Sequence-based classification of glycoside hydrolases - Revision history

Spencer Williams: Redirected page to Sequence-based classification

2010-08-10T11:22:18Z

Redirected page to Sequence-based classification

Spencer Williams at 11:21, 10 August 2010

2010-08-10T11:21:16Z

Spencer Williams: /* Classification of glycoside hydrolases into 'clans' */

2010-08-10T11:16:05Z

Classification of glycoside hydrolases into 'clans'

Spencer Williams at 11:15, 10 August 2010

2010-08-10T11:15:45Z

Spencer Williams at 11:14, 10 August 2010

2010-08-10T11:14:57Z

Spencer Williams at 11:07, 10 August 2010

2010-08-10T11:07:37Z

Spencer Williams at 23:21, 9 August 2010

2010-08-09T23:21:37Z

Spencer Williams at 23:17, 9 August 2010

2010-08-09T23:17:30Z

Spencer Williams at 23:16, 9 August 2010

2010-08-09T23:16:43Z

Spencer Williams at 23:16, 9 August 2010

2010-08-09T23:16:08Z

← Older revision		Revision as of 11:22, 10 August 2010
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−	~~{{CuratorApproved}}~~
−	* Authors: ^^^Steve Withers^^^, ^^^Spencer Williams^^^
−	* Responsible Curator: ^^^Spencer Williams^^^
−	~~----~~
−	~~=== Sequence-based classification ===~~

−	Sequence classification methods require knowledge of at least part of the amino acid sequence for an protein. Algorithmic methods are then used to compare sequences. Each of the resulting families contain proteins that are related by sequence, and by corollary, 3D 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 complimentary) to the Enzyme Commission classification scheme, which assigns proteins to groups based on the nature of the reactions that they catalyze.

−	~~=== Classification of glycoside hydrolases ===~~	+	#Redirect [[Sequence-based classification]]
−
−	Using a combination of comparison algorithms the glycoside hydrolases have been classified into more than 100 GH families <cite>1</cite>. This classification is permanently available through the Carbohydrate Active enZyme database <cite>2</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>3</cite> as well as the geometry around the glycosidic bond (irrespective of naming conventions) <cite>4</cite>.
−
−	~~=== Classification of glycoside hydrolases into 'clans' ===~~
−
−	Classification of GH families into larger groups, termed 'clans', has been proposed <cite>5</cite>. A `clan' is a group of families that possess significant similarity in their tertiary structure, catalytic residues and mechanism. Thus knowledge of 3D 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>6</cite>.
−
−	~~=== Classification of glycosyltransferases ===~~
−	Using sequence comparison algorithms glycosyltransferases that use nucleotide diphospho-sugar, nucleotide monophospho-sugars and sugar phosphates have been group into over 90 GT families <cite>7 8</cite>. This classification is permanently available through the Carbohydrate Active enZyme database<cite>2</cite>. As for the GH families above, the same three-dimensional fold is expected to occur within each of the GT families. Just as for the glycoside hydrolases, several of the families defined on the basis of sequence similarities turn out to have similar three-~~dimensional structures.~~
−
−	~~== References ==~~
−	~~<biblio>~~
−
−	~~#1 pmid=1747104~~
−	~~#2 Carbohydrate Active Enzymes database; URL http://www.cazy.org/~~
−	~~#3 pmid=1618761~~
−	~~#4 pmid=7624375~~
−	~~#5 pmid=8687420~~
−	~~#6 Carbohydrate Active Enzymes database, glycoside hydrolase~~ classification~~; URL http://www.cazy.org/Glycoside-Hydrolases.html~~
−
−	~~#7 pmid=9334165~~
−
−	~~#8 pmid=12691742~~
−	~~</biblio>~~

← Older revision		Revision as of 11:21, 10 August 2010
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	#8 pmid=12691742		#8 pmid=12691742
	</biblio>		</biblio>
−	~~[[Category:Definitions and explanations]]~~
−	~~[[Category:Curator approved]]~~

@@ Line 13: / Line 13: @@
 === Classification of glycoside hydrolases into 'clans' ===
-Classification of families into larger groups, termed 'clans', has been proposed <cite>5</cite>. A `clan' is a group of families that possess significant similarity in their tertiary structure, catalytic residues and mechanism. Thus knowledge of 3D 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>6</cite>.
+Classification of GH families into larger groups, termed 'clans', has been proposed <cite>5</cite>. A `clan' is a group of families that possess significant similarity in their tertiary structure, catalytic residues and mechanism. Thus knowledge of 3D 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>6</cite>.
 === Classification of glycosyltransferases ===

