Glycoside Hydrolase Family 2 - Revision history

Kazune Tamura: /* Three-dimensional structures */

2019-02-23T23:35:52Z

Three-dimensional structures

Harry Brumer: /* References */

2016-08-11T22:54:49Z

References

Harry Brumer: /* References */

2016-08-11T22:54:15Z

References

Harry Brumer: /* References */

2016-08-11T22:51:59Z

References

Harry Brumer: /* References */

2016-08-11T22:51:25Z

References

Harry Brumer: /* References */

2016-08-11T22:50:55Z

References

Harry Brumer at 22:49, 11 August 2016

2016-08-11T22:49:59Z

Harry Brumer at 22:44, 11 August 2016

2016-08-11T22:44:59Z

Harry Brumer: Added one primary ebg evolution ref.

2013-12-29T20:39:48Z

Added one primary ebg evolution ref.

Harry Brumer: Updated reference tags to AuthorYear format for future page maintenance

2013-12-29T20:31:43Z

Updated reference tags to AuthorYear format for future page maintenance

@@ Line 35: / Line 35: @@
 == Three-dimensional structures ==
-Three-dimensional structures are available for five Family GH2 enzymes currently, the first solved being that of the ''E. coli'' (lacZ) β-galactosidase in a ''tour de force'' of X-ray crystallography at that time, given its huge size (4  x  125,000 Da) <cite>Jacobson1994</cite>. The enzyme is multidomain, but as members of Clan GHA the catalytic domains a classical (α/β)<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).
+Three-dimensional structures are available for five Family GH2 enzymes currently, the first solved being that of the ''E. coli'' (lacZ) β-galactosidase in a ''tour de force'' of X-ray crystallography at that time, given its huge size (4  x  125,000 Da) <cite>Jacobson1994</cite>. The enzyme is multidomain, but as members of Clan GHA the catalytic domain is a classical (α/β)<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).
 == Family Firsts ==

@@ Line 48: / Line 48: @@
 #Hall1999 pmid=10234816
 #Sly1973 pmid=4265197
-#Wallenfels1951 Wallenfels K. ''Enzymatische Synthese von Oligosacchariden aus Disacchariden.'' Naturwissenschaften, 1951; 38: 306-307. [http://dx.doi.org/10.1007/BF00636782 DOI:10.1007/BF00636782]
+#Wallenfels1951 Wallenfels K. ''Enzymatische synthese von oligosacchariden aus disacchariden.'' Naturwissenschaften, 1951; 38: 306-307. [http://dx.doi.org/10.1007/BF00636782 DOI:10.1007/BF00636782]
 #SinnottSouchard1973 pmid=4578762
 #SinnottViratelle1973 pmid=4721624

@@ Line 48: / Line 48: @@
 #Hall1999 pmid=10234816
 #Sly1973 pmid=4265197
-#Wallenfels1951 Wallenfels K. Enzymatische Synthese von Oligosacchariden aus Disacchariden, Naturwissenschaften, 1951; 38: 306-307. [http://dx.doi.org/10.1007/BF00636782 DOI:10.1007/BF00636782]
+#Wallenfels1951 Wallenfels K. ''Enzymatische Synthese von Oligosacchariden aus Disacchariden.'' Naturwissenschaften, 1951; 38: 306-307. [http://dx.doi.org/10.1007/BF00636782 DOI:10.1007/BF00636782]
 #SinnottSouchard1973 pmid=4578762
 #SinnottViratelle1973 pmid=4721624

@@ Line 48: / Line 48: @@
 #Hall1999 pmid=10234816
 #Sly1973 pmid=4265197
-#Wallenfels1951 Wallenfels K. Enzymatische Synthese von Oligosacchariden aus Disacchariden, Naturwissenschaften, 1951; 38: 306-307. [http://dx.doi.org/10.1007/BF00636782 doi:10.1007/BF00636782]
+#Wallenfels1951 Wallenfels K. Enzymatische Synthese von Oligosacchariden aus Disacchariden, Naturwissenschaften, 1951; 38: 306-307. [http://dx.doi.org/10.1007/BF00636782 DOI:10.1007/BF00636782]
 #SinnottSouchard1973 pmid=4578762
 #SinnottViratelle1973 pmid=4721624

