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 See a page that's out-of-date and just needs a touch-up?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.

Talk:Glycoside Hydrolase Family 3

From CAZypedia
Jump to navigation Jump to search

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 | PubMed ID:23201198 [Thongpoo2012]

    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 | PubMed ID:23177201 [Bacik2012]

    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 | PubMed ID:20826810 [Litzinger2010]

    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 | PubMed ID:20138890 [Pozzo2010]

    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 | PubMed ID:20662765 [Yoshida2010]

    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 | PubMed ID:16717412 [Li2006]

    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 | PubMed ID:14561218 [Paal2004]

    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 | PubMed ID:11978178 [Chir2002]

    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 | PubMed ID:11851422 [Li2002]

    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 | PubMed ID:10625486 [Vocadlo2000]
  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 | PubMed ID:10671536 [Dan2000]

All Medline abstracts: PubMed


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