them for different purposes. This tends towards periplasmic trehalases being metabolically relevant while cytoplasmic trehalases participate in osmoregulation <cite>Arguelles2000</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
GH37 trehalases follow an [[inverting]] mechanism. This was first demonstrated through incubation of GH37 trehalases obtained from ''S. barbata'', the flesh fly, with <sup>18</sup>O-labelled water and observing its incorporation primarily into the beta-epimer <cite>Clifford1980</cite>. This was further supported by the solved structure of ''E. coli'' Tre37A which demonstrated that the proposed catalytic residues were in a position consistent with an [[inverting]] mechanism <cite>Gibson2007</cite>. <br />
<br />
Several fungal neutral trehalases; ''S. cerevisiae'', ''A. nidulans'', ''N. crassa'', and ''C. albicans'', show evidence of activation by calcium ion binding and cAMP-dependent phosphorylation <cite>DEnfert1999 Alblova2017 Alblova2019</cite>. <br />
<br />
== Catalytic Residues ==<br />
The catalytic residues were first predicted through structural determination of ''E. coli'' Tre37A in complex with inhibitors 1-thiatrehazolin (PDB ID [https://www.rcsb.org/structure/2JG0 2JG0]) and validoxylamine A (PDB ID [https://www.rcsb.org/structure/2JF4 2JF4]) <cite>Gibson2007</cite>. These structures implicate an aspartate residue (Asp312 in ''E. coli'') as the catalytic [[general acid/base|general acid]], and a glutamate residue (Glu496 in ''E. coli'') as the catalytic [[general acid/base|general base]]. A crystal structure of ''S. cerevisiae'' Nth1 with bound trehalose identified an aspartate residue (Asp478 in ''S. cerevisiae'') as the catalytic [[general acid/base|general acid]], and a glutamate residue (Glu674 in ''S. cerevisiae'') as the [[general acid/base|general base]]. Superimposition of these structures indicates that the proposed catalytic residues align in both the ''E. coli'' Tre37A inhibitor bound and ''S. cerevisiae'' Nth1 trehalose bound structures. <br />
<br />
Kinetic evidence for the catalytic residues was provided by site-directed mutagenesis of an ''S. frugiperda'' trehalase <cite>Silva2010</cite>. Mutation of the proposed catalytic acid and base residues; Asp322 and Glu520 respectively, resulted in dramatically reduced Kcat values compared to that of the Wild-type protein, and in the loss of ionization reflective of their predicted pKa values. The reduction in Kcat combined with loss of ionization strongly indicates that these function as catalytic residues <cite>Silva2010</cite>. <br />
<br />
== Three-dimensional structures ==<br />
The first three-dimensional structure of a GH37 trehalase was obtained from ''E. coli'' Tre37A in complex with the inhibitors 1-thiatrehazolin (PDB ID [https://www.rcsb.org/structure/2JG0 2JG0]) and validoxylamine A (PDB ID [https://www.rcsb.org/structure/2JF4 2JF4]) by x-ray crystallography <cite>Gibson2007</cite>. The structure revealed a monomeric enzyme consisting of an (α/α)6 barrel fold, similar to other α-toroidal glycosidases. The structure revealed extensive hydrogen bonding and a distinct lack of hydrophobic stacking within the +1 subsite. The bound structure also revealed that the +1 and -1 subsites were buried within the enzyme structure and significant conformation changes would be required for substrate recognition.<br />
<br />
The first eukaryotic GH37 structure was determined from an ''S. cerevisiae'' Nth1:Bmh1 complex, and provided the first structure in the presence of trehalose (PDB ID [https://www.rcsb.org/structure/5M4A 5M4A]) <cite>Alblova2017</cite>. The catalytic domain consists of an (α/α)6 barrel formed by the interaction of one Bmh1 C-terminus with Nth1. Similar to the ''E. coli'' Tre37A structure, the substrate was found in a deep pocket. This structure provided the first evidence of a flexible “lid loop” structure, which would undergo significant conformational changes and complete the active site of Nth1. A similar, but shorter, structure was revealed in ''E. coli'' Tre37A once the solved structures were superimposed <cite>Alblova2017</cite>. <br />
<br />