@@ Line 48: / Line 48: @@
 #Hall1999 pmid=10234816
 #Sly1973 pmid=4265197
-#Wallenfels1951 Wallenfels K. Enzymatische Synthese von Oligosacchariden aus Disacchariden, Naturwissenschaften, 1951, 38, 306-307. [http://dx.doi.org/10.1007/BF00636782 doi:10.1007/BF00636782]
+#Wallenfels1951 Wallenfels K. Enzymatische Synthese von Oligosacchariden aus Disacchariden, Naturwissenschaften, 1951; 38: 306-307. [http://dx.doi.org/10.1007/BF00636782 doi:10.1007/BF00636782]
 #SinnottSouchard1973 pmid=4578762
 #SinnottViratelle1973 pmid=4721624

@@ Line 29: / Line 29: @@
 == Kinetics and Mechanism ==
-Family 2 β-glycosidases are [[retaining]] enzymes and follow a classical [[Koshland double-displacement mechanism]].  This was first evidenced in 1951 by  Wallenfels, who demonstrated the transglycosylastion of lactose via an implicated glycosyl-enzyme intermediate <cite>Wallenfels1951</cite>  The best studied enzyme kinetically must be the ''E. coli'' (lacZ) β-galactosidase, for which a key set of studies defining the two-step mechanism and elucidating rate-limiting steps was published by the groups of Yon and Sinnott in the early 1970’s <cite>SinnottSouchard1973 SinnottViratelle1973 ViratelleYon1973</cite>. Indeed the approaches developed on that system laid the foundations for many subsequent studies on other glycosidases.  An analysis of the roles of each substrate hydroxyl in catalysis, based upon kinetic studies with modified sugars has also been published <cite>McCarter1992</cite>. Some GH2 glycosidases require Mg<sup>2+</sup> for activity and in ''E. coli'' β-galactosidase this Mg<sup>2+</sup> requirement is associated with the binding of the cation in the active site such that it places the acid/base residue appropriately.  Others, such as the human β-glucuronidase, have no such metal ion requirement.
+Family 2 β-glycosidases are [[retaining]] enzymes and follow a classical [[Koshland double-displacement mechanism]].  This was first evidenced in 1951 by  Wallenfels, who demonstrated the transglycosylation of lactose via an implicated glycosyl-enzyme intermediate <cite>Wallenfels1951</cite>  The best studied enzyme kinetically must be the ''E. coli'' (lacZ) β-galactosidase, for which a key set of studies defining the two-step mechanism and elucidating rate-limiting steps was published by the groups of Yon and Sinnott in the early 1970’s <cite>SinnottSouchard1973 SinnottViratelle1973 ViratelleYon1973</cite>. Indeed the approaches developed on that system laid the foundations for many subsequent studies on other glycosidases.  An analysis of the roles of each substrate hydroxyl in catalysis, based upon kinetic studies with modified sugars has also been published <cite>McCarter1992</cite>. Some GH2 glycosidases require Mg<sup>2+</sup> for activity and in ''E. coli'' β-galactosidase this Mg<sup>2+</sup> requirement is associated with the binding of the cation in the active site such that it places the acid/base residue appropriately.  Others, such as the human β-glucuronidase, have no such metal ion requirement.
 == Catalytic Residues ==
@@ Line 38: / Line 38: @@
 == Family Firsts ==
-;First stereochemistry determination:  <cite>Wallenfels1951</cite>
+;First stereochemistry determination:  Via transglycosylation of lactose <cite>Wallenfels1951</cite>
 ;First [[catalytic nucleophile]] identification: ''E. coli'' (lacZ) β-galactosidase by 2-fluorogalactose labeling <cite>Gebler1992</cite>
 ;First [[general acid/base]] residue identification: ''E. coli'' (lacZ) β-galactosidase by re-interpretation of kinetic studies with mutants <cite>Gebler1992 Cupples1990</cite>

