https://www.cazypedia.org/api.php?action=feedcontributions&user=Daniil+Naumoff&feedformat=atomCAZypedia - User contributions [en-ca]2024-03-29T11:07:27ZUser contributionsMediaWiki 1.35.10https://www.cazypedia.org/index.php?title=User_talk:Warren_Wakarchuk&diff=9635User talk:Warren Wakarchuk2013-12-10T11:16:15Z<p>Daniil Naumoff: /* Comment on tertiary structural relatedness of GH101 and GH13 */</p>
<hr />
<div>== Comment on tertiary structural relatedness of GH101 and GH13 ==<br />
<br />
Dear Warren,<br />
<br />
I would like to pay your attention on some data about [[GH101]] family:<br />
<br />
* You have written, that '[[Glycoside Hydrolase Family 101|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)<sub>8</sub>-barrel glycoside hydrolases [1, 2].<br />
* According to BLAST searches, the seventh domain of SpGH101 and BlGH101 belongs to [http://pfam.sanger.ac.uk/family?entry=NPCBM_assoc family NEW3] of the functionally uncharacterized domains [3].<br />
<br />
References:<br />
1. [http://link.springer.com/article/10.1134/S0026893309040189 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.]<br />
<br />
2. [http://www.bionet.nsc.ru/meeting/bgrs2008/BGRS2008_Proceedings.pdf 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.]<br />
<br />
3. [http://link.springer.com/article/10.1023/B:MBIL.0000032210.97006.de D.G. Naumoff. 2004. Phylogenetic analysis of α-galactosidases of the GH27 family. Molecular Biology (Engl Transl). V.38. N.3. P.388-399.]<br />
<br />
--[[User:Daniil Naumoff|Daniil Naumoff]] 11:36, 10 December 2009 (UTC)<br />
<br />
* Six subfamilies have been recognized in GH101 family [4].<br />
<br />
References:<br />
4. [http://www.worldscinet.com/jbcb/08/0803/S0219720010004628.html 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.]<br />
--[[User:Daniil Naumoff|Daniil Naumoff]] 21:37, 5 May 2010 (UTC)</div>Daniil Naumoffhttps://www.cazypedia.org/index.php?title=User_talk:Warren_Wakarchuk&diff=4970User talk:Warren Wakarchuk2010-06-18T11:28:46Z<p>Daniil Naumoff: /* Comment on tertiary structural relatedness of GH101 and GH13 */</p>
<hr />
<div>== Comment on tertiary structural relatedness of GH101 and GH13 ==<br />
<br />
Dear Warren,<br />
<br />
I would like to pay your attention on some data about [[GH101]] family:<br />
<br />
* You have written, that '[[Glycoside Hydrolase Family 101|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)<sub>8</sub>-barrel glycoside hydrolases [1, 2].<br />
* According to BLAST searches, the seventh domain of SpGH101 and BlGH101 belongs to [http://pfam.sanger.ac.uk/family?entry=NPCBM_assoc family NEW3] of the functionally uncharacterized domains [3].<br />
<br />
References:<br />
1. [http://bioinform.genetika.ru/members/Naumoff/MB2009E.pdf 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.]<br />
<br />
2. [http://www.bionet.nsc.ru/meeting/bgrs2008/BGRS2008_Proceedings.pdf 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.]<br />
<br />
3. [http://bioinform.genetika.ru/members/Naumoff/MB2004E.pdf D.G. Naumoff. 2004. Phylogenetic analysis of α-galactosidases of the GH27 family. Molecular Biology (Engl Transl). V.38. N.3. P.388-399.]<br />
<br />
--[[User:Daniil Naumoff|Daniil Naumoff]] 11:36, 10 December 2009 (UTC)<br />
<br />
* Six subfamilies have been recognized in GH101 family [4].<br />
<br />
References:<br />
4. [http://www.worldscinet.com/jbcb/08/0803/S0219720010004628.html 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.]<br />
--[[User:Daniil Naumoff|Daniil Naumoff]] 21:37, 5 May 2010 (UTC)</div>Daniil Naumoffhttps://www.cazypedia.org/index.php?title=User_talk:Warren_Wakarchuk&diff=4620User talk:Warren Wakarchuk2010-05-05T21:37:44Z<p>Daniil Naumoff: /* Comment on tertiary structural relatedness of GH101 and GH13 */</p>
