Glycoside Hydrolase Family 22 - Revision history

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

2021-12-18T21:19:31Z

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

Spencer Williams at 22:31, 17 April 2017

2017-04-17T22:31:35Z

Spencer Williams at 22:29, 17 April 2017

2017-04-17T22:29:46Z

Spencer Williams at 22:27, 17 April 2017

2017-04-17T22:27:58Z

Harry Brumer: /* References */

2017-04-10T18:29:01Z

References

Harry Brumer: /* References */ improved PDB MOTM reference

2017-04-10T18:28:28Z

References: improved PDB MOTM reference

Harry Brumer: /* Three-dimensional structures */

2017-04-10T18:23:05Z

Three-dimensional structures

Harry Brumer: /* Three-dimensional structures */ Added links to GH22 structure page in the CAZy DB

2017-04-10T18:22:22Z

Three-dimensional structures: Added links to GH22 structure page in the CAZy DB

Spencer Williams at 11:46, 10 April 2017

2017-04-10T11:46:22Z

Spencer Williams at 11:45, 10 April 2017

2017-04-10T11:45:52Z

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 <!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
-* [[Author]]: ^^^Spencer Williams^^^
+* [[Author]]: [[User:Spencer Williams|Spencer Williams]]
-* [[Responsible Curator]]:  ^^^David Vocadlo^^^
+* [[Responsible Curator]]:  [[User:David Vocadlo|David Vocadlo]]
 ----

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 == Catalytic Residues ==
-Inspection of complexes of lysozyme with chitooligosaccharides and chemical reasoning led to the proposal of Glu35 as a proton donor <cite>Blake1967</cite>. Site directed mutagenesis of Glu35 to Gln35 resulted in a complete loss of activity against ''Micrococcus luteus'' cell wall <cite>Malcolm1989</cite>. Together these data support the identity of Glu35 as the [[general acid/base]] in a [[classical Koshland retaining mechanism]]. In an early study Asp52 was highlighted as a catalytic residue, and proposed to play a role in stablizing an oxocarbenium ion intermediate as noted above <cite>Blake1967</cite>. An early example of unnatural amino acid mutagenesis realized by chemical mutagenesis of Asp52 to Homoser52 yielded an enzyme with greatly reduced catalytic activity <cite>Eshdat1974</cite>. Unexpectedly, the Asp52Asn mutant exhibited approximately 5% wild-type lytic ability against ''Micrococcus luteus'' cell wall <cite>Malcolm1989</cite> and this residual activity was shown to arise from the presence of carboxylate groups within the stem peptide of certain peptidoglycan fragments, which presumably act by substrate-assisted catalysis to provide chemical rescue of the mutant <cite>Matsumura1996</cite>. Asp52 is generally now believed to function as a [[catalytic nucleophile]], as shown by X-ray crystallographic observation of a covalent bond for the 2-fluoroglycosyl enzyme formed on the E35Q mutant of HEWL using ''N''-acetylglucosaminyl-(1,4)-2-deoxy-2-fluoroglycosyl fluoride, and by mass spectrometric observation of a covalent adduct of the same complex <cite>Vocadlo2001</cite>.
+Inspection of complexes of lysozyme with chitooligosaccharides and chemical reasoning led to the proposal of Glu35 as a proton donor <cite>Blake1967</cite>. Site directed mutagenesis of Glu35 to Gln35 provided a mutant with no activity against ''Micrococcus luteus'' cell wall <cite>Malcolm1989</cite>. Together these data support the identity of Glu35 as the [[general acid/base]] in a [[classical Koshland retaining mechanism]]. In an early study Asp52 was highlighted as a catalytic residue, and proposed to play a role in stablizing an oxocarbenium ion intermediate as noted above <cite>Blake1967</cite>. An early example of unnatural amino acid mutagenesis realized by chemical mutagenesis of Asp52 to Homoser52 yielded an enzyme with greatly reduced catalytic activity <cite>Eshdat1974</cite>. Unexpectedly, the Asp52Asn mutant exhibited approximately 5% wild-type lytic ability against ''Micrococcus luteus'' cell wall <cite>Malcolm1989</cite> and this residual activity was shown to arise from the presence of carboxylate groups within the stem peptide of certain peptidoglycan fragments, which presumably act by substrate-assisted catalysis to provide chemical rescue of the mutant <cite>Matsumura1996</cite>. Asp52 is generally now believed to function as a [[catalytic nucleophile]], as shown by X-ray crystallographic observation of a covalent bond for the 2-fluoroglycosyl enzyme formed on the E35Q mutant of HEWL using ''N''-acetylglucosaminyl-(1,4)-2-deoxy-2-fluoroglycosyl fluoride, and by mass spectrometric observation of a covalent adduct of the same complex <cite>Vocadlo2001</cite>.
 α-Lactalbumins typically lack the conserved catalytic residues present in lysozymes. Two naturally occurring variants of human lysozyme, Ile56Thr and Asp67His, are amyloidogenic <cite>Jeyashekar2005</cite>. In both cases, decreased protein stability is believed to contribute to amyloid formation, with fibrils forming more readily at low pH or at slightly elevated temperatures.

