Talk:Glycoside Hydrolase Family 3

Litzinger et al. (2010) suggested that the acid/base catalyst of 2 domain NagZs (and also 1 domain NagZs) is an Asp-His dyad in the (β/α)₈ domain. pmid: 20826810.

Update to Catalytic Residues section needed?

Given the growing amount of information about the identity of the GH3 catalytic residues - and in particular the acid/base - in different enzymes/subfamilies, I wonder if a update of this section isn't needed?

Here are some key acid/base ID references [1, 2, 3, 4, 5, 6, 7, 8, 9], one of which also confirms the catalytic nucleophile [7]. These references are nucleophile-specific studies [10, 11]:

References

1. Thongpoo P, McKee LS, Araújo AC, Kongsaeree PT, and Brumer H. (2013). Identification of the acid/base catalyst of a glycoside hydrolase family 3 (GH3) beta-glucosidase from Aspergillus niger ASKU28. Biochim Biophys Acta. 2013;1830(3):2739-49. DOI:10.1016/j.bbagen.2012.11.014 |

   Subfamily 4, via kinetic analysis & azide rescue

2. Bacik JP, Whitworth GE, Stubbs KA, Vocadlo DJ, and Mark BL. (2012). Active site plasticity within the glycoside hydrolase NagZ underlies a dynamic mechanism of substrate distortion. Chem Biol. 2012;19(11):1471-82. DOI:10.1016/j.chembiol.2012.09.016 |

   NagZ subfamily, ligand complex

3. Litzinger S, Fischer S, Polzer P, Diederichs K, Welte W, and Mayer C. (2010). Structural and kinetic analysis of Bacillus subtilis N-acetylglucosaminidase reveals a unique Asp-His dyad mechanism. J Biol Chem. 2010;285(46):35675-84. DOI:10.1074/jbc.M110.131037 |

   NagZ sunfamily, kinetic analysis

4. Pozzo T, Pasten JL, Karlsson EN, and Logan DT. (2010). Structural and functional analyses of beta-glucosidase 3B from Thermotoga neapolitana: a thermostable three-domain representative of glycoside hydrolase 3. J Mol Biol. 2010;397(3):724-39. DOI:10.1016/j.jmb.2010.01.072 |

   Subfamily 5

5. Yoshida E, Hidaka M, Fushinobu S, Koyanagi T, Minami H, Tamaki H, Kitaoka M, Katayama T, and Kumagai H. (2010). Role of a PA14 domain in determining substrate specificity of a glycoside hydrolase family 3 β-glucosidase from Kluyveromyces marxianus. Biochem J. 2010;431(1):39-49. DOI:10.1042/BJ20100351 |

   Subfamily 5

6. Li H, Zhao G, Miyake H, Umekawa H, Kimura T, Ohmiya K, and Sakka K. (2006). Identification of a catalytic residue of Clostridium paraputrificum N-acetyl-beta-D-glucosaminidase Nag3A by site-directed mutagenesis. Biosci Biotechnol Biochem. 2006;70(5):1127-33. DOI:10.1271/bbb.70.1127 |

   double-check

7. Paal K, Ito M, and Withers SG. (2004). Paenibacillus sp. TS12 glucosylceramidase: kinetic studies of a novel sub-family of family 3 glycosidases and identification of the catalytic residues. Biochem J. 2004;378(Pt 1):141-9. DOI:10.1042/BJ20031028 |

   Subfamily 5

8. Chir J, Withers S, Wan CF, and Li YK. (2002). Identification of the two essential groups in the family 3 beta-glucosidase from Flavobacterium meningosepticum by labelling and tandem mass spectrometric analysis. Biochem J. 2002;365(Pt 3):857-63. DOI:10.1042/BJ20020186 |

   Subfamily 5

9. Li YK, Chir J, Tanaka S, and Chen FY. (2002). Identification of the general acid/base catalyst of a family 3 beta-glucosidase from Flavobacterium meningosepticum. Biochemistry. 2002;41(8):2751-9. DOI:10.1021/bi016049e |

   Nag - relevant? Mis-identification.

10. Vocadlo DJ, Mayer C, He S, and Withers SG. (2000). Mechanism of action and identification of Asp242 as the catalytic nucleophile of Vibrio furnisii N-acetyl-beta-D-glucosaminidase using 2-acetamido-2-deoxy-5-fluoro-alpha-L-idopyranosyl fluoride. Biochemistry. 2000;39(1):117-26. DOI:10.1021/bi991958d |
11. Dan S, Marton I, Dekel M, Bravdo BA, He S, Withers SG, and Shoseyov O. (2000). Cloning, expression, characterization, and nucleophile identification of family 3, Aspergillus niger beta-glucosidase. J Biol Chem. 2000;275(7):4973-80. DOI:10.1074/jbc.275.7.4973 |

Harry Brumer (talk) 17:55, 14 December 2012 (PST)