<hr />
<div>== Comment on tertiary structural relatedness of GH101 and GH13 ==<br />
<br />
Dear Warren,<br />
<br />
I would like to pay your attention on some data about [[GH101]] family:<br />
<br />
* You have written, that '[[Glycoside Hydrolase Family 101|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)<sub>8</sub>-barrel glycoside hydrolases [1, 2].<br />
* According to BLAST searches, the seventh domain of SpGH101 and BlGH101 belongs to [http://pfam.sanger.ac.uk/family?entry=NPCBM_assoc family NEW3] of the functionally uncharacterized domains [3].<br />
<br />
References:<br />
1. [http://bioinform.genetika.ru/members/Naumoff/MB2009E.pdf 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.]<br />
<br />
2. [http://www.bionet.nsc.ru/meeting/bgrs2008/BGRS2008_Proceedings.pdf 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.]<br />
<br />
3. [http://bioinform.genetika.ru/members/Naumoff/MB2004E.pdf D.G. Naumoff. 2004. Phylogenetic analysis of α-galactosidases of the GH27 family. Molecular Biology (Engl Transl). V.38. N.3. P.388-399.]<br />
<br />
--[[User:Daniil Naumoff|Daniil Naumoff]] 11:36, 10 December 2009 (UTC)<br />
<br />
* Six subfamilies have been recognized in GH101 family [4].<br />
<br />
References:<br />
4. [http://www.worldscinet.com/jbcb/00/0001/S0219720010004628.html D.G. Naumoff. 2010. GH101 family of glycoside hydrolases: subfamily structure and evolutionary connections with other families. Journal of Bioinformatics and Computational Biology. (in press)]<br />
<br />
--[[User:Daniil Naumoff|Daniil Naumoff]] 21:37, 5 May 2010 (UTC)</div>Daniil Naumoffhttps://www.cazypedia.org/index.php?title=User_talk:Warren_Wakarchuk&diff=3029User talk:Warren Wakarchuk2009-12-14T07:43:23Z<p>Daniil Naumoff: </p>
<hr />
<div>Dear Warren,<br />
<br />
I would like to pay your attention on some data about [[GH101]] family:<br />
<br />
* You have written, that '[[Glycoside Hydrolase Family 101|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)<sub>8</sub>-barrel glycoside hydrolases [1, 2].<br />
* According to BLAST searches, the seventh domain of SpGH101 and BlGH101 belongs to [http://pfam.sanger.ac.uk/family?entry=NPCBM_assoc family NEW3] of the functionally uncharacterized domains [3].<br />
* Six subfamilies have been recognized in GH101 family [4, 5].<br />
<br />
<br />
<br />
References:<br />
<br />
1. [http://bioinform.genetika.ru/members/Naumoff/MB2009E.pdf 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.]<br />
<br />
2. [http://www.bionet.nsc.ru/meeting/bgrs2008/BGRS2008_Proceedings.pdf 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.]<br />
<br />
3. [http://bioinform.genetika.ru/members/Naumoff/MB2004E.pdf D.G. Naumoff. 2004. Phylogenetic analysis of α-galactosidases of the GH27 family. Molecular Biology (Engl Transl). V.38. N.3. P.388-399.]<br />
<br />
4. [http://mccmb.genebee.msu.su/2009/MCCMB09_Proceedings.pdf D.G. Naumoff. 2009. Sequence analysis of endo-α-N-acetylgalactosaminidases and their homologues. Proceedings of the International Moscow Conference on Computational Molecular Biology (MCCMB’09). July 20-23, 2009. Moscow. Russia. P.251-252.]<br />
<br />
5. [http://www.springerlink.com/content/5464020317174jx9/fulltext.pdf D.G. Naumoff. 2009. Sequence analysis of endo-α-N-acetylgalactosaminidases (Abstracts of 20th International Symposium on Glycoconjugates Glycans "GLYCO XX", November 29 – December 4, 2009, San Juan, Puerto Rico, USA). Glycoconjugate Journal. V.26. N.7. P.847.]<br />
<br />
