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Difference between revisions of "Glycoside Hydrolase Family 62"
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== Kinetics and Mechanism == | == Kinetics and Mechanism == | ||
| − | While the catalytic mechanism of this family have not been formerly determined, likely reflecting the extremely quick rate of mutarotation displayed by arabinose, the enzyme is predicted to display a single displacement or “inverting” mechanism. This prediction is based on the location of GH62 in Clan F, the same clan occupied by GH43 (ClanF), which is an inverting family. Similarly, although the catalytic residues have not been determined using either biochemical or mutagenesis strategies, the identity of these residues is predicted from sequence homology with GH43 enzymes, given that both the catalytic mechanism and the catalytic apparatus are conserved in glycoside hydrolase families belonging to the same clan. Thus <cite># | + | While the catalytic mechanism of this family have not been formerly determined, likely reflecting the extremely quick rate of mutarotation displayed by arabinose, the enzyme is predicted to display a single displacement or “inverting” mechanism. This prediction is based on the location of GH62 in Clan F, the same clan occupied by GH43 (ClanF), which is an inverting family. Similarly, although the catalytic residues have not been determined using either biochemical or mutagenesis strategies, the identity of these residues is predicted from sequence homology with GH43 enzymes, given that both the catalytic mechanism and the catalytic apparatus are conserved in glycoside hydrolase families belonging to the same clan. Thus <cite>#4</cite> predicts that the catalytic general acid and base will be a Glu and Asp, respectively, while a second Asp modulates the pKa of the general acid. |
== Catalytic Residues == | == Catalytic Residues == | ||
Revision as of 03:18, 30 July 2009
| Glycoside Hydrolase Family GH62 | |
| Clan | GH-F |
| Mechanism | assumed to be inverting |
| Active site residues | inferred |
| CAZy DB link | |
| http://www.cazy.org/fam/GH62.html | |
Substrate specificities
This small family comprises an equal number of eukaryotic and prokaryotic enzymes. All the characterized enzymes in this family are arabinofuranosidases that specifically cleave either alpha1,2 or alpha1,3 L-arabinofuranose side chains from xylans [1, 2]. The enzyme will not act on xylose moieties in xylan that are decorated at both O2 and O3 with an arabinose side chain. The enzyme also displays no non-specific arabinofuranosidase activity; for example it does not hydrolyse 4-nitrophenyl-alpha-L-arabinofuranose. Several of these enzymes contain cellulose #1 or xylan #2 binding CBMs.
Kinetics and Mechanism
While the catalytic mechanism of this family have not been formerly determined, likely reflecting the extremely quick rate of mutarotation displayed by arabinose, the enzyme is predicted to display a single displacement or “inverting” mechanism. This prediction is based on the location of GH62 in Clan F, the same clan occupied by GH43 (ClanF), which is an inverting family. Similarly, although the catalytic residues have not been determined using either biochemical or mutagenesis strategies, the identity of these residues is predicted from sequence homology with GH43 enzymes, given that both the catalytic mechanism and the catalytic apparatus are conserved in glycoside hydrolase families belonging to the same clan. Thus [3] predicts that the catalytic general acid and base will be a Glu and Asp, respectively, while a second Asp modulates the pKa of the general acid.
Catalytic Residues
Predicted to be an Asp (genral acid) and Glu (genral base)
Three-dimensional structures
Based on its location in Clan F GH62s are preducted to display a 5-fold beta-propeller fold
Family Firsts
- First sterochemistry determination
- No experimental proof.
- First catalytic nucleophile identification
- No experimental proof.
- First general acid/base residue identification
- No experimental proof.
- First 3-D structure
- No experimental proof.
""
References
- Kellett LE, Poole DM, Ferreira LM, Durrant AJ, Hazlewood GP, and Gilbert HJ. (1990). Xylanase B and an arabinofuranosidase from Pseudomonas fluorescens subsp. cellulosa contain identical cellulose-binding domains and are encoded by adjacent genes. Biochem J. 1990;272(2):369-76. DOI:10.1042/bj2720369 |
- Pons T, Naumoff DG, Martínez-Fleites C, and Hernández L. (2004). Three acidic residues are at the active site of a beta-propeller architecture in glycoside hydrolase families 32, 43, 62, and 68. Proteins. 2004;54(3):424-32. DOI:10.1002/prot.10604 |
- Vincent P, Shareck F, Dupont C, Morosoli R, and Kluepfel D. (1997). New alpha-L-arabinofuranosidase produced by Streptomyces lividans: cloning and DNA sequence of the abfB gene and characterization of the enzyme. Biochem J. 1997;322 ( Pt 3)(Pt 3):845-52. DOI:10.1042/bj3220845 |
- Dupont C, Roberge M, Shareck F, Morosoli R, and Kluepfel D. (1998). Substrate-binding domains of glycanases from Streptomyces lividans: characterization of a new family of xylan-binding domains. Biochem J. 1998;330 ( Pt 1)(Pt 1):41-5. DOI:10.1042/bj3300041 |