Sequence-based classification - Revision history

Harry Brumer: Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

2021-12-18T21:20:28Z

Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

Harry Brumer: Fixed broken link to Sorting the Diverse - new DOI link added

2020-04-19T01:11:53Z

Fixed broken link to Sorting the Diverse - new DOI link added

Harry Brumer: /* Clans */

2019-06-06T16:27:49Z

Clans

Harry Brumer at 16:25, 6 June 2019

2019-06-06T16:25:56Z

Harry Brumer at 16:24, 6 June 2019

2019-06-06T16:24:20Z

Harry Brumer at 18:33, 3 August 2016

2016-08-03T18:33:47Z

Harry Brumer: /* References */

2016-08-03T18:17:01Z

References

Harry Brumer at 15:31, 7 July 2015

2015-07-07T15:31:40Z

Harry Brumer at 21:48, 18 December 2013

2013-12-18T21:48:38Z

Harry Brumer at 10:16, 18 December 2013

2013-12-18T10:16:02Z

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 {{CuratorApproved}}
-* Authors: ^^^Steve Withers^^^, ^^^Spencer Williams^^^
+* Authors: [[User:Steve Withers|Steve Withers]], [[User:Spencer Williams|Spencer Williams]]
-* Responsible Curator:  ^^^Spencer Williams^^^
+* Responsible Curator:  [[User:Spencer Williams|Spencer Williams]]
 ----
 Sequence classification methods require knowledge of at least part of the amino acid or nucleotide sequence for a protein. Algorithmic methods are then used to compare and classify sequences (''e.g.'' the original classification of [[Glycoside Hydrolase Families]] relied largely on hydrophobic cluster analysis and multiple sequence alignment <cite>Henrissat1989 Henrissat1991</cite>, while sequence alignment and Hidden Markov Model methods have become dominant with the evolution of the [[carbohydrate-active enzymes]] classification <cite>Cantarel2009 Lombard2013</cite>). Each of the resulting sequence-based families contain proteins that are related by sequence, and by corollary, three-dimensional fold. An obvious shortcoming of sequence-based classifications is that they can only be applied to proteins for which sequence information is available. On the other hand sequence-based classification schemes allow classification of proteins for which no biochemical evidence has been obtained such as the thousands of uncharacterized sequences of [[carbohydrate-active enzymes]] that originate from genome sequencing efforts worldwide. Sequence-based classification methods are rather different (and in many ways complementary) to the Enzyme Commission classification scheme, which assigns proteins to groups based on the nature of the reactions that they catalyze <cite>ECWikipedia</cite>.

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 #Cantarel2009 pmid=18838391
 #Lombard2013 pmid=24270786
-#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].
+#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [https://doi.org/10.1042/BIO03004026 Download PDF version].
 </biblio>
 [[Category:Definitions and explanations]]

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 === Clans ===
-Classification of GH families into larger groups, termed "clans", has been proposed <cite>Henrissat1996 DaviesSinnott2008</cite>. A clan is a group of families that possess significant similarity in their tertiary structure, catalytic residues and mechanism. Thus knowledge of three-dimensional structure and the functional assignment of catalytic residues is required for classification into clans. Families within clans are thought to have a common evolutionary ancestry. Please  see the CAZy Database for an updated table of [http://www.cazy.org/Glycoside-Hydrolases.html glycoside hydrolase clans].
+Classification of GH families into larger groups, termed "clans", has been proposed <cite>Henrissat1996 DaviesSinnott2008</cite>. A clan is a group of families that possess significant similarity in their tertiary structure, catalytic residues and mechanism. Thus knowledge of three-dimensional structure and the functional assignment of catalytic residues is required for classification into clans. Families within clans are thought to have a common evolutionary ancestry. Please  see the CAZy Database for a current table of [http://www.cazy.org/Glycoside-Hydrolases.html glycoside hydrolase clans].
 == Classification of glycosyltransferases ==

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 == Classification of glycoside hydrolases ==
 === Families ===
-Using a combination of comparison algorithms the [[glycoside hydrolases]] have been classified into more than 100 GH families <cite>Henrissat1991</cite>. This classification is permanently available through the Carbohydrate Active enZyme database <cite>CAZyURL</cite>. Classification of [[glycoside hydrolases]] into families allows many useful predictions to be made since it has long been noted that the catalytic machinery and molecular mechanism is conserved for the vast majority of the GH families <cite>Gebler1992</cite> as well as the geometry around the glycosidic bond (irrespective of naming conventions) <cite>Henrissat1995</cite>. Usually, the mechanism used (ie [[retaining]] or [[inverting]]) is conserved within a GH family. One notable exception is the [[glycoside hydrolases]] of family [[GH97]], which contains both [[retaining]] and [[inverting]] enzymes; a glutamate acts as a [[general base]] in inverting members, whereas an aspartate likely acts as a [[catalytic nucleophile]] in retaining members <cite>Gloster2008</cite>. Another mechanistic curiosity are the [[glycoside hydrolases]] of familes [[GH4]] and [[GH109]] which operate through an [[NAD-dependent hydrolysis]] mechanism that proceeds through oxidation-elimination-addition-reduction steps via anionic [[transition state]]s <cite>Yip2007</cite>. This allows a single enzyme to hydrolyze both alpha- and beta-glycosides.
+Using a combination of comparison algorithms the [[glycoside hydrolases]] have been classified into more than 100 GH families <cite>Henrissat1991</cite>. This classification is permanently available through the [http://www.cazy.org/ Carbohydrate Active enZyme database] <cite>Lombard2013</cite>. Classification of [[glycoside hydrolases]] into families allows many useful predictions to be made since it has long been noted that the catalytic machinery and molecular mechanism is conserved for the vast majority of the GH families <cite>Gebler1992</cite> as well as the geometry around the glycosidic bond (irrespective of naming conventions) <cite>Henrissat1995</cite>. Usually, the mechanism used (ie [[retaining]] or [[inverting]]) is conserved within a GH family. One notable exception is the [[glycoside hydrolases]] of family [[GH97]], which contains both [[retaining]] and [[inverting]] enzymes; a glutamate acts as a [[general base]] in inverting members, whereas an aspartate likely acts as a [[catalytic nucleophile]] in retaining members <cite>Gloster2008</cite>. Another mechanistic curiosity are the [[glycoside hydrolases]] of familes [[GH4]] and [[GH109]] which operate through an [[NAD-dependent hydrolysis]] mechanism that proceeds through oxidation-elimination-addition-reduction steps via anionic [[transition state]]s <cite>Yip2007</cite>. This allows a single enzyme to hydrolyze both alpha- and beta-glycosides.
 As a consequence of the evolution of the classification, several GH families have been deleted. Once deleted, family numbers are never reused in order to prevent confusion.
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 <biblio>
 #Henrissat1991 pmid=1747104
 #Gebler1992 pmid=1618761
 #Henrissat1995 pmid=7624375