--[[User:Daniil Naumoff|Daniil Naumoff]] 11:36, 10 December 2009 (UTC)</div>Daniil Naumoffhttps://www.cazypedia.org/index.php?title=User_talk:Warren_Wakarchuk&diff=3026User talk:Warren Wakarchuk2009-12-10T11:36:26Z<p>Daniil Naumoff: Created page with 'Dear Warren, I would like to pay your attention on some data about GH101 family: * You have written, that '[[Glycoside Hydrolase Family 101|the recently solved 3D structure…'</p>
<hr />
<div>Dear Warren,<br />
<br />
I would like to pay your attention on some data about [[GH101]] family:<br />
<br />
* You have written, that '[[Glycoside Hydrolase Family 101|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 (beta/alpha)<sub>8</sub>-barrel glycoside hydrolases [1].<br />
* According to BLAST searches, the seventh domain of SpGH101 and BlGH101 belongs to [http://pfam.sanger.ac.uk/family?entry=NPCBM_assoc family NEW3] of the functionally uncharacterized domains [2].<br />
* Six subfamilies have been recognized in GH101 family [3, 4].<br />
<br />
<br />
<br />
References:<br />
<br />
1. [http://bioinform.genetika.ru/members/Naumoff/MB2009E.pdf 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.]<br />
<br />
2. [http://bioinform.genetika.ru/members/Naumoff/MB2004E.pdf D.G. Naumoff. 2004. Phylogenetic analysis of α-galactosidases of the GH27 family. Molecular Biology (Engl Transl). V.38. N.3. P.388-399.]<br />
<br />
3. [http://mccmb.genebee.msu.su/2009/MCCMB09_Proceedings.pdf D.G. Naumoff. 2009. Sequence analysis of endo-α-N-acetylgalactosaminidases and their homologues. Proceedings of the International Moscow Conference on Computational Molecular Biology (MCCMB’09). July 20-23, 2009. Moscow. Russia. P.251-252.]<br />
<br />
4. [http://www.springerlink.com/content/5464020317174jx9/fulltext.pdf D.G. Naumoff. 2009. Sequence analysis of endo-α-N-acetylgalactosaminidases (Abstracts of 20th International Symposium on Glycoconjugates Glycans "GLYCO XX", November 29 – December 4, 2009, San Juan, Puerto Rico, USA). Glycoconjugate Journal. V.26. N.7. P.847.]<br />
<br />
--[[User:Daniil Naumoff|Daniil Naumoff]] 11:36, 10 December 2009 (UTC)</div>Daniil Naumoffhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_27&diff=444Glycoside Hydrolase Family 272008-03-13T16:08:27Z<p>Daniil Naumoff: </p>
<hr />
<div>* Author: [[User:hbrumer3|Harry Brumer]]<br />
* Responsible Editor: [[User:hbrumer3|Harry Brumer]]<br />
----<br />
<br />
<div style="float:right"><br />
{| {{Prettytable}}<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH27'''<br />
|-<br />
|'''Clan''' <br />
|[[GH-D]]<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH27.html<br />
|}<br />
</div><br />
<br />
== Substrate specificities ==<br />
α-Galactosidase activity has been observed in both bacterial and eukaryotic members of GH27, while α-''N''-acetylgalactosaminidase activity has been observed in certain eukaryotic enzymes, including human, mouse, and chicken. Bacterial GH27 isomaltodextranases have also been identified. Notably, this family contains both human α-galactosidase A and human α-''N''-acetylgalactosaminidase (also known as α-galactosidase B), defects in which produce the phenotypes associated with [http://en.wikipedia.org/wiki/Fabry%27s_disease Fabry] and [http://children.webmd.com/schindler-disease Schindler] lysosomal storage disorders, respectively <cite>4 5</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Family GH27 α-galactosidases are anomeric configuration-retaining enzymes, as first demonstrated by proton NMR studies of the hydrolysis of ''p''-nitrophenyl α-galactopyranoside by an α-galactosidase isolated from the white-rot fungus ''Phanerochaete chrysosporium'' <cite>1</cite>. GH27 enzymes are thus expected to use a classical Koshland double-displacement mechanism <cite>6</cite>, which involves the formation of a covalent glycosyl-enzyme intermediate <cite>7</cite>. As predicted based on their common clanship in [[Clan GH-D]], [[Glycoside Hydrolase Family 36 (GH36)]] enzymes also operate through the same "retaining" mechanism <cite>8</cite>.<br />
