Glycoside Hydrolase Family 104 - Revision history

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

2021-12-18T21:16:41Z

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

Harry Brumer at 19:48, 26 August 2013

2013-08-26T19:48:09Z

Harry Brumer: increased figure size

2013-08-26T19:47:38Z

increased figure size

Harry Brumer: updated CAZyDBlink

2012-09-10T16:46:37Z

updated CAZyDBlink

Harry Brumer: updated CAZyDBlink

2012-09-10T16:46:08Z

updated CAZyDBlink

Spencer Williams at 03:18, 14 June 2011

2011-06-14T03:18:25Z

Harry Brumer at 17:52, 22 February 2010

2010-02-22T17:52:07Z

Harry Brumer at 17:51, 22 February 2010

2010-02-22T17:51:04Z

Anthony Clarke at 18:19, 21 February 2010

2010-02-21T18:19:56Z

Anthony Clarke at 18:18, 21 February 2010

2010-02-21T18:18:49Z

@@ Line 1: / Line 1: @@
 <!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
-* [[Author]]: ^^^Anthony Clarke^^^
+* [[Author]]: [[User:Anthony Clarke|Anthony Clarke]]
-* [[Responsible Curator]]:  ^^^Anthony Clarke^^^
+* [[Responsible Curator]]:  [[User:Anthony Clarke|Anthony Clarke]]
 ----

@@ Line 12: / Line 12: @@
 |-
 |'''Clan'''
-|none
+|none, α+β “lysozyme fold
 |-
 |'''Mechanism'''

@@ Line 29: / Line 29: @@
 == Substrate specificities ==
-[[Image:LTreaction.jpg|thumb|right|'''Figure 1.''' Reaction catalyzed by family GH104 enzymes. LT, lytic transglycosylase.  (''click to enlarge'').]]The [[glycoside hydrolases]] of this family are lytic transglyosylases (also referred to as peptidoglycan lyases) of bacteriophage origin and they constitute family 4 of the classification scheme of Blackburn and Clarke <cite>1</cite>.  Unfortunately, the origin of many of the hypothetical enzymes listed in GH104 is misleading because they are encoded within prophages which have been integrated into the chromosome of their bacterial host.   In other cases, the phage enzyme has been acquired by  pathogenicity islands on the bacterial chromosome.  The prototype for this family is the enzyme from ''lambda'' phage.
+[[Image:LTreaction.jpg|thumb|400px|right|'''Figure 1.''' Reaction catalyzed by family GH104 enzymes. LT, lytic transglycosylase.]]The [[glycoside hydrolases]] of this family are lytic transglyosylases (also referred to as peptidoglycan lyases) of bacteriophage origin and they constitute family 4 of the classification scheme of Blackburn and Clarke <cite>1</cite>.  Unfortunately, the origin of many of the hypothetical enzymes listed in GH104 is misleading because they are encoded within prophages which have been integrated into the chromosome of their bacterial host.   In other cases, the phage enzyme has been acquired by  pathogenicity islands on the bacterial chromosome.  The prototype for this family is the enzyme from ''lambda'' phage.
 These enzymes cleave the β-1,4 linkage between ''N''-acetylmuramoyl and ''N''-acetylglucosaminyl residues in peptidoglycan (Figure 1).  No other activities have been observed.

@@ Line 23: / Line 23: @@
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 |-
-| colspan="2" |{{CAZyDBlink}}GH105.html
+| colspan="2" |{{CAZyDBlink}}GH104.html
 |}
 </div>

@@ Line 23: / Line 23: @@
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 |-
-| colspan="2" |http://www.cazy.org/fam/GH104.html
+| colspan="2" |{{CAZyDBlink}}GH105.html
 |}
 </div>