@@ Line 26: / Line 26: @@
 == Substrate specificities ==
-The most common activities for [[glycoside hydrolases]] of this family include β-galactosidases, β-glucuronidases, β-mannosidases, [[exo]]-β-glucosaminidases and, in plants, a mannosylglycoprotein [[endo]]-β-mannosidase. The enzymes are found across a broad spectrum of life forms, but are concentrated in bacteria. The most famous enzyme in this family is the ''E. coli'' (lacZ) β-galactosidase, a component of the lac operon. Not only did this enzyme play a key role in developing the understanding of operon structure and control of gene expression, but also it continues to play a key role as a cell biological probe. Another matter of note is that this remains the largest protein monomer to be sequenced entirely at the peptide level <cite>FowlerZabin1978</cite>.  ''E. coli'' also contains a second, vestigial β-galactosidase (ebg) whose activity has been shown to evolve in lacZ<sup>-</sup> strains of ''E. coli''  grown under selective pressure with lactose as sole carbon source <cite>Hall1999</cite>. Another reasonably well-studied GH2 enzyme is the ''E. coli'' β-glucuronidase, whose activity is used to detect the presence of ''E. coli'' (http://www.cfsan.fda.gov/~ebam/bam-4.html), though interestingly not the nasty O157 strain. The principal enzyme of medical interest in GH2 is the lysosomal β-glucuronidase whose deficiency leads to Sly syndrome <cite>Sly1973</cite>. The only other human GH2 enzyme is the lysosomal β-mannosidase.
+The most common activities for [[glycoside hydrolases]] of this family include β-galactosidases, β-glucuronidases, β-mannosidases, [[exo]]-β-glucosaminidases and, in plants, a mannosylglycoprotein [[endo]]-β-mannosidase. The enzymes are found across a broad spectrum of life forms, but are concentrated in bacteria. The most famous enzyme in this family is the ''E. coli'' (lacZ) β-galactosidase, a component of the lac operon. Not only did this enzyme play a key role in developing the understanding of operon structure and control of gene expression, but also it continues to play a key role as a cell biological probe. Another matter of note is that this remains the largest protein monomer to be sequenced entirely at the peptide level <cite>FowlerZabin1978</cite>.  ''E. coli'' also contains a second, vestigial β-galactosidase (ebg) whose activity has been shown to evolve in lacZ<sup>-</sup> strains of ''E. coli''  grown under selective pressure with lactose as sole carbon source <cite>Hall1999 Krishnan1995</cite>. Another reasonably well-studied GH2 enzyme is the ''E. coli'' β-glucuronidase, whose activity is used to detect the presence of ''E. coli'' (http://www.cfsan.fda.gov/~ebam/bam-4.html), though interestingly not the nasty O157 strain. The principal enzyme of medical interest in GH2 is the lysosomal β-glucuronidase whose deficiency leads to Sly syndrome <cite>Sly1973</cite>. The only other human GH2 enzyme is the lysosomal β-mannosidase.
 == Kinetics and Mechanism ==
@@ Line 57: / Line 57: @@
 #Cupples1990 pmid=1969405
 #Jacobson1994 pmid=8008071
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH002]]