<br />
== Catalytic Residues ==<br />
The conserved amino acid sidechain that functions as the catalytic nucleophile in GH27 has been identified in two different eukaryotic family members by mechanism-based labelling, proteolytic digestion, and mass spectrometric analysis. Identification of Asp-130 in the YLKY'''D'''NC sequence fragment of the ''Phanerochaete chrysosporium'' α-galactosidase by labelling with 2',4',6'-trinitrophenyl 2-deoxy-2,2-difluoro-α-D-''lyxo''-hexopyranoside ("2,2-difluoro-α-galactosyl picrate") <cite>2</cite> only slightly predated the identification of the same conserved aspartate in the green coffee bean α-galactosidase (Asp-145 in the sequence LKY'''D'''NCNNN) using 5-fluoro-α-D-galactopyranosyl fluoride as a labelling agent <cite>9</cite>.<br />
<br />
The catalytic acid/base residue in this family was first identified by X-ray structural analysis of the chicken (''Gallus gallus'') α-''N''-acetylgalactosaminidase in complex with ''N''-acetylgalactosamine <cite>3</cite>. The position of the product within the enzyme active site indicated that Asp-201 in the sequence CNLWRNYD'''D'''IQDSW was the obvious candidate to fulfill this role. Subsequent product complexes of the rice α-galactosidase <cite>11</cite>, human α-galactosidase A <cite>10</cite>, and the ''Hypocrea jecorina'' (née ''Trichoderma reesei'') α-galactosidase <cite>12</cite> have similarly implicated the homologous residue in these enzymes in catalysis.<br />
<br />
Interestingly, of the over 200 known point mutations in human α-galactosidase A that lead to Fabry disease, very few involve the catalytic residues <cite>3 4 10</cite>. While many mutations are thought to disrupt the hydrophobic core of the enzyme or otherwise disrupt protein folding, only the D170V, D170H, and D231N genotypic variants are known, with obvious catalytic implications <cite>4 10</cite>. Several other mutations are known to affect key active site structural or substrate-binding residues in human α-galactosidase A <cite>10</cite>. Whereas Fabry disease is X-linked and therefore comparatively more common, the autosomal recessive Schindler disease is rare <cite>4</cite>. Comparative analysis using the structurally similar human α-galactosidase A <cite>10</cite> and chicken ''N''-acetylgalactosaminidase <cite>3</cite> enzymes has indicated that none of the few known mutations in the human GH27 α-''N''-acetylgalactosaminidase occur in the catalytic nor active site residues <cite>4</cite>.<br />
<br />
== Three-dimensional structures ==<br />
Published in 2002, the 3-D structure of the chicken (''Gallus gallus'') α-''N''-acetylgalactosaminidase solved by Garman ''et al.'' using X-ray crystallography (1.9 Å resolution) represented the first structure of an enzyme from GH27, and indeed [[Clan GH-D]] <cite>3</cite>. Futhermore, the simultaneous solution of an enzyme-product complex (2.4 Å), was instrumental in defining the catalytic acid/base residue in this GH family and clan <cite>3</cite>, as described above. Soon thereafter, structures of the rice (''Oryza sativa'') α-galactosidase (2003) <cite>11</cite>, human (''Homo sapiens'') α-galactosidase A (2004) <cite>10</cite>, and ''Hypocrea jecorina'' (née ''Trichoderma reesei'') α-galactosidase (2004) <cite>12</cite> were presented in both free and product-complexed forms. All of these structures indicated that GH27 enzymes are comprised of an N-terminal (β/α)<sub>8</sub> (TIM) barrel domain and a C-terminal anti-parallel β-jellyroll domain, the former of which contains the enzyme catalytic center composed by loop residues at the ends of β-strands 1-7.<br />