@@ Line 29: / Line 29: @@
 == Substrate specificities ==
-[[Image:LTreaction.jpg|thumb|right|'''Figure 1.''' Reaction catalyzed by family GH104 enzymes. LT, lytic transglycosylase.  (''click to enlarge'').]]The glycoside hydrolases of this family are lytic transglyosylases (also referred to as peptidoglycan lyases) of bacteriophage origin and they constitute family 4 of the classification scheme of Blackburn and Clarke <cite>1</cite>.  Unfortunately, the origin of many of the hypothetical enzymes listed in GH104 is misleading because they are encoded within prophages which have been integrated into the chromosome of their bacterial host.   In other cases, the phage enzyme has been acquired by  pathogenicity islands on the bacterial chromosome.  The prototype for this family is the enzyme from ''lambda'' phage.
+[[Image:LTreaction.jpg|thumb|right|'''Figure 1.''' Reaction catalyzed by family GH104 enzymes. LT, lytic transglycosylase.  (''click to enlarge'').]]The [[glycoside hydrolases]] of this family are lytic transglyosylases (also referred to as peptidoglycan lyases) of bacteriophage origin and they constitute family 4 of the classification scheme of Blackburn and Clarke <cite>1</cite>.  Unfortunately, the origin of many of the hypothetical enzymes listed in GH104 is misleading because they are encoded within prophages which have been integrated into the chromosome of their bacterial host.   In other cases, the phage enzyme has been acquired by  pathogenicity islands on the bacterial chromosome.  The prototype for this family is the enzyme from ''lambda'' phage.
 These enzymes cleave the β-1,4 linkage between ''N''-acetylmuramoyl and ''N''-acetylglucosaminyl residues in peptidoglycan (Figure 1).  No other activities have been observed.
 == Kinetics and Mechanism ==
-The lytic transglycosidases, strictly speaking, are retaining enzymes.  However, they are not hydrolases but rather catalyse an intramolecular glycosyl transferase reaction onto the C-6 hydroxyl group of the muramoyl residue leading to the generation of a terminal 1,6-anhdyromuramoyl product (Figure 1) thus lacking a reducing end <cite>2</cite>.   No detailed analyses involving either steady state or pre-steady state kinetic studies have been reported.
+The lytic transglycosidases, strictly speaking, are retaining enzymes.  However, they are not hydrolases but rather catalyse an intramolecular glycosyl transferase reaction onto the C-6 hydroxyl group of the muramoyl residue leading to the generation of a terminal 1,6-anhydromuramoyl product (Figure 1) thus lacking a reducing end <cite>2</cite>.   No detailed analyses involving either steady state or pre-steady state kinetic studies have been reported.
 == Catalytic Residues ==
-As with other lytic transglycosylases (families [[GH23]], [[GH102]], and [[GH103]]), the GH104 enzymes are thought to possess a single catalytic acid/base residue.   This residue in lambda bacteriophage lytic transglycosylase has been inferred as Glu19 by X-ray crystallography of the enzyme alone <cite>3</cite> and in complex with two chitohexaose oligomers <cite>4</cite>.  The role of an essential carboxyl group in the enzyme was confirmed by chemical modification <cite>4</cite>, thus supporting the identification of Glu19.  The mechanism of action of the family GH104 enzymes has not been investigated and hence it is not known if they follow that of the lytic transglycosylases of families [[GH23]], [[GH102]], or [[GH103]].
+As with other lytic transglycosylases (families [[GH23]], [[GH102]], and [[GH103]]), the GH104 enzymes are thought to possess a single catalytic [[general acid/base]] residue.   This residue in lambda bacteriophage lytic transglycosylase has been inferred as Glu19 by X-ray crystallography of the enzyme alone <cite>3</cite> and in complex with two chitohexaose oligomers <cite>4</cite>.  The role of an essential carboxyl group in the enzyme was confirmed by chemical modification <cite>4</cite>, thus supporting the identification of Glu19.  The mechanism of action of the family GH104 enzymes has not been investigated and hence it is not known if they follow that of the lytic transglycosylases of families [[GH23]], [[GH102]], or [[GH103]].
 == Three-dimensional structures ==
@@ Line 45: / Line 45: @@
 ;First identification of lytic transglycosylase: Bacteriophage lambda <cite>3</cite>.
 ;First catalytic nucleophile identification: Not applicable for lytic transglycosylases.
-;First general acid/base residue identification: Inferred by X-ray crystallography of lambda bacteriophage <cite>3</cite>.
+;First [[general acid/base]] residue identification: Inferred by X-ray crystallography of lambda bacteriophage <cite>3</cite>.
 ;First 3-D structure: Lambda bacteriophage <cite>3</cite>.

@@ Line 32: / Line 32: @@
 These enzymes cleave the β-1,4 linkage between ''N''-acetylmuramoyl and ''N''-acetylglucosaminyl residues in peptidoglycan (Figure 1).  No other activities have been observed.
 == Kinetics and Mechanism ==
 The lytic transglycosidases, strictly speaking, are retaining enzymes.  However, they are not hydrolases but rather catalyse an intramolecular glycosyl transferase reaction onto the C-6 hydroxyl group of the muramoyl residue leading to the generation of a terminal 1,6-anhdyromuramoyl product (Figure 1) thus lacking a reducing end <cite>2</cite>.   No detailed analyses involving either steady state or pre-steady state kinetic studies have been reported.
 == Catalytic Residues ==
 As with other lytic transglycosylases (families [[GH23]], [[GH102]], and [[GH103]]), the GH104 enzymes are thought to possess a single catalytic acid/base residue.   This residue in lambda bacteriophage lytic transglycosylase has been inferred as Glu19 by X-ray crystallography of the enzyme alone <cite>3</cite> and in complex with two chitohexaose oligomers <cite>4</cite>.  The role of an essential carboxyl group in the enzyme was confirmed by chemical modification <cite>4</cite>, thus supporting the identification of Glu19.  The mechanism of action of the family GH104 enzymes has not been investigated and hence it is not known if they follow that of the lytic transglycosylases of families [[GH23]], [[GH102]], or [[GH103]].
 == Three-dimensional structures ==
 The three-dimensional structure of only the lambda phage enzyme has been solved  <cite>3 4</cite>, and like the other lytic transglycosylases of families [[GH23]], and [[GH103]], it possesses the well characterized α+β “lysozyme fold.”
 == Family Firsts ==
@@ Line 51: / Line 47: @@
 ;First general acid/base residue identification: Inferred by X-ray crystallography of lambda bacteriophage <cite>3</cite>.
 ;First 3-D structure: Lambda bacteriophage <cite>3</cite>.
 == References ==
@@ Line 59: / Line 54: @@
 #3 pmid=9514719
 #4 pmid=11341831
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH104]]

@@ Line 9: / Line 9: @@
 {| {{Prettytable}}
 |-
-|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GHnn'''
+|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH104'''
 |-
 |'''Clan'''
@@ Line 23: / Line 23: @@
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 |-
-| colspan="2" |http://www.cazy.org/fam/GHnn.html
+| colspan="2" |http://www.cazy.org/fam/GH104.html
 |}
 </div>