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Difference between revisions of "Glycoside Hydrolase Family 107"

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== Substrate specificities ==
 
== Substrate specificities ==
The [[glycoside hydrolases]] of this family are [[endo]]-acting α-fucosidases active on sulfated fucans (or fucoidans) from brown algae.
+
The [[glycoside hydrolases]] of this family are [[endo]]-acting α-fucosidases active on sulfated fucans (or fucoidans) from brown algae. All described GH107 family members are endo-1,4-fucanase of bacterial origin, and together with enzymes from the CAZY family [[GH29]], they form the clan GH-R. Members of the GH107 family were first described in 2006.<cite>Colin2006</cite>
 
 
All described GH107 family members are endo-1,4-fucanase of bacterial origin.
 
 
 
With enzymes from the CAZY family [[GH29]] they form the clan GH-R.
 
  
 
== Kinetics and Mechanism ==
 
== Kinetics and Mechanism ==
Content is to be added here.
+
The mechanism was proven to be [[retaining]]  by observation of the formation of an alpha-linked mercaptoethanol by transglycosylation.<cite>Vickers2018</cite> It  should then follow a [[classical Koshland double-displacement mechanism]] similarly to  [[GH29]].
 
 
 
== Catalytic Residues ==
 
== Catalytic Residues ==
The catalytic nucleophile is an aspartate, while the catalytic acid-base is a histidine. The later is unusual in GHs, and a divergence from [[GH29]], but is likely necessary to avoid electronic repulsion with the substrate sulfate groups.
+
The catalytic nucleophile is an aspartate, while the catalytic acid-base is a histidine. The later is unusual in GHs, and a divergence from [[GH29]], but is likely necessary to avoid electronic repulsion with the substrate sulfate groups. These two residues have been identified by structural superimposition with GH29 enzymes, and are conserved within the few members of the GH107 family. The catalytic His has been confirmed by the lack of activity of th H294Q mutant of ''Mariniflexile fucanivorans'', despite its structure was maintained.<cite>Vickers2018</cite>
  
 
== Three-dimensional structures ==
 
== Three-dimensional structures ==
The crystal structures of ''Mariniflexile fucanivorans'' (PDB: [{{PDBlink}}6dns 6dns],[{{PDBlink}}6dms 6dms],[{{PDBlink}}6dlh 6dlh]) and ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]). have been determined in 2018. The''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) enzyme showed a single catalytic domain with a (β/α)<sub>8</sub> / TIM-barrel fold, while in the  ''Mariniflexile fucanivorans'' enzyme, this catalytic domain is followed by three Ig-like domains that wrap around the catalytic one.<cite>Vickers2018</cite>
+
The crystal structures of ''Mariniflexile fucanivorans'' (PDB: [{{PDBlink}}6dns 6dns],[{{PDBlink}}6dms 6dms],[{{PDBlink}}6dlh 6dlh]) and ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) have been determined in 2018.<cite>Vickers2018</cite>  The''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) enzyme showed a single catalytic domain with a (β/α)<sub>8</sub> / TIM-barrel fold, while in the  ''Mariniflexile fucanivorans'' enzyme, this catalytic domain is followed by three Ig-like domains that wrap around the catalytic one.<cite>Vickers2018</cite>
  
 
== Family Firsts ==
 
== Family Firsts ==
 
;First stereochemistry determination: Content is to be added here.
 
;First stereochemistry determination: Content is to be added here.
;First catalytic nucleophile identification: Content is to be added here.
+
;First catalytic nucleophile identification: Both catalytic residues have been identified at the same time, in 2018.<cite>Vickers2018</cite>
;First general acid/base residue identification: Content is to be added here.
+
;First general acid/base residue identification: Both catalytic residues have been identified at the same time, in 2018.<cite>Vickers2018</cite>
;First 3-D structure: Content is to be added here.
+
;First 3-D structure: The crystal structures of ''Mariniflexile fucanivorans'' (PDB: [{{PDBlink}}6dns 6dns],[{{PDBlink}}6dms 6dms],[{{PDBlink}}6dlh 6dlh]) and ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) have been released at the same time, in 2018.<cite>Vickers2018</cite>
  