<br />
The known overall structures of GH27 enzymes are all highly conserved and the N-terminal domains are all closely superimposable, with minor exceptions including the ''H. jecorina'' (''T. reesei'') α-galactosidase <cite>12</cite>, which contains a 40 amino acid insertion in loop β4-α4, and the animal enzymes <cite>3 10</cite>, which contain a short 10 residue insertion in the α1-β1 loop <cite>4</cite>. The C-terminal domains, although similar, are less well conserved, both at the primary and tertiary structural levels <cite>4</cite>. In keeping with the ''exo'' mode of action of these enzymes, which cleave α-Gal from the non-reducing terminii of their substrates, the active sites are pocket-shaped <cite>3 11 12 10</cite>. Specificity for the 2-hydroxyl substituent, in the case of α-galactosidases in the family, and the 2-deoxy-2-''N''-acetyl substituent, in the case of the α-''N''-acetylgalactosaminidases, is dictated by the presence of correspondingly large or small active-site binding residues, respectively <cite>10</cite> (reviewed in <cite>4</cite>). Based on these observations, phylogenetic analysis has been presented which may have some power to predict specificity within GH27 <cite>10</cite>.<br />
<br />
As predicted by their common membership in [[Clan GH-D]], [[GH36]] enzymes likewise present active sites on (β/α)<sub>8</sub>- barrel domains <cite>8</cite>. [[GH36]] enzymes also contain a related C-terminal β-sheet domain, in addition to a large β-supersandwich N-terminal domain not found in GH27 enzymes <cite>8</cite>. Structural analysis of a [[GH31]] enzyme has led to the addition of this family to [[Clan GH-D]] <cite>13</cite>.<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Retention of anomeric stereochemistry demonstrated by H-1 NMR for the main α-galactosidase from the white-rot fungus ''Phanerochaete chrysosporium'' <cite>1</cite>.<br />
;First catalytic nucleophile identification: ''Phanerochaete chrysosporium'' α-galactosidase by mechanism-based labelling with 2',4',6'-trinitrophenyl 2-deoxy-2,2-difluoro-α-D-''lyxo''-hexopyranoside ("2,2-difluoro-α-galactosyl picrate"), pepsin digestion, and mass spectrometry <cite>2</cite>.<br />
;First general acid/base residue identification: Chicken (''Gallus gallus'') α-''N''-acetylgalactosaminidase by X-ray structural analysis of an enzyme-''N''-acetylgalactosamine complex <cite>3</cite>.<br />
;First 3-D structure: Chicken α-''N''-acetylgalactosaminidase, both free enzyme and in complex with ''N''-acetylgalactosamine <cite>3</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#1 pmid=10085226<br />
#2 pmid=10933800<br />
#3 pmid=12005440<br />
#4 Garman, S.C. (2006) ''Structural studies on α-GAL and α-NAGAL: The atomic basis of Fabry and Schindler diseases.'' Biocatalysis and Biotransformation 24 (1/2) 129-136. [http://dx.doi.org/10.1080/10242420600598194 DOI: 10.1080/10242420600598194]<br />
#5 pmid=17391432<br />
#6 Sinnott, M.L. (1990) ''Catalytic mechanisms of enzymatic glycosyl transfer.'' Chem. Rev. 90 (7) 1171-1202. [http://dx.doi.org/10.1021/cr00105a006 DOI: 10.1021/cr00105a006]<br />
#7 pmid=11518970<br />
#8 pmid=17323919<br />
#9 pmid=11128583<br />
#10 pmid=15003450<br />
#11 pmid=12657636<br />
#12 pmid=15136043<br />