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 === Clans ===
-Classification of GH families into larger groups, termed "clans", has been proposed <cite>Henrissat1996 DaviesSinnott2008</cite>. A clan is a group of families that possess significant similarity in their tertiary structure, catalytic residues and mechanism. Thus knowledge of three-dimensional structure and the functional assignment of catalytic residues is required for classification into clans. Families within clans are thought to have a common evolutionary ancestry. For an updated table of glycoside hydrolase clans see the CAZy Database <cite>CAZyGHURL</cite>.
+Classification of GH families into larger groups, termed "clans", has been proposed <cite>Henrissat1996 DaviesSinnott2008</cite>. A clan is a group of families that possess significant similarity in their tertiary structure, catalytic residues and mechanism. Thus knowledge of three-dimensional structure and the functional assignment of catalytic residues is required for classification into clans. Families within clans are thought to have a common evolutionary ancestry. Please  see the CAZy Database for an updated table of [http://www.cazy.org/Glycoside-Hydrolases.html glycoside hydrolase clans].
 == Classification of glycosyltransferases ==
@@ Line 30: / Line 30: @@
 #Henrissat1995 pmid=7624375
 #Henrissat1996 pmid=8687420
 #Campbell1997 pmid=9334165
 #Countinho2003 pmid=12691742

@@ Line 35: / Line 35: @@
 #Gloster2008 pmid=18848471
 #Yip2007 pmid=17676871
-#ECWikipedia http://en.wikipedia.org/wiki/EC_number
+#ECWikipedia http://en.wikipedia.org/wiki/Enzyme_Commission_number
 #Henrissat1989 pmid=2806912
 #Cantarel2009 pmid=18838391

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 * Responsible Curator:  ^^^Spencer Williams^^^
 ----
-Sequence classification methods require knowledge of at least part of the amino acid or nucleotide sequence for a protein. Algorithmic methods are then used to compare and classify sequences (''e.g.'' the original [[glycoside hydrolase]] classification relied largely on hydrophobic cluster analysis and multiple sequence alignment <cite>Henrissat1989 Henrissat1991</cite>, with sequence alignment and Hidden Markov Model methods becoming dominant with the evolution of the [[carbohydrate-active enzymes]] classification <cite>Cantarel2009 Lombard2013</cite>). Each of the resulting sequence-based families contain proteins that are related by sequence, and by corollary, three-dimensional fold. An obvious shortcoming of sequence-based classifications is that they can only be applied to proteins for which sequence information is available. On the other hand sequence-based classification schemes allow classification of proteins for which no biochemical evidence has been obtained such as the thousands of uncharacterized sequences of [[carbohydrate-active enzymes]] that originate from genome sequencing efforts worldwide. Sequence-based classification methods are rather different (and in many ways complementary) to the Enzyme Commission classification scheme, which assigns proteins to groups based on the nature of the reactions that they catalyze <cite>ECWikipedia</cite>.
+Sequence classification methods require knowledge of at least part of the amino acid or nucleotide sequence for a protein. Algorithmic methods are then used to compare and classify sequences (''e.g.'' the original [[glycoside hydrolase]] classification relied largely on hydrophobic cluster analysis and multiple sequence alignment <cite>Henrissat1989 Henrissat1991</cite>, while sequence alignment and Hidden Markov Model methods have become dominant with the evolution of the [[carbohydrate-active enzymes]] classification <cite>Cantarel2009 Lombard2013</cite>). Each of the resulting sequence-based families contain proteins that are related by sequence, and by corollary, three-dimensional fold. An obvious shortcoming of sequence-based classifications is that they can only be applied to proteins for which sequence information is available. On the other hand sequence-based classification schemes allow classification of proteins for which no biochemical evidence has been obtained such as the thousands of uncharacterized sequences of [[carbohydrate-active enzymes]] that originate from genome sequencing efforts worldwide. Sequence-based classification methods are rather different (and in many ways complementary) to the Enzyme Commission classification scheme, which assigns proteins to groups based on the nature of the reactions that they catalyze <cite>ECWikipedia</cite>.
 == Classification of glycoside hydrolases ==