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Difference between revisions of "Glycoside Hydrolase Family 105"

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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: <cite>DaviesSinnott2008 Cantarel2009</cite>
  
 
== Kinetics and Mechanism ==
 
== Kinetics and Mechanism ==

Revision as of 14:43, 18 July 2019


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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 [1]. 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 [2, 3]. 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 [2, 4]. Some of the various carbohydrate sources targeted by GH105 enzymes include: rhamnogalacturonan-I, ulvan, and the arabinogalactan decoration on certain cell wall proteins [2, 5, 6, 7].

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: [8, 9]

Kinetics and Mechanism

GH105 enzymes do not act via a typical Koshland retaining or inverting mechanism [10], 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 [5]. 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 [6], but has been confirmed through kinetic isotope effects and NMR analysis in the highly related unsaturated glucuronyl hydrolase GH88 family [3, 11]

Catalytic Residues

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Three-dimensional structures

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Family Firsts

First stereochemistry determination
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First catalytic nucleophile identification
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First general acid/base residue identification
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First 3-D structure
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References

  1. Cantarel2009 pmid=18838391
  2. Munoz-Munoz2017 pmid=28637865
  3. Jongkees2011 pmid=22047074
  4. Zhang2009 pmid=15906318
  5. Itoh2006 pmid=16870154
  6. Itoh2006-1 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.