#13 pmid=16580018<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families]]</div>Daniil Naumoffhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_GH97_(GH97)&diff=443Glycoside Hydrolase Family GH97 (GH97)2008-03-12T12:25:02Z<p>Daniil Naumoff: Redirecting to Glycoside Hydrolase Family 97</p>
<hr />
<div>#redirect [[Glycoside Hydrolase Family 97]]</div>Daniil Naumoffhttps://www.cazypedia.org/index.php?title=Glycosyl_Hydrolase_Family_97&diff=441Glycosyl Hydrolase Family 972008-03-12T12:21:56Z<p>Daniil Naumoff: Redirecting to Glycoside Hydrolase Family 97</p>
<hr />
<div>#redirect [[Glycoside Hydrolase Family 97]]</div>Daniil Naumoffhttps://www.cazypedia.org/index.php?title=User:Daniil_Naumoff&diff=439User:Daniil Naumoff2008-03-12T11:57:12Z<p>Daniil Naumoff: New page: This is the user page of Daniil G. Naumoff, Ph.D. I am a Leading Research Scientist (PI) in the Laboratory of Bioinformatics of State Institute for Genetics and Selection of Industrial Mic...</p>
<hr />
<div>This is the user page of Daniil G. Naumoff, Ph.D. I am a Leading Research Scientist (PI) in the Laboratory of Bioinformatics of State Institute for Genetics and Selection of Industrial Microorganisms (Moscow, Russia). <br />
Details about my current areas of research in the sequence-based classification of glycoside hydrolases can be found at my [http://bioinform.genetika.ru/members/Naumoff/index.htm home page].<br />
<br />
[[Category:Biographies|Naumoff, Daniil]]</div>Daniil Naumoffhttps://www.cazypedia.org/index.php?title=CAZypedia:Community_Portal&diff=438CAZypedia:Community Portal2008-03-12T11:50:26Z<p>Daniil Naumoff: /* More pages needed... */</p>
<hr />
<div>'''''Please write your ideas/suggestions/etc. for the improvement of CAZypedia on this page. Community participation is essential for the continued development of this resource!'''''<br />
<br />
== More pages needed... ==<br />
We are looking for CAZyme researchers to author new pages - please contact the [[Editorial Board]] if you'd like to help.<br />
* Is it still actual? --[[User:Daniil Naumoff|Daniil Naumoff]] 12:50, 12 March 2008 (CET)</div>Daniil Naumoffhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_43&diff=437Glycoside Hydrolase Family 432008-03-12T11:40:23Z<p>Daniil Naumoff: /* References */</p>
<hr />
<div>* Author: ''NONE ASSIGNED''<br />
* Responsible Editor: ''NONE ASSIGNED''<br />
----<br />
<br />
<br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH43'''<br />
|-<br />
|'''Clan''' <br />
|GH-F<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|not known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH43.html<br />
|}<br />
</div><br />
<br />
== Substrate specificities ==<br />
<br />
== Kinetics and Mechanism ==<br />
<br />
<br />
<br />
== Catalytic Residues ==<br />
<br />
<br />
<br />
== Three-dimensional structures ==<br />
<br />
<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Cite some reference here, with a ''short'' explanation <cite>1</cite>.<br />
;First catalytic nucleophile identification: <br />
;First general acid/base residue identification: <br />
;First 3-D structure: <br />
<br />
== References ==<br />
<biblio><br />
#1 pmid=1268883<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families]]</div>Daniil Naumoffhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_1&diff=436Glycoside Hydrolase Family 12008-03-12T09:28:05Z<p>Daniil Naumoff: </p>
<hr />
<div>* Author: [[User:Withers|Stephen Withers]]<br />
* Responsible Editor: [[User:Withers|Stephen Withers]]<br />
----<br />
<br />
<br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH1'''<br />
|-<br />
|'''Clan''' <br />
|GH-A<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH1.html<br />
