Talk:Glycoside Hydrolase Family 3

Comment from Brian Mark, April 2013

The GH3 page has received a comprehensive update. The following comments have been addressed. Thank-you for the input!

Comment from Shinya Fushinobu, Sept. 2011

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, 3-D homology model, mutagenesis, kinetic analysis, pH profile, 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 |

   1-domain Nag, experimental structure, ligand complex, mobile loop bearing acid/base

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 |

   2-domain Nag, strucuture, mutagenesis, kinetic analysis, pH profile, azide rescue unsuccessful

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, experimental structure, complexes, reduced Km for mutant with PNP-Glc

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, experimental structure, product complex

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 |

   Nag - relevant? Appears to be mis-identification.

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, kinetic analysis, pH profile, azide rescue

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, Glu-473 labelled by N-bromoacetyl-beta-d-glucosylamine

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 |

   Subfamily 5, kinetic analysis, pH profile, azide rescue

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)