@@ Line 41: / Line 41: @@
 == Catalytic Residues ==
-Inspection of complexes of lysozyme with chitooligosaccharides and chemical reasoning led to the proposal of Glu35 as a proton donor <cite>Blake1967</cite>. Site directed mutagenesis of Glu35 to Gln35 resulted in a complete loss of activity against ''Micrococcus luteus'' cell wall <cite>Malcolm1989</cite>. Together these data support the identity of Glu35 as the [[general acid/base]] in a [[classical Koshland retaining mechanism]]. In an early study Asp52 was highlighted as a catalytic residue, and proposed to play a role in stablizing an oxocarbenium ion intermediate as noted above <cite>Blake1967</cite>. An early example of unnatural amino acid mutagenesis realized by chemical mutagenesis of Asp52 to Homoser52 yielded an enzyme with greatly reduced catalytic activity <cite>Eshdat1974</cite>. Unexpectedly, the Asp52Asn mutant exhibited approximately 5% wild-type lytic ability against ''Micrococcus luteus'' cell wall <cite>Malcolm1989</cite> and this was shown to arise from the presence of carboxylate groups within the stem peptide of genuine peptidoglycan fragments, which presumably act by chemical rescue of the mutant <cite>Matsumura1996</cite>. Asp52 is generally now believed to function as a [[catalytic nucleophile]], as shown by X-ray crystallographic observation of a covalent bond for the 2-fluoroglycosyl enzyme formed on the E35Q mutant of HEWL using ''N''-acetylglucosaminyl-(1,4)-2-deoxy-2-fluoroglycosyl fluoride, and by mass spectrometric observation of a covalent adduct of the same complex <cite>Vocadlo2001</cite>.
+Inspection of complexes of lysozyme with chitooligosaccharides and chemical reasoning led to the proposal of Glu35 as a proton donor <cite>Blake1967</cite>. Site directed mutagenesis of Glu35 to Gln35 resulted in a complete loss of activity against ''Micrococcus luteus'' cell wall <cite>Malcolm1989</cite>. Together these data support the identity of Glu35 as the [[general acid/base]] in a [[classical Koshland retaining mechanism]]. In an early study Asp52 was highlighted as a catalytic residue, and proposed to play a role in stablizing an oxocarbenium ion intermediate as noted above <cite>Blake1967</cite>. An early example of unnatural amino acid mutagenesis realized by chemical mutagenesis of Asp52 to Homoser52 yielded an enzyme with greatly reduced catalytic activity <cite>Eshdat1974</cite>. Unexpectedly, the Asp52Asn mutant exhibited approximately 5% wild-type lytic ability against ''Micrococcus luteus'' cell wall <cite>Malcolm1989</cite> and this residual activity was shown to arise from the presence of carboxylate groups within the stem peptide of certain peptidoglycan fragments, which presumably act by substrate-assisted catalysis to provide chemical rescue of the mutant <cite>Matsumura1996</cite>. Asp52 is generally now believed to function as a [[catalytic nucleophile]], as shown by X-ray crystallographic observation of a covalent bond for the 2-fluoroglycosyl enzyme formed on the E35Q mutant of HEWL using ''N''-acetylglucosaminyl-(1,4)-2-deoxy-2-fluoroglycosyl fluoride, and by mass spectrometric observation of a covalent adduct of the same complex <cite>Vocadlo2001</cite>.
 α-Lactalbumins typically lack the conserved catalytic residues present in lysozymes. Two naturally occurring variants of human lysozyme, Ile56Thr and Asp67His, are amyloidogenic <cite>Jeyashekar2005</cite>. In both cases, decreased protein stability is believed to contribute to amyloid formation, with fibrils forming more readily at low pH or at slightly elevated temperatures.

