Page 104 - Read Online
P. 104
Page 16 of 17 Gotoh et al. Microbiome Res Rep 2023;2:20 https://dx.doi.org/10.20517/mrr.2023.14
PubMed PMC
21. Sasaki Y, Komeno M, Ishiwata A, et al. Mechanism of cooperative degradation of gum arabic arabinogalactan protein by
Bifidobacterium longum surface enzymes. Appl Environ Microbiol 2022;88:e0218721. DOI PubMed PMC
22. Sasaki Y, Yanagita M, Hashiguchi M, et al. Assimilation of arabinogalactan side chains with novel 3-O-β-L-arabinopyranosyl-α-L-
arabinofuranosidase in Bifidobacterium pseudocatenulatum. Microbiome Res Rep 2023;2:12. DOI
23. Hidaka M, Fushinobu S, Ohtsu N, et al. Trimeric crystal structure of the glycoside hydrolase family 42 β-galactosidase from Thermus
thermophilus A4 and the structure of its complex with galactose. J Mol Biol 2002;322:79-91. DOI PubMed
24. Godoy AS, Camilo CM, Kadowaki MA, et al. Crystal structure of β1→6-galactosidase from Bifidobacterium bifidum S17: trimeric
architecture, molecular determinants of the enzymatic activity and its inhibition by α-galactose. FEBS J 2016;283:4097-112. DOI
PubMed
25. Viborg AH, Fredslund F, Katayama T, et al. A β1-6/β1-3 galactosidase from Bifidobacterium animalis subsp. lactis Bl-04 gives
insight into sub-specificities of β-galactoside catabolism within Bifidobacterium. Mol Microbiol 2014;94:1024-40. DOI PubMed
26. Maksimainen M, Paavilainen S, Hakulinen N, Rouvinen J. Structural analysis, enzymatic characterization, and catalytic mechanisms
of β-galactosidase from Bacillus circulans sp. alkalophilus. FEBS J 2012;279:1788-98. DOI PubMed
27. Solomon HV, Tabachnikov O, Feinberg H, et al. Crystallization and preliminary crystallographic analysis of GanB, a GH42
intracellular β-galactosidase from Geobacillus stearothermophilus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013;69:1114-
9. DOI PubMed PMC
28. Fan Y, Hua X, Zhang Y, et al. Cloning, expression and structural stability of a cold-adapted β-galactosidase from Rahnella sp. R3.
Protein Expr Purif 2015;115:158-64. DOI
29. Karan R, Mathew S, Muhammad R, et al. Understanding high-salt and cold adaptation of a polyextremophilic enzyme.
Microorganisms 2020;8:1594. DOI PubMed PMC
30. Mangiagalli M, Lapi M, Maione S, et al. The co-existence of cold activity and thermal stability in an Antarctic GH42 β-galactosidase
relies on its hexameric quaternary arrangement. FEBS J 2021;288:546-65. DOI PubMed
31. Viborg AH, Katayama T, Arakawa T, et al. Discovery of α-l-arabinopyranosidases from human gut microbiome expands the diversity
within glycoside hydrolase family 42. J Biol Chem 2017;292:21092-101. DOI PubMed PMC
32. Ojima MN, Asao Y, Nakajima A, et al. Diversification of a fucosyllactose transporter within the genus Bifidobacterium. Appl Environ
Microbiol 2022;88:e0143721. DOI PubMed PMC
33. Nishimoto M, Kitaoka M. Practical preparation of lacto-N-biose I, a candidate for the bifidus factor in human milk. Biosci Biotechnol
Biochem 2007;71:2101-4. DOI PubMed
34. Nihira T, Nakajima M, Inoue K, Nishimoto M, Kitaoka M. Colorimetric quantification of alpha-D-galactose 1-phosphate. Anal
Biochem 2007;371:259-61. DOI PubMed
35. Kabsch W. XDS. Acta Crystallogr D Biol Crystallogr 2010;66:125-32. DOI
36. Evans PR, Murshudov GN. How good are my data and what is the resolution? Acta Crystallogr D Biol Crystallogr 2013;69:1204-14.
DOI PubMed PMC
37. Vagin A, Teplyakov A. Molecular replacement with MOLREP. Acta Crystallogr D Biol Crystallogr 2010;66:22-5. DOI PubMed
38. Casañal A, Lohkamp B, Emsley P. Current developments in Coot for macromolecular model building of Electron Cryo-microscopy
and Crystallographic Data. Protein Sci 2020;29:1069-78. DOI PubMed PMC
39. Murshudov GN, Skubák P, Lebedev AA, et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D
Biol Crystallogr 2011;67:355-67. DOI PubMed PMC
40. Holm L, Laakso LM. Dali server update. Nucleic Acids Res 2016;44:W351-5. DOI PubMed PMC
41. Krissinel E, Henrick K. Inference of macromolecular assemblies from crystalline state. J Mol Biol 2007;372:774-97. DOI
42. Henrissat B, Davies G. Structural and sequence-based classification of glycoside hydrolases. Curr Opin Struct Biol 1997;7:637-44.
DOI PubMed
43. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol
Biol Evol 2018;35:1547-9. DOI PubMed PMC
44. Larkin MA, Blackshields G, Brown NP, et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007;23:2947-8. DOI
45. Holm L. DALI and the persistence of protein shape. Protein Sci 2020;29:128-40. DOI PubMed PMC
46. Di Lauro B, Strazzulli A, Perugino G, et al. Isolation and characterization of a new family 42 β-galactosidase from the
thermoacidophilic bacterium Alicyclobacillus acidocaldarius: identification of the active site residues. Biochim Biophys Acta
2008;1784:292-301. DOI PubMed
47. Shaikh FA, Müllegger J, He S, Withers SG. Identification of the catalytic nucleophile in Family 42 β-galactosidases by intermediate
trapping and peptide mapping: YesZ from Bacillus subtilis. FEBS Lett 2007;581:2441-6. DOI PubMed
48. Cremer D, Pople JA. General definition of ring puckering coordinates. J Am Chem Soc 1975;97:1354-8. DOI
49. Wheatley RW, Huber RE. An allolactose trapped at the lacZ β-galactosidase active site with its galactosyl moiety in a (4)H3
conformation provides insights into the formation, conformation, and stabilization of the transition state. Biochem Cell Biol
2015;93:531-40. DOI PubMed
50. Davies GJ, Ducros VM, Varrot A, Zechel DL. Mapping the conformational itinerary of β-glycosidases by X-ray crystallography.
Biochem Soc Trans 2003;31:523-7. DOI PubMed
51. Hinz SW, van den Brock LA, Beldman G, Vincken JP, Voragen AG. β-galactosidase from Bifidobacterium adolescentis DSM20083

