CAZypedia needs your help!
We have many unassigned pages in need of Authors and Responsible Curators. See a page that's out-of-date and just needs a touch-up? - You are also welcome to become a CAZypedian. Here's how.
Scientists at all career stages, including students, are welcome to contribute.
Learn more about CAZypedia's misson here and in this article.
Totally new to the CAZy classification? Read this first.
Difference between revisions of "Glycoside Hydrolase Family 134"
Harry Brumer (talk | contribs) (Created page with "<!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --> {{UnderConstruct...") |
Harry Brumer (talk | contribs) m (Text replacement - "\^\^\^(.*)\^\^\^" to "$1") |
||
| (17 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
| − | + | {{CuratorApproved}} | |
| − | + | * [[Author]]: [[User:Spencer Williams|Spencer Williams]] | |
| − | * [[Author]]: | + | * [[Responsible Curator]]: [[User:Spencer Williams|Spencer Williams]] |
| − | * [[Responsible Curator]]: | ||
---- | ---- | ||
| − | |||
<div style="float:right"> | <div style="float:right"> | ||
{| {{Prettytable}} | {| {{Prettytable}} | ||
| Line 12: | Line 10: | ||
|- | |- | ||
|'''Clan''' | |'''Clan''' | ||
| − | | | + | |none |
|- | |- | ||
|'''Mechanism''' | |'''Mechanism''' | ||
| − | | | + | |inverting |
|- | |- | ||
|'''Active site residues''' | |'''Active site residues''' | ||
| − | | | + | |known |
|- | |- | ||
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link''' | |{{Hl2}} colspan="2" align="center" |'''CAZy DB link''' | ||
| Line 29: | Line 27: | ||
== Substrate specificities == | == Substrate specificities == | ||
| − | + | [[Glycoside hydrolase]] family 134 exclusively contains β-1,4-mannanases, and was created based on the discovery of Man134A from ''Aspergillus nidulans'' <cite>Shimizu2015</cite>. Man134A exhibits weak activity on galactomannan but robust activity on glucomannan, and activity on β-1,4-linked mannopentaose and hexaose <cite>Shimizu2015</cite>. ''Ss''GH134 from ''Streptomyces'' sp. NRRL B-24484 possesses a strong preference for unsubstituted linear β-mannans over gluco- and galactomannans <cite>Jin2016</cite>. ''Ss''GH134 possesses activity on β-1,4-linked mannotetraose, pentaose and hexaose. | |
| − | |||
| − | |||
| − | |||
| − | |||
== Kinetics and Mechanism == | == Kinetics and Mechanism == | ||
| − | + | <sup>1</sup>H NMR spectroscopic analysis of ''Ss''GH134 catalyzed cleavage of a benzoylhydrazine derivative of β-mannohexaose provided evidence for the formation of the α-anomer, consistent with an [[inverting]] mechanism <cite>Jin2016</cite>. Crystallographic evidence from binary complexes of ''Ss''GH134 with substrate and product, complemented by quantum mechanics/molecular mechanics calculations, supports a "southern hemisphere" <sup>1</sup>''C''<sub>4</sub>→<sup>3</sup>''H''<sub>4</sub><sup>‡</sup>→<sup>3</sup>''S''<sub>1</sub> [[conformational itinerary]] along the reaction coordinate <cite>Jin2016</cite>. | |
== Catalytic Residues == | == Catalytic Residues == | ||
| − | + | Structural analysis of ''Ss''GH134 from ''Streptomyces'' sp. (see below) suggested roles for Glu45 as a [[general acid]] catalyst and for Asp57 as a [[general base]] catalyst <cite>Jin2016</cite>. These roles were supported by mutagenesis with the corresponding Glu45Ala and Asp57Ala single mutants inactive on β-mannopentaose and hexaose. | |
| − | |||
== Three-dimensional structures == | == Three-dimensional structures == | ||
| − | + | The three dimensional structure was first reported for ''Ss''GH134, and exists as a mixed α-helix/β-sheet fold with resemblance to HEWL ([[GH22]]), as well as [[GH19]] chitinases, [[GH23]] G-type lysozyme, and [[GH124]] cellulases <cite>Jin2016</cite>. A binary Michaelis complex of the E45A variant of ''Ss''GH134 with mannopentaose bound in the active site defined the -3 to +2 subsites, and showed the sugar binding in the -1 subsite in a <sup>1</sup>''C''<sub>4</sub> conformation; a similar conformation was observed for the reducing-end mannose of a complex of mannotriose bound to the -3 to -1 subsites of wild-type ''Ss''GH134 <cite>Jin2016</cite>. Within the Michaelis complex, the carboxylate of the highly conserved C-terminal residue Ile173 is hydrogen bonded to O6 of the –2 mannosyl unit, and also forms a salt-bridge with the highly conserved K59. Within only the Michaelis complex, this interaction results in the formation of an active cleft tunnel reminiscent of processive glycoside hydrolases; the C-terminal segment is disordered in both ''apo'' and mannotriose product-bound forms <cite>Jin2016</cite>. ''Ss''GH134 can be classified as a [[syn/anti lateral protonation|''syn'' protonator]], with the acid residue situated ''syn'' to the C1-O5 bond. | |
| − | |||
== Family Firsts == | == Family Firsts == | ||
| − | ;First stereochemistry determination: | + | ;First stereochemistry determination: ''Ss''GH134 was shown to be [[inverting]] by <sup>1</sup>H NMR spectroscopy <cite>Jin2016</cite>. |
| − | ;First | + | ;First [[general acid]] residue identification: Glu45 in ''Ss''GH134 by structural study supported by kinetic analysis of mutants <cite>Jin2016</cite>. |
| − | ;First general | + | ;First [[general base]] residue identification: Asp57 in ''Ss''GH134 by structural study supported by kinetic analysis of mutants <cite>Jin2016</cite>. |
| − | ;First 3-D structure: | + | ;First 3-D structure: ''Ss''GH134 from ''Streptomyces'' sp. (PDB ID [{{PDBlink}}5JTS 5JTS]) <cite>Jin2016</cite>. |
== References == | == References == | ||
<biblio> | <biblio> | ||
| − | # | + | #Shimizu2015 pmid=26385921 |
| − | # | + | #Jin2016 pmid=28058278 |
</biblio> | </biblio> | ||
| + | |||
[[Category:Glycoside Hydrolase Families|GH134]] | [[Category:Glycoside Hydrolase Families|GH134]] | ||
Latest revision as of 13:18, 18 December 2021
This page has been approved by the Responsible Curator as essentially complete. CAZypedia is a living document, so further improvement of this page is still possible. If you would like to suggest an addition or correction, please contact the page's Responsible Curator directly by e-mail.
