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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?
- 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. 1830, 2739-49. DOI:10.1016/j.bbagen.2012.11.014 | Subfamily 4, 3-D homology model, mutagenesis, kinetic analysis, pH profile, azide rescue
- 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. 19, 1471-82. DOI:10.1016/j.chembiol.2012.09.016 | 1-domain Nag, experimental structure, ligand complex, mobile loop bearing acid/base
- 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. 285, 35675-84. DOI:10.1074/jbc.M110.131037 | 2-domain Nag, strucuture, mutagenesis, kinetic analysis, pH profile, azide rescue unsuccessful
- 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. 397, 724-39. DOI:10.1016/j.jmb.2010.01.072 | Subfamily 5, experimental structure, complexes, reduced Km for mutant with PNP-Glc
- 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. 431, 39-49. DOI:10.1042/BJ20100351 | Subfamily 5, experimental structure, product complex
- 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. 70, 1127-33. DOI:10.1271/bbb.70.1127 | Nag - relevant? Appears to be mis-identification.
- 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. 378, 141-9. DOI:10.1042/BJ20031028 | Subfamily 5, kinetic analysis, pH profile, azide rescue
- 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. 365, 857-63. DOI:10.1042/BJ20020186 | Subfamily 5, Glu-473 labelled by N-bromoacetyl-beta-d-glucosylamine
- 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. 41, 2751-9. DOI:10.1021/bi016049e | Subfamily 5, kinetic analysis, pH profile, azide rescue
- 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. 39, 117-26. DOI:10.1021/bi991958d |
- 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. 275, 4973-80. DOI:10.1074/jbc.275.7.4973 |