CAZypedia needs your help! We have many unassigned GH, PL, CE, AA, GT, and CBM pages in need of Authors and Responsible Curators.
Scientists at all career stages, including students, are welcome to contribute to CAZypedia. Read more here, and in the 10th anniversary article in Glycobiology.
New to the CAZy classification? Read this first.
*
Consider attending the 15th Carbohydrate Bioengineering Meeting in Ghent, 5-8 May 2024.

Difference between revisions of "Glycoside Hydrolase Family 105"

From CAZypedia
Jump to navigation Jump to search
Line 1: Line 1:
 
<!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 
<!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 +
 
{{UnderConstruction}}
 
{{UnderConstruction}}
 +
 
* [[Author]]: ^^^James Stevenson^^^
 
* [[Author]]: ^^^James Stevenson^^^
−
* [[Responsible Curator]]: ^^^Joel Weadge^^^
+
* [[Responsible Curator]]: ^^^Joel Weadge^^^
 +
 
 
----
 
----
  
 
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family -->
 
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family -->
−
<div style="float:right">
+
<div style="float: right">
−
{| {{Prettytable}}  
+
{| {{Prettytable}}
 
|-
 
|-
−
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH105'''
+
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH105'''
 
|-
 
|-
−
|'''Clan'''  
+
| '''Clan'''
−
|GH-x
+
| GH-x
 
|-
 
|-
−
|'''Mechanism'''
+
| '''Mechanism'''
−
|retaining/inverting
+
| retaining/inverting
 
|-
 
|-
−
|'''Active site residues'''
+
| '''Active site residues'''
−
|known/not known
+
| known/not known
 
|-
 
|-
−
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
+
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 
|-
 
|-
 
| colspan="2" |{{CAZyDBlink}}GH105.html
 
| colspan="2" |{{CAZyDBlink}}GH105.html
 
|}
 
|}
 
</div>
 
</div>
 +
 
<!-- This is the end of the table -->
 
<!-- This is the end of the table -->
  
 +
== Substrate specificities ==
  
−
== 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 ''Cantarel2009''. 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 ''Munoz-Munoz2017''. 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
−
Content is to be added here.
 
  
 
Authors may get an idea of what to put in each field from ''Curator Approved'' [[Glycoside Hydrolase Families]]. ''(TIP: Right click with your mouse and open this link in a new browser window...)''
 
Authors may get an idea of what to put in each field from ''Curator Approved'' [[Glycoside Hydrolase Families]]. ''(TIP: Right click with your mouse and open this link in a new browser window...)''
  
−
In the meantime, please see these references for an essential introduction to the CAZy classification system: <cite>DaviesSinnott2008 Cantarel2009</cite>.
+
In the meantime, please see these references for an essential introduction to the CAZy classification system: ''DaviesSinnott2008 Cantarel2009''.
  
 
== Kinetics and Mechanism ==
 
== Kinetics and Mechanism ==
 +
 
Content is to be added here.
 
Content is to be added here.
  
 
== Catalytic Residues ==
 
== Catalytic Residues ==
 +
 
Content is to be added here.
 
Content is to be added here.
  
 
== Three-dimensional structures ==
 
== Three-dimensional structures ==
 +
 
Content is to be added here.
 
Content is to be added here.
  
 
== Family Firsts ==
 
== Family Firsts ==
−
;First stereochemistry determination: Content is to be added here.
+
 
−
;First catalytic nucleophile identification: Content is to be added here.
+
; First stereochemistry determination: Content is to be added here.
−
;First general acid/base residue identification: Content is to be added here.
+
; First catalytic nucleophile identification: Content is to be added here.
−
;First 3-D structure: 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 ==
 
== References ==
−
<biblio>
 
 
#Cantarel2009 pmid=18838391
 
#Cantarel2009 pmid=18838391
 +
#Munoz-Munoz2017 pmid=28637865
 +
#Jongkees2011 pmid=22047074
 +
#Zhang2009 pmid=15906318
 +
#Itoh2006 pmid=16870154
 +
#Itoh2006 pmid=16781735
 +
#Colle2014 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=26239707
 +
#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].
 
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
 
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
−
</biblio>
 
−
 
  
 
[[Category:Glycoside Hydrolase Families|GH105]]
 
[[Category:Glycoside Hydrolase Families|GH105]]

Revision as of 14:24, 18 July 2019


Under construction icon-blue-48px.png

This page is currently under construction. This means that the Responsible Curator has deemed that the page's content is not quite up to CAZypedia's standards for full public consumption. All information should be considered to be under revision and may be subject to major changes.

Glycoside Hydrolase Family GH105
Clan GH-x
Mechanism retaining/inverting
Active site residues known/not known
CAZy DB link
http://www.cazy.org/GH105.html


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 Cantarel2009. 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 Munoz-Munoz2017. 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

Authors may get an idea of what to put in each field from Curator Approved Glycoside Hydrolase Families. (TIP: Right click with your mouse and open this link in a new browser window...)

In the meantime, please see these references for an essential introduction to the CAZy classification system: DaviesSinnott2008 Cantarel2009.

Kinetics and Mechanism

Content is to be added here.

Catalytic Residues

Content is to be added here.

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

  1. Cantarel2009 pmid=18838391
  2. Munoz-Munoz2017 pmid=28637865
  3. Jongkees2011 pmid=22047074
  4. Zhang2009 pmid=15906318
  5. Itoh2006 pmid=16870154
  6. Itoh2006 pmid=16781735
  7. Colle2014 pmid=24407291
  8. Koshland1953 Koshland, D.E. (1953) Stereochemistry and the Mechanism of Enzymatic Reactions. Biological Reviews, vol. 28, no. 4., pp. 416-436. [1].
  9. Jongkees2014 pmid=24573682
  10. Rye2000 pmid=11006547
  11. Pettersen2004 pmid=15264254
  12. 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. [2].
  13. Osipiuk2014 Osipiuk, J., Li, H., Endres, M., Joachimiak, A. (2014) Glycosyl hydrolase family 88 from Bacteroides vulgatus. RCSB Protein Data Bank. [3].
  14. Germane2015 pmid=26239707
  15. 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. [4].
  16. 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. [5].
  17. 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. [6].
  18. DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. The Biochemist, vol. 30, no. 4., pp. 26-32. Download PDF version.
Retrieved from "http://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_105&oldid=13952"