Further evidence of the “lid loop”, also referred to as a “hood-like domain”, in bacterial trehalases was observed in ''E. cloacae'' Tre <cite>Adhav2019</cite>. Comparison of the solved structures for unbound (PDB ID [https://www.rcsb.org/structure/5Z6H 5Z6H]) and validoxylamine A bound trehalase (PDB ID [https://www.rcsb.org/structure/5Z66 5Z66]) revealed both “side loop” and “lid loop” residues which undergo significant conformational changes upon ligand binding. Structural comparisons to ''E. coli'' Tre37A with validoxylamine A ligand highlighted identically positioned loop structures <cite>Adhav2019 Gibson2007</cite>. Three conserved residues identified within the lid loop structure were observed to contact validoxylamine A, one of which was also observed to form a salt bridge upon lid loop closure. Mutation of this residue; Glu 511, resulted in significant decrease of enzyme activity likely resulting from incomplete loop closure. <br />
<br />
GH37 enzymes belong to the [[clans|clan]] GH-G. <br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: The inversion of stereochemistry for a trehalase from the flesh fly ''Sarcophaga barbata'' was first demonstrated by Clifford in 1980 <cite>Clifford1980</cite>.<br />
;First [[general acid]] identification: First predicted in ''E. coli'' Tre37A from structure determination with inhibitors <cite>Gibson2007</cite>, experimentally observed in ''S. frugiperda'' through site-directed mutagenesis and kinetic determination <cite>Silva2010</cite>.<br />
;First [[general base]] identification: First predicted in ''E. coli'' Tre37A from structure determination with inhibitors <cite>Gibson2007</cite>, experimentally observed in ''S. frugiperda'' through site-directed mutagenesis and kinetic determination <cite>Silva2010</cite>.<br />
;First 3-D structure: The GH37 trehalase from ''Escherichia coli'' was solved by X-ray crystallography <cite>Gibson2007</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#DEnfert1999 pmid=10320571<br />
<br />
#Arguelles2000 pmid=11081789<br />
<br />
#Clifford1980 pmid=7341233<br />
<br />
#Gibson2007 pmid=17455176<br />
<br />
#Alblova2017 pmid=29087344<br />
<br />
#Alblova2019 pmid=30628830<br />
<br />
#Silva2010 pmid=20691783<br />
<br />
#Adhav2019 pmid=30657252<br />
<br />
<br />
</biblio><br />
<br />
<br />
[[Category:Glycoside Hydrolase Families|GH037]]</div>Cecelia Garciahttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_37&diff=16262Glycoside Hydrolase Family 372021-09-09T19:34:43Z<p>Cecelia Garcia: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Tracey Gloster^^^, ^^^Cecelia Garcia^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH37'''<br />
|-<br />
|'''Clan''' <br />
|GH-G<br />
|-<br />
|'''Mechanism'''<br />
|Inverting<br />
|-<br />
|'''Active site residues'''<br />
|Inferred<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH37.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
To date, GH37 [[glycoside hydrolases]] have been shown to hydrolyze the α-1,1 bound trehalose (α-D-glucopyranosyl-(1→1)-α-D-glucopyranoside) into two molecules of D-glucose (EC [{{EClink}}3.2.1.28 3.2.1.28]). GH37 enzymes are further classified by their optimal pH; neutral or acidic, and also by their cellular localization; soluble or membrane bound <cite>DEnfert1999</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH37 trehalases follow an [[inverting]] mechanism. This was first demonstrated through incubation of GH37 trehalases obtained from ''S. barbata'', the flesh fly, with <sup>18</sup>O-labelled water and observing its incorporation primarily into the beta-epimer <cite>Clifford1980</cite>. This was further supported by the solved structure of ''E. coli'' Tre37A which demonstrated that the proposed catalytic residues were in a position consistent with an [[inverting]] mechanism <cite>Gibson2007</cite>. <br />
<br />
Several fungal neutral trehalases; ''S. cerevisiae'', ''A. nidulans'', ''N. crassa'', and ''C. albicans'', show evidence of activation by calcium ion binding and cAMP-dependent phosphorylation <cite>DEnfert1999 Alblova2017 Alblova2019</cite>. <br />
<br />
== Catalytic Residues ==<br />