@@ Line 26: / Line 26: @@
 == Substrate specificities ==
-The most common activities for [[glycoside hydrolases]] of this family include β-galactosidases, β-glucuronidases, β-mannosidases, [[exo]]-β-glucosaminidases and, in plants, a mannosylglycoprotein [[endo]]-β-mannosidase. The enzymes are found across a broad spectrum of life forms, but are concentrated in bacteria. The most famous enzyme in this family is the ''E. coli'' (lacZ) β-galactosidase, a component of the lac operon. Not only did this enzyme play a key role in developing the understanding of operon structure and control of gene expression, but also it continues to play a key role as a cell biological probe. Another matter of note is that this remains the largest protein monomer to be sequenced entirely at the peptide level <cite>1</cite>.  ''E. coli'' also contains a second, vestigial β-galactosidase (ebg) whose activity has been shown to evolve in lacZ<sup>-</sup> strains of ''E. coli''  grown under selective pressure with lactose as sole carbon source <cite>2</cite>. Another reasonably well-studied GH2 enzyme is the ''E. coli'' β-glucuronidase, whose activity is used to detect the presence of ''E. coli'' (http://www.cfsan.fda.gov/~ebam/bam-4.html), though interestingly not the nasty O157 strain. The principal enzyme of medical interest in GH2 is the lysosomal β-glucuronidase whose deficiency leads to Sly syndrome <cite>3</cite>. The only other human GH2 enzyme is the lysosomal β-mannosidase.
+The most common activities for [[glycoside hydrolases]] of this family include β-galactosidases, β-glucuronidases, β-mannosidases, [[exo]]-β-glucosaminidases and, in plants, a mannosylglycoprotein [[endo]]-β-mannosidase. The enzymes are found across a broad spectrum of life forms, but are concentrated in bacteria. The most famous enzyme in this family is the ''E. coli'' (lacZ) β-galactosidase, a component of the lac operon. Not only did this enzyme play a key role in developing the understanding of operon structure and control of gene expression, but also it continues to play a key role as a cell biological probe. Another matter of note is that this remains the largest protein monomer to be sequenced entirely at the peptide level <cite>FowlerZabin1978</cite>.  ''E. coli'' also contains a second, vestigial β-galactosidase (ebg) whose activity has been shown to evolve in lacZ<sup>-</sup> strains of ''E. coli''  grown under selective pressure with lactose as sole carbon source <cite>Hall1999</cite>. Another reasonably well-studied GH2 enzyme is the ''E. coli'' β-glucuronidase, whose activity is used to detect the presence of ''E. coli'' (http://www.cfsan.fda.gov/~ebam/bam-4.html), though interestingly not the nasty O157 strain. The principal enzyme of medical interest in GH2 is the lysosomal β-glucuronidase whose deficiency leads to Sly syndrome <cite>Sly1973</cite>. The only other human GH2 enzyme is the lysosomal β-mannosidase.
 == Kinetics and Mechanism ==
-Family 2 β-glycosidases are [[retaining]] enzymes, as first shown by XXXXX <cite>4</cite> and follow a classical [[Koshland double-displacement mechanism]]. The best studied enzyme kinetically must be the ''E. coli'' (lacZ) β-galactosidase, for which a key set of studies defining the two-step mechanism and elucidating rate-limiting steps was published by the groups of Yon and Sinnott in the early 1970’s <cite>5 6 7</cite>. Indeed the approaches developed on that system laid the foundations for many subsequent studies on other glycosidases.  An analysis of the roles of each substrate hydroxyl in catalysis, based upon kinetic studies with modified sugars has also been published <cite>8</cite>. Some GH2 glycosidases require Mg<sup>2+</sup> for activity and in ''E. coli'' β-galactosidase this Mg<sup>2+</sup> requirement is associated with the binding of the cation in the active site such that it places the acid/base residue appropriately.  Others, such as the human β-glucuronidase, have no such metal ion requirement.
+Family 2 β-glycosidases are [[retaining]] enzymes, as first shown by XXXXX <cite>TBA</cite> and follow a classical [[Koshland double-displacement mechanism]]. The best studied enzyme kinetically must be the ''E. coli'' (lacZ) β-galactosidase, for which a key set of studies defining the two-step mechanism and elucidating rate-limiting steps was published by the groups of Yon and Sinnott in the early 1970’s <cite>SinnottSouchard1973 SinnottViratelle1973 ViratelleYon1973</cite>. Indeed the approaches developed on that system laid the foundations for many subsequent studies on other glycosidases.  An analysis of the roles of each substrate hydroxyl in catalysis, based upon kinetic studies with modified sugars has also been published <cite>McCarter1992</cite>. Some GH2 glycosidases require Mg<sup>2+</sup> for activity and in ''E. coli'' β-galactosidase this Mg<sup>2+</sup> requirement is associated with the binding of the cation in the active site such that it places the acid/base residue appropriately.  Others, such as the human β-glucuronidase, have no such metal ion requirement.