<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Wikipedia link'''<br />
|-<br />
| colspan="2" |http://en.wikipedia.org/wiki/Glycoside_hydrolase_family_1<br />
|}<br />
</div><br />
<br />
== Substrate specificities ==<br />
The most common known enzymatic activities in this family, at the current time, are those of β-glucosidases and β-galactosidases: indeed typically both activities are found within the same active site, often with similar ''k''<sub>cat</sub> values, but with substantially higher ''K''<sub>m</sub> values for the galactosides. However, other commonly found activities are 6-phospho-β-glucosidase and 6-phospho-β-galactosidase, β-mannosidase, β-D-fucosidase and β-glucuronidase. Family GH1 enzymes are found across a broad spectrum of life forms. Enzymes of medical interest include the human lactase/phlorizin hydrolase whose deficiency leads to lactose intolerance. In plants Family GH1 enzymes are often involved in the processing of glycosylated aromatics such as saponins and some plant hormones stored in inactive glycosylated forms. Indeed some have been identified as plant oncogenes due to aberrant control of auxin levels. Some plants also use Family GH1 enzymes as part of their defense system in order to release toxic aglycons, the most known examples being ''Trifolium repens'' β-glucosidase and ''Sinapis alba'' myrosinase, which respectively hydrolyse linamarin and glucosinolates. One of the work horses of glycosidase enzymology, the almond emulsin β-glucosidase, even though not fully sequenced, is deduced to belong to Family GH1 by limited sequence analysis <cite>1</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Family GH1 β-glycosidases are retaining enzymes, as first shown by NMR <cite>2</cite> and follow a classical Koshland double-displacement mechanism. Enzymes that have been well-studied kinetically include the almond emulsin enzyme, for which a particularly nice and important set of studies on rate-limiting steps and inhibition was reported in the mid 1980’s <cite>3 4</cite> and the ''Agrobacterium'' sp. β-glucosidase which has been the subject of a series of kinetic evaluations, including detailed steady state <cite>5 6</cite> and pre-steady state kinetic analyses in which the roles of each substrate hydroxyl in catalysis have also been carefully probed <cite>7</cite>.<br />
<br />
== Catalytic Residues ==<br />
The catalytic nucleophile was first identified in the ''Agrobacterium'' sp. β-glucosidase as Glu358 in the sequence YIT'''<u>E</u>'''NG through trapping of the 2-deoxy-2-fluoroglucosyl-enzyme intermediate and subsequent peptide mapping <cite>8</cite>. The acid/base catalyst was first identified as Glu170 in this same enzyme through detailed mechanistic analysis of mutants at that position, which included azide rescue experiments <cite>9</cite>. Family GH1 enzymes, as is typical of [http://www.cazy.org/fam/acc_GH.html#table Clan GH-A], have an asparagine residue preceding the acid/base catalyst in a typical NEP sequence. The asparagine engages in important hydrogen bonding interactions with the substrate 2-hydroxyl. Interestingly, the plant myrosinases cleave thioglycosides bearing an anionic aglycone (glucosinolates), and have evolved an active site in which the acid/base glutamate is replaced by glutamine. Substrates are sufficiently reactive not to require the acid catalyst, while the role of base catalyst is played by exogenous ascorbate, which binds to the glycosyl enzyme <cite>13</cite>.<br />
<br />
== Three-dimensional structures ==<br />