The catalytic residues were first predicted through structural determination of ''E. coli'' Tre37A in complex with inhibitors 1-thiatrehazolin (PDB ID [https://www.rcsb.org/structure/2JG0 2JG0]) and validoxylamine A (PDB ID [https://www.rcsb.org/structure/2JF4 2JF4]) <cite>Gibson2007</cite>. These structures implicate an aspartate residue (Asp312 in ''E. coli'') as the catalytic [[general acid/base|general acid]], and a glutamate residue (Glu496 in ''E. coli'') as the catalytic [[general acid/base|general base]]. A crystal structure of ''S. cerevisiae'' Nth1 with bound trehalose identified an aspartate residue (Asp478 in ''S. cerevisiae'') as the catalytic [[general acid/base|general acid]], and a glutamate residue (Glu674 in ''S. cerevisiae'') as the [[general acid/base|general base]]. Superimposition of these structures indicates that the proposed catalytic residues align in both the ''E. coli'' Tre37A inhibitor bound and ''S. cerevisiae'' Nth1 trehalose bound structures. <br />
<br />
== Three-dimensional structures ==<br />
The first three-dimensional structure of a GH37 trehalase was obtained from ''E. coli'' Tre37A in complex with the inhibitors 1-thiatrehazolin (PDB ID [https://www.rcsb.org/structure/2JG0 2JG0]) and validoxylamine A (PDB ID [https://www.rcsb.org/structure/2JF4 2JF4]) by x-ray crystallography <cite>Gibson2007</cite>. The structure revealed a monomeric enzyme consisting of an (α/α)6 barrel fold, similar to other α-toroidal glycosidases. The structure revealed extensive hydrogen bonding and a distinct lack of hydrophobic stacking within the +1 subsite. The bound structure also revealed that the +1 and -1 subsites were buried within the enzyme structure and significant conformation changes would be required for substrate recognition.<br />
<br />
The first eukaryotic GH37 structure was determined from an ''S. cerevisiae'' Nth1:Bmh1 complex, and provided the first structure in the presence of trehalose (PDB ID [https://www.rcsb.org/structure/5M4A 5M4A]) <cite>Alblova2017</cite>. The catalytic domain consists of an (α/α)6 barrel formed by the interaction of one Bmh1 C-terminus with Nth1. Similar to the ''E. coli'' Tre37A structure, the substrate was found in a deep pocket. A flexible “lid” loop structure was observed to undergo significant conformational changes and complete the active site of Nth1. A similar, but shorter, structure was revealed in ''E. coli'' Tre37A once the solved structures were superimposed <cite>Alblova2017</cite>. <br />
<br />
GH37 enzymes belong to the [[clans|clan]] GH-G. <br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: The inversion of stereochemistry for a trehalase from the flesh fly ''Sarcophaga barbata'' was first demonstrated by Clifford in 1980 <cite>Clifford1980</cite>.<br />
;First [[general acid]] identification: First predicted in E. coli Tre37A from structure determination with inhibitors <cite>Gibson2007</cite>, observed in structural determination of S. cerevisiae complexed with trehalose <cite>Alblova2017</cite>.<br />
;First [[general base]] identification: First predicted in E. coli Tre37A from structure determination with inhibitors <cite>Gibson2007</cite>, observed in structural determination of S. cerevisiae complexed with trehalose <cite>Alblova2017</cite>.<br />
;First 3-D structure: The GH37 trehalase from ''Escherichia coli'' was solved by X-ray crystallography <cite>Gibson2007</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#DEnfert1999 pmid=10320571<br />
#Clifford1980 pmid=7341233<br />
#Gibson2007 pmid=17455176<br />
#Alblova2017 pmid=29087344<br />
#Alblova2019 pmid=30628830<br />
<br />
<br />
</biblio><br />
<br />
<br />
[[Category:Glycoside Hydrolase Families|GH037]]</div>Cecelia Garciahttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_37&diff=16259Glycoside Hydrolase Family 372021-09-08T21:19:10Z<p>Cecelia Garcia: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Tracey Gloster^^^, ^^^Cecelia Garcia^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH37'''<br />
|-<br />
|'''Clan''' <br />
|GH-G<br />
|-<br />
|'''Mechanism'''<br />
|Inverting<br />
|-<br />
|'''Active site residues'''<br />
|Inferred<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH37.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