@@ Line 5: / Line 5: @@
 === Sequence-based classification ===
-Sequence classification methods require knowledge of at least part of the amino acid sequence for an protein. Algorithmic methods are then used to compare sequences. Each of the resulting families contain proteins that are related by sequence, and by corollary, 3D 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 [[carbohydrate-active enzyme]] sequences that originate from genome sequencing efforts worldwide. Sequence based classification methods are rather different (and in many ways complimentary) to the Enzyme Commission classification scheme, which assigns proteins to groups based on the nature of the reactions that they catalyze.
+Sequence classification methods require knowledge of at least part of the amino acid sequence for an protein. Algorithmic methods are then used to compare sequences. Each of the resulting families contain proteins that are related by sequence, and by corollary, 3D 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 complimentary) to the Enzyme Commission classification scheme, which assigns proteins to groups based on the nature of the reactions that they catalyze.
 === Classification of glycoside hydrolases ===

@@ Line 5: / Line 5: @@
 === Sequence-based classification ===
-Sequence classification methods require knowledge of at least part of the amino acid sequence for an enzyme. Algorithmic methods are then used to compare sequences. Each of the resulting families contain proteins that are related by sequence, and by corollary, 3D 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 glycosidase-related sequences that originate from genome sequencing efforts worldwide. Sequence based classification methods are rather different (and in many ways complimentary) to the Enzyme Commission classification scheme, which assigns proteins to groups based on the nature of the reactions that they catalyze.
+Sequence classification methods require knowledge of at least part of the amino acid sequence for an protein. Algorithmic methods are then used to compare sequences. Each of the resulting families contain proteins that are related by sequence, and by corollary, 3D 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 [[carbohydrate-active enzyme]] sequences that originate from genome sequencing efforts worldwide. Sequence based classification methods are rather different (and in many ways complimentary) to the Enzyme Commission classification scheme, which assigns proteins to groups based on the nature of the reactions that they catalyze.
 === Classification of glycoside hydrolases ===
@@ Line 16: / Line 16: @@
 === Classification of glycosyltransferases ===
 == References ==
@@ Line 26: / Line 27: @@
 #5 pmid=8687420
 #6 Carbohydrate Active Enzymes database, glycoside hydrolase classification; URL http://www.cazy.org/Glycoside-Hydrolases.html
 </biblio>
 [[Category:Definitions and explanations]]
 [[Category:Curator approved]]

@@ Line 5: / Line 5: @@
 === Sequence-based classification ===
-Sequence classification methods require knowledge of at least part of the amino acid sequence for an enzyme. Algorithmic methods are then used to compare sequences. Using a combination of comparison algorithms the glycoside hydrolases have been classified into more than 100 families <cite>1</cite>. This classification is permanently available through the Carbohydrate Active enZyme database <cite>2</cite>. Each family (GH family) contains proteins that are related by sequence, and by corollary, fold. An obvious shortcoming of sequence-based classifications is that they can only be applied to enzymes 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 glycosidase-related sequences that originate from genome sequencing efforts worldwide. This allows a number of 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 glycosidase families <cite>3</cite> as well as the geometry around the glycosidic bond (irrespective of naming conventions) <cite>4</cite>. As such sequence based classification methods are rather different (and in many ways complimentary) to the EC method discussed above.
+Sequence classification methods require knowledge of at least part of the amino acid sequence for an enzyme. Algorithmic methods are then used to compare sequences. Using a combination of comparison algorithms the glycoside hydrolases have been classified into more than 100 families <cite>1</cite>. This classification is permanently available through the Carbohydrate Active enZyme database <cite>2</cite>. Each family (GH family) contains proteins that are related by sequence, and by corollary, fold. An obvious shortcoming of sequence-based classifications is that they can only be applied to enzymes 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 glycosidase-related sequences that originate from genome sequencing efforts worldwide. This allows a number of 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 glycosidase families <cite>3</cite> as well as the geometry around the glycosidic bond (irrespective of naming conventions) <cite>4</cite>. As such sequence based classification methods are rather different (and in many ways complimentary) to the Enzyme Commission classification scheme, which assigns proteins to groups based on the nature of the reactions that they catalyze.
 === Classification into 'clans' ===

@@ Line 9: / Line 9: @@
 === Classification into 'clans' ===
-Classification of families into larger groups, termed 'clans', has been proposed <cite>18</cite>. A `clan' is a group of families that possess significant similarity in their tertiary structure, catalytic residues and mechanism. Thus knowledge of 3D 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>5</cite>.
+Classification of families into larger groups, termed 'clans', has been proposed <cite>5</cite>. A `clan' is a group of families that possess significant similarity in their tertiary structure, catalytic residues and mechanism. Thus knowledge of 3D 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>6</cite>.
 == References ==
@@ Line 20: / Line 20: @@
 #3 pmid=1618761
 #4 pmid=7624375
 #5 Carbohydrate Active Enzymes database, glycoside hydrolase classification; URL http://www.cazy.org/Glycoside-Hydrolases.html
 [[Category:Definitions and explanations]]
 [[Category:Curator approved]]

@@ Line 1: / Line 1: @@
-#redirect [[Glycoside hydrolases#Sequence-based classification]]
+{{CuratorApproved}}
 [[Category:Definitions and explanations]]
 [[Category:Curator approved]]