Three-dimensional structures are available for a large number of Family 1 enzymes, the first solved being that of the white clover (''Trifolium repens'') cyanogenic β-glucosidase <cite>12</cite>. As members of Clan GH-A they have a classical (&alpha;/&beta;)<sub>8</sub> TIM barrel fold with the two key active site glutamic acids being approximately 200 residues apart in sequence and located at the C-terminal ends of β-strands 4 (acid/base) and 7 (nucleophile) <cite>10</cite>.<br />
<br />
== "Family Firsts" ==<br />
;First sterochemistry determination: ''Agrobacterium'' sp. (formerly ''Alcaligenes faecalis'') β-glucosidase by NMR <cite>2</cite><br />
;First catalytic nuclepohile identification: ''Agrobacterium'' sp. (formerly ''Alcaligenes faecalis'') β-glucosidase by 2-fluoroglucose labeling <cite>8</cite><br />
;First general acid/base residue identification: ''Agrobacterium'' sp. (formerly ''Alcaligenes faecalis'') β-glucosidase by rescue kinetics with mutants (<cite>9</cite><br />
;First 3-D structure of a GH1 enzyme: White clover (''Trifolium repens'') cyanogenic β-glucosidase <cite>12</cite><br />
<br />
== References ==<br />
<biblio><br />
#1 pmid=9312086 <br />
#2 pmid=3094517<br />
#3 pmid=3929833<br />
#4 pmid=3087421<br />
#5 pmid=1390780<br />
#6 pmid=139078<br />
#7 pmid=8519777<br />
#8 Withers, S. G.; Warren, R. A. J.; Street, I. P.; Rupitz, K.; Kempton, J. B.; Aebersold, R. ''Journal of the American Chemical Society '1990''', ''112'', 5887-5889.<br />
#9 pmid=7578061<br />
#10 pmid=7624375<br />
#12 pmid=8535788<br />
#13 pmid=10978344<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families]]</div>Daniil Naumoffhttps://www.cazypedia.org/index.php?title=User:Bernard_Henrissat&diff=435User:Bernard Henrissat2008-03-12T09:17:46Z<p>Daniil Naumoff: </p>
<hr />
<div>[[Image:Resize of bernie.jpg|right]]<br />
<br />
This is the user page of Bernard Henrissat. I am a CNRS Director of Research at the Architecture et Fonction des Macromolecules Biologiques Laboratory in Marseille, France. I have developed the family classification of glycoside hydrolases and subsequently applied it to other categories of carbohydrate-active enzymes. Together with Pedro M. Coutinho we developed and continuously update the Carbohydrate-Active enZYme database (CAZy at http://www.cazy.org/).<br />
<br />
[[Category:Biographies|Henrissat, Bernard]]</div>Daniil Naumoffhttps://www.cazypedia.org/index.php?title=User:Steve_Withers&diff=434User:Steve Withers2008-03-12T09:14:09Z<p>Daniil Naumoff: </p>
<hr />
<div>[[Image:Resize of Resize of withers.jpg|right]]<br />
<br />
'''Steve Withers''' obtained his BSc in Chemistry from the University of Bristol, U.K. in 1974, then completed his PhD at Bristol with Mike Sinnott in 1977, working on the catalytic mechanism of ''E. coli'' (lac z) Beta-galactosidase (GH2). His postdoctoral fellowship was carried out at the University of Alberta, Edmonton, Canada, working with Neil Madsen and Brian Sykes doing 31P-NMR studies on the role of PLP in the mechanism of glycogen phosphorylase (GT35). In 1982 he moved as Assistant Professor to the Department of Chemistry, University of British Columbia and now holds the Khorana Chair in Chemistry and Biochemistry at UBC. During this time he has spent sabbatical leaves at the University of Oxford (Louise Johnson, 1991/2: Raymond Dwek, 1998/9) and AFMB, Marseille (Bernard Henrissat, 2006/7). His research interests concern mechanisms of glycosidases and glycosyl transferases, engineering of these enzymes, particularly for enzymatic glycoside synthesis (glycosynthases and thioglycoligases), and development of inhibitors as potential pharmaceuticals.<br />
<br />
[[Category:Biographies|Withers, Steve]]</div>Daniil Naumoff