| Glycoside Hydrolase Family GH134 | |
| Clan | none |
| Mechanism | inverting |
| Active site residues | known |
| CAZy DB link | |
| https://www.cazy.org/GH134.html | |
Substrate specificities
Glycoside hydrolase family 134 exclusively contains β-1,4-mannanases, and was created based on the discovery of Man134A from Aspergillus nidulans [1]. Man134A exhibits weak activity on galactomannan but robust activity on glucomannan, and activity on β-1,4-linked mannopentaose and hexaose [1]. SsGH134 from Streptomyces sp. NRRL B-24484 possesses a strong preference for unsubstituted linear β-mannans over gluco- and galactomannans [2]. SsGH134 possesses activity on β-1,4-linked mannotetraose, pentaose and hexaose.
Kinetics and Mechanism
1H NMR spectroscopic analysis of SsGH134 catalyzed cleavage of a benzoylhydrazine derivative of β-mannohexaose provided evidence for the formation of the α-anomer, consistent with an inverting mechanism [2]. Crystallographic evidence from binary complexes of SsGH134 with substrate and product, complemented by quantum mechanics/molecular mechanics calculations, supports a "southern hemisphere" 1C4→3H4‡→3S1 conformational itinerary along the reaction coordinate [2].
Catalytic Residues
Structural analysis of SsGH134 from Streptomyces sp. (see below) suggested roles for Glu45 as a general acid catalyst and for Asp57 as a general base catalyst [2]. These roles were supported by mutagenesis with the corresponding Glu45Ala and Asp57Ala single mutants inactive on β-mannopentaose and hexaose.
Three-dimensional structures
The three dimensional structure was first reported for SsGH134, and exists as a mixed α-helix/β-sheet fold with resemblance to HEWL (GH22), as well as GH19 chitinases, GH23 G-type lysozyme, and GH124 cellulases [2]. A binary Michaelis complex of the E45A variant of SsGH134 with mannopentaose bound in the active site defined the -3 to +2 subsites, and showed the sugar binding in the -1 subsite in a 1C4 conformation; a similar conformation was observed for the reducing-end mannose of a complex of mannotriose bound to the -3 to -1 subsites of wild-type SsGH134 [2]. Within the Michaelis complex, the carboxylate of the highly conserved C-terminal residue Ile173 is hydrogen bonded to O6 of the –2 mannosyl unit, and also forms a salt-bridge with the highly conserved K59. Within only the Michaelis complex, this interaction results in the formation of an active cleft tunnel reminiscent of processive glycoside hydrolases; the C-terminal segment is disordered in both apo and mannotriose product-bound forms [2]. SsGH134 can be classified as a syn protonator, with the acid residue situated syn to the C1-O5 bond.
Family Firsts
- First stereochemistry determination
- SsGH134 was shown to be inverting by 1H NMR spectroscopy [2].
- First general acid residue identification
- Glu45 in SsGH134 by structural study supported by kinetic analysis of mutants [2].
- First general base residue identification
- Asp57 in SsGH134 by structural study supported by kinetic analysis of mutants [2].
- First 3-D structure
- SsGH134 from Streptomyces sp. (PDB ID 5JTS) [2].
References
- Shimizu M, Kaneko Y, Ishihara S, Mochizuki M, Sakai K, Yamada M, Murata S, Itoh E, Yamamoto T, Sugimura Y, Hirano T, Takaya N, Kobayashi T, and Kato M. (2015). Novel β-1,4-Mannanase Belonging to a New Glycoside Hydrolase Family in Aspergillus nidulans. J Biol Chem. 2015;290(46):27914-27. DOI:10.1074/jbc.M115.661645 |
- Jin Y, Petricevic M, John A, Raich L, Jenkins H, Portela De Souza L, Cuskin F, Gilbert HJ, Rovira C, Goddard-Borger ED, Williams SJ, and Davies GJ. (2016). A β-Mannanase with a Lysozyme-like Fold and a Novel Molecular Catalytic Mechanism. ACS Cent Sci. 2016;2(12):896-903. DOI:10.1021/acscentsci.6b00232 |