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Comment on tertiary structural relatedness of GH101 and GH13

Dear Warren,

I would like to pay your attention on some data about GH101 family:

• You have written, that 'the recently solved 3D structure of SpGH101 reveals that this protein surprisingly shares some structural features with GH13 alpha-amylases', but it is not so surprising. According to PSI-BLAST searches, GH101 is related to GH13, GH31 and many other (β/α)₈-barrel glycoside hydrolases [1, 2].
• According to BLAST searches, the seventh domain of SpGH101 and BlGH101 belongs to family NEW3 of the functionally uncharacterized domains [3].

References: 1. D.G. Naumoff and M. Carreras. 2009. PSI Protein Classifier: a new program automating PSI-BLAST search results. Molecular Biology (Engl Transl). V.43. N.4. P.652-664.

2. D.G. Naumoff. 2008. The GH31 family of glycoside hydrolases: subfamily structure and evolutionary connections. The Sixth International Conference on Bioinformatics of Genome Regulation and Structure. June 22-28, 2008. Novosibirsk. Russia. P.169.

3. D.G. Naumoff. 2004. Phylogenetic analysis of α-galactosidases of the GH27 family. Molecular Biology (Engl Transl). V.38. N.3. P.388-399.

--Daniil Naumoff 11:36, 10 December 2009 (UTC)

• Six subfamilies have been recognized in GH101 family [4].

References: 4. D.G. Naumoff. 2010. GH101 family of glycoside hydrolases: subfamily structure and evolutionary connections with other families. Journal of Bioinformatics and Computational Biology. V.8. N.3. P.437-451. --Daniil Naumoff 21:37, 5 May 2010 (UTC)