 
== References ==
 
== References ==
 
<biblio>
 
<biblio>
 +
#Colin2006 pmid=16880504
 +
#Vickers2018 pmid=30282808
  
#Vickers2018 pmid=30282808
 
 
#Cantarel2009 pmid=18838391
 
#Cantarel2009 pmid=18838391
  

Revision as of 03:23, 13 December 2019

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Glycoside Hydrolase Family GH107
Clan GH-R
Mechanism retaining
Active site residues known
CAZy DB link
http://www.cazy.org/GH107.html


Substrate specificities

The glycoside hydrolases of this family are endo-acting α-fucosidases active on sulfated fucans (or fucoidans) from brown algae. All described GH107 family members are endo-1,4-fucanase of bacterial origin, and together with enzymes from the CAZY family GH29, they form the clan GH-R. Members of the GH107 family were first described in 2006.[1]

Kinetics and Mechanism

The mechanism was proven to be retaining by observation of the formation of an alpha-linked mercaptoethanol by transglycosylation.[2] It should then follow a classical Koshland double-displacement mechanism similarly to GH29.

Catalytic Residues

The catalytic nucleophile is an aspartate, while the catalytic acid-base is a histidine. The later is unusual in GHs, and a divergence from GH29, but is likely necessary to avoid electronic repulsion with the substrate sulfate groups. These two residues have been identified by structural superimposition with GH29 enzymes, and are conserved within the few members of the GH107 family. The catalytic His has been confirmed by the lack of activity of th H294Q mutant of Mariniflexile fucanivorans, despite its structure was maintained.[2]

Three-dimensional structures

The crystal structures of Mariniflexile fucanivorans (PDB: 6dns,6dms,6dlh) and Psychromonas sp. (PDB: 6m8n) have been determined in 2018.[2] ThePsychromonas sp. (PDB: 6m8n) enzyme showed a single catalytic domain with a (β/α)8 / TIM-barrel fold, while in the Mariniflexile fucanivorans enzyme, this catalytic domain is followed by three Ig-like domains that wrap around the catalytic one.[2]

Family Firsts

First stereochemistry determination
Content is to be added here.
First catalytic nucleophile identification
Both catalytic residues have been identified at the same time, in 2018.[2]
First general acid/base residue identification
Both catalytic residues have been identified at the same time, in 2018.[2]
First 3-D structure
The crystal structures of Mariniflexile fucanivorans (PDB: 6dns,6dms,6dlh) and Psychromonas sp. (PDB: 6m8n) have been released at the same time, in 2018.[2]

References

  1. Colin S, Deniaud E, Jam M, Descamps V, Chevolot Y, Kervarec N, Yvin JC, Barbeyron T, Michel G, and Kloareg B. (2006) Cloning and biochemical characterization of the fucanase FcnA: definition of a novel glycoside hydrolase family specific for sulfated fucans. Glycobiology. 16, 1021-32. DOI:10.1093/glycob/cwl029 | PubMed ID:16880504 | HubMed [Colin2006]
  2. Vickers C, Liu F, Abe K, Salama-Alber O, Jenkins M, Springate CMK, Burke JE, Withers SG, and Boraston AB. (2018) Endo-fucoidan hydrolases from glycoside hydrolase family 107 (GH107) display structural and mechanistic similarities to α-l-fucosidases from GH29. J Biol Chem. 293, 18296-18308. DOI:10.1074/jbc.RA118.005134 | PubMed ID:30282808 | HubMed [Vickers2018]
  3. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, and Henrissat B. (2009) The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res. 37, D233-8. DOI:10.1093/nar/gkn663 | PubMed ID:18838391 | HubMed [Cantarel2009]
  4. 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.
    [DaviesSinnott2008]
All Medline abstracts: PubMed | HubMed