To date, GH37 [[glycoside hydrolases]] have been shown to hydrolyze the α-1,1 bound trehalose (α-D-glucopyranosyl-(1→1)-α-D-glucopyranoside) into two molecules of D-glucose (EC [{{EClink}}3.2.1.28 3.2.1.28]). GH37 enzymes are further classified by their optimal pH; neutral or acidic, and also by their cellular localization; soluble or membrane bound <cite>DEnfert1999</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH37 trehalases follow an [[inverting]] mechanism. This was first demonstrated through incubation of GH37 trehalases obtained from ''S. barbata'', the flesh fly, with <sup>18</sup>O-labelled water and observing its incorporation primarily into the beta-epimer <cite>Clifford1980</cite>. This was further supported by the solved structure of ''E. coli'' Tre37A which demonstrated that the proposed catalytic residues were in a position consistent with an [[inverting]] mechanism <cite>Gibson2007</cite>. <br />
<br />
Several fungal neutral trehalases; ''S. cerevisiae'', ''A. nidulans'', ''N. crassa'', and ''C. albicans'', show evidence of activation by calcium ion binding and cAMP-dependent phosphorylation <cite>DEnfert1999 Alblova2017 Alblova2019</cite>. <br />
<br />
== Catalytic Residues ==<br />
The catalytic residues have not been demonstrated unequivocally, but structural determination of the trehalase from ''Escherichia coli'' in complex with inhibitors in the active site implicate an aspartate residue (Asp312 in ''E. coli'') as the catalytic [[general acid]] and a glutamate residue (Glu496 in ''E. coli'') as the catalytic [[general base]] <cite>Gibson2007</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The only structural representative from GH37 to date is the trehalase from ''Escherichia coli'', which was solved using X-ray crystallography <cite>Gibson2007</cite>. The structure revealed a (α/α)<sub>6</sub> barrel fold, similar to other α-toroidal glycosidases such as those in families [[GH94]], [[GH15]] and [[GH65]]. GH37 falls into [[clans|clan]] GH-G. Structures have been solved with the inhibitors validoxylamine A, 1-thiatrehazolin and casuarine analogues <cite>Gibson2007,Cardona2009,Cardona2010</cite>.<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: The inversion of stereochemistry for a trehalase from the flesh fly ''Sarcophaga barbata'' was first demonstrated by Clifford in 1980 <cite>Clifford1980</cite>.<br />
;First [[general acid]] identification: Predicted from structure determination <cite>Gibson2007</cite>, but not shown unequivocally. <br />
;First [[general base]] identification: Predicted from structure determination <cite>Gibson2007</cite>, but not shown unequivocally.<br />
;First 3-D structure: The GH37 trehalase from ''Escherichia coli'' was solved by X-ray crystallography <cite>Gibson2007</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#DEnfert1999 pmid=10320571<br />
#Clifford1980 pmid=7341233<br />
#Gibson2007 pmid=17455176<br />
#Alblova2017 pmid=29087344<br />
#Alblova2019 pmid=30628830<br />
<br />
#Cardona2009 pmid=19123216<br />
#Cardona2010 pmid=20461849 <br />
<br />
<br />
</biblio><br />
<br />
<br />
[[Category:Glycoside Hydrolase Families|GH037]]</div>Cecelia Garciahttps://www.cazypedia.org/index.php?title=User:Cecelia_Garcia&diff=16258User:Cecelia Garcia2021-09-08T20:48:24Z<p>Cecelia Garcia: </p>
<hr />
<div>[[Image:Blank_user-200px.png|200px|right]]<br />
<br />
Cecelia Garcia obtained her B.Sc. in Biology from York College of Pennsylvania. She is currently working on her Biology PhD at the University of Maryland, Baltimore County under the supervision of Dr. Jeffrey Gardner. <br />
<br />
Her work combines bioinformatics with biochemistry and microbial physiology to characterize glycoside hydrolases from the soil bacterium C. japonicus. Of particular interest are glycoside hydrolases capable of acting on small ɑ-diglucosides <cite>Garcia2021</cite>. Cecelia has largely contributed to the functional characterization of C. japonicus GH37 trehalases <cite>Garcia2020</cite> and is focusing on elucidating the physiology of C. japonicus strains adapted to novel alpha-diglucosides <cite>Garcia2019</cite>. She has also contributed to developing systems for studying physiological responses to microcrystalline insoluble materials '''[in review]'''. <br />
<br />
<br />
----<br />
<br />
<biblio><br />
#Garcia2021 pmid=33961116<br />
#Garcia2020 pmid=32917758<br />
#Garcia2019 pmid=31672746<br />
</biblio><br />
<br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Garcia,Cecelia]]</div>Cecelia Garcia