 == Catalytic Residues ==
-The [[catalytic nucleophile]] in GH2 was first correctly identified in the ''E. coli'' (lacZ) β-galactosidase as Glu537 in the sequence ILC'''<u>E</u>'''YAH through trapping of the 2-deoxy-2-fluorogalactosyl-enzyme [[intermediate]] and subsequent peptide mapping via HPLC techniques using radiolabeled tracers <cite>9</cite>. Earlier studies, carefully done using conduritol C cis-epoxide as affinity label, had identified Glu461 as the labeled residue, <cite>10</cite> on which basis a series of beautifully executed kinetic studies were performed on mutants modified at this position that appeared initially to support this conclusion <cite>11</cite>. However, doubts were raised when similar kinetic analysis of nucleophile mutants of the GH1 Agrobacterium sp. β-glucosidase yielded quite different results, leading to the above labeling study <cite>9</cite>.  The [[general acid/base]] catalyst was then identified as Glu461 by re-interpretation <cite>9</cite> of the published kinetic results on mutants at that position <cite>11</cite>, which had included azide rescue experiments. These conclusions were fully supported by subsequent 3-dimensional structural analyses (below).
+The [[catalytic nucleophile]] in GH2 was first correctly identified in the ''E. coli'' (lacZ) β-galactosidase as Glu537 in the sequence ILC'''<u>E</u>'''YAH through trapping of the 2-deoxy-2-fluorogalactosyl-enzyme [[intermediate]] and subsequent peptide mapping via HPLC techniques using radiolabeled tracers <cite>Gebler1992</cite>. Earlier studies, carefully done using conduritol C cis-epoxide as affinity label, had identified Glu461 as the labeled residue, <cite>HerrchenLegler1984</cite> on which basis a series of beautifully executed kinetic studies were performed on mutants modified at this position that appeared initially to support this conclusion <cite>Cupples1990</cite>. However, doubts were raised when similar kinetic analysis of nucleophile mutants of the GH1 Agrobacterium sp. β-glucosidase yielded quite different results, leading to the above labeling study <cite>Gebler1992</cite>.  The [[general acid/base]] catalyst was then identified as Glu461 by re-interpretation <cite>Gebler1992</cite> of the published kinetic results on mutants at that position <cite>Cupples1990</cite>, which had included azide rescue experiments. These conclusions were fully supported by subsequent 3-dimensional structural analyses (below).
 == Three-dimensional structures ==
-Three-dimensional structures are available for five Family GH2 enzymes currently, the first solved being that of the ''E. coli'' (lacZ) β-galactosidase in a ''tour de force'' of X-ray crystallography at that time, given its huge size (4  x  125,000 Da) <cite>12</cite>. The enzyme is multidomain, but as members of Clan GHA the catalytic domains a classical (α/β)<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).
+Three-dimensional structures are available for five Family GH2 enzymes currently, the first solved being that of the ''E. coli'' (lacZ) β-galactosidase in a ''tour de force'' of X-ray crystallography at that time, given its huge size (4  x  125,000 Da) <cite>Jacobson1994</cite>. The enzyme is multidomain, but as members of Clan GHA the catalytic domains a classical (α/β)<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).
 == Family Firsts ==
-;First stereochemistry determination:   (pmid=TBA)
+;First stereochemistry determination:  (pmid=TBA)
-;First [[catalytic nucleophile]] identification: ''E. coli'' (lacZ) β-galactosidase by 2-fluorogalactose labeling <cite>9</cite>
+;First [[catalytic nucleophile]] identification: ''E. coli'' (lacZ) β-galactosidase by 2-fluorogalactose labeling <cite>Gebler1992</cite>
-;First [[general acid/base]] residue identification: ''E. coli'' (lacZ) β-galactosidase by re-interpretation of kinetic studies with mutants <cite>9 11</cite>
+;First [[general acid/base]] residue identification: ''E. coli'' (lacZ) β-galactosidase by re-interpretation of kinetic studies with mutants <cite>Gebler1992 Cupples1990</cite>
-;First 3-D structure: ''E. coli'' (lacZ) β-galactosidase <cite>12</cite>
+;First 3-D structure: ''E. coli'' (lacZ) β-galactosidase <cite>Jacobson1994</cite>
 == References ==
 <biblio>
-#1 pmid=97298
+#FowlerZabin1978 pmid=97298
-#2 pmid=10234816
+#Hall1999 pmid=10234816
-#3 pmid=4265197
+#Sly1973 pmid=4265197
-#4 pmid=TBA
+#TBA pmid=TBA
-#5 pmid=4578762
+#SinnottSouchard1973 pmid=4578762
-#6 pmid=4721624
+#SinnottViratelle1973 pmid=4721624
-#7 pmid=4691347
+#ViratelleYon1973 pmid=4691347
-#8 pmid=1417731
+#McCarter1992 pmid=1417731
-#9 pmid=1350782
+#Gebler1992 pmid=1350782
-#10 pmid=6420154
+#HerrchenLegler1984 pmid=6420154
-#11 pmid=1969405
+#Cupples1990 pmid=1969405
-#12 pmid=8008071
+#Jacobson1994 pmid=8008071
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH002]]