@@ Line 41: / Line 41: @@
 == Catalytic Residues ==
-Inspection of complexes of lysozyme with chitooligosaccharides and chemical reasoning led to the proposal of Glu35 as a proton donor <cite>Blake1967</cite>. Site directed mutagenesis of Glu35 to Gln35 resulted in a complete loss of activity against ''Micrococcus luteus'' cell wall <cite>Malcolm1989</cite>. Together these data support the identity of Glu35 as the [[general acid/base]] in a [[classical Koshland retaining mechanism]]. In an early study Asp52 was highlighted as a catalytic residue, and proposed to play a role in stablizing an oxocarbenium ion intermediate as noted above <cite>Blake1967</cite>. An early example of unnatural amino acid mutagenesis realized by chemical mutagenesis of Asp52 to Homoser52 yielded an enzyme with greatly reduced catalytic activity <cite>Eshdat1974</cite>. Unexpectedly, the Asp52Asn mutant exhibited approximately 5% wild-type lytic ability against ''Micrococcus luteus'' cell wall and this was shown to arise from the presence of carboxylate groups within the stem peptide of genuine peptidoglycan fragments, which presumably act by chemical rescue of the mutant <cite>Malcolm1989</cite>. Asp52 is generally now believed to function as a [[catalytic nucleophile]], as shown by X-ray crystallographic observation of a covalent bond for the 2-fluoroglycosyl enzyme formed on the E35Q mutant of HEWL using ''N''-acetylglucosaminyl-(1,4)-2-deoxy-2-fluoroglycosyl fluoride, and by mass spectrometric observation of a covalent adduct of the same complex <cite>Vocadlo2001</cite>.
+Inspection of complexes of lysozyme with chitooligosaccharides and chemical reasoning led to the proposal of Glu35 as a proton donor <cite>Blake1967</cite>. Site directed mutagenesis of Glu35 to Gln35 resulted in a complete loss of activity against ''Micrococcus luteus'' cell wall <cite>Malcolm1989</cite>. Together these data support the identity of Glu35 as the [[general acid/base]] in a [[classical Koshland retaining mechanism]]. In an early study Asp52 was highlighted as a catalytic residue, and proposed to play a role in stablizing an oxocarbenium ion intermediate as noted above <cite>Blake1967</cite>. An early example of unnatural amino acid mutagenesis realized by chemical mutagenesis of Asp52 to Homoser52 yielded an enzyme with greatly reduced catalytic activity <cite>Eshdat1974</cite>. Unexpectedly, the Asp52Asn mutant exhibited approximately 5% wild-type lytic ability against ''Micrococcus luteus'' cell wall <cite>Malcolm1989</cite> and this was shown to arise from the presence of carboxylate groups within the stem peptide of genuine peptidoglycan fragments, which presumably act by chemical rescue of the mutant <cite>Matsumura1996</cite>. Asp52 is generally now believed to function as a [[catalytic nucleophile]], as shown by X-ray crystallographic observation of a covalent bond for the 2-fluoroglycosyl enzyme formed on the E35Q mutant of HEWL using ''N''-acetylglucosaminyl-(1,4)-2-deoxy-2-fluoroglycosyl fluoride, and by mass spectrometric observation of a covalent adduct of the same complex <cite>Vocadlo2001</cite>.
 α-Lactalbumins typically lack the conserved catalytic residues present in lysozymes. Two naturally occurring variants of human lysozyme, Ile56Thr and Asp67His, are amyloidogenic <cite>Jeyashekar2005</cite>. In both cases, decreased protein stability is believed to contribute to amyloid formation, with fibrils forming more readily at low pH or at slightly elevated temperatures.
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 #Malcolm1989 pmid=2563161
 #Mackie2002 pmid=21708724
 #Mitani1986 pmid=3087980
 #Prager1988 pmid=3146643

@@ Line 71: / Line 71: @@
 #Eshdat1974 pmid=4525456
 #Ford1974 pmid=4453000
-#Goodsell2000 Goodsell DS, Lysozyme, RCSB PDB Molecule of the Month, September 2000, [http://dx.doi.org/10.2210/rcsb_pdb/mom_2000_9 DOI:10.2210/rcsb_pdb/mom_2000_9]
+#Goodsell2000 Goodsell DS, ''Lysozyme'', RCSB PDB Molecule of the Month, September 2000, [http://dx.doi.org/10.2210/rcsb_pdb/mom_2000_9 DOI:10.2210/rcsb_pdb/mom_2000_9]
 #Jeyashekar2005 pmid=15657495
 #Lowe1967 pmid=6049930

@@ Line 46: / Line 46: @@
 == Three-dimensional structures ==
-[http://www.cazy.org/GH22_structure.html A large number of structures] is available for family GH22 members. The bulk of the discussion here will focus on hen egg white lysozyme (HEWL), as it was the first structure reported for a GH22 member <cite>Blake1962 Blake1965</cite>. In fact, HEWL has a distinguished history as the first enzyme for which atomic resolution X-ray data was reported, and has attracted great interest as it provided the first molecular view of enzyme catalysis, launching the field of structural enzymology. An extensive range of lysozyme structures have been determined, including hundreds of structures of mutants, such that lysozyme is the most commonly deposited protein in the Protein Databank <cite> Goodsell2000</cite>. Lysozyme adopts a compact globular structure comprised of just 127 amino acids. There are five helical regions comprising around 40% of the amino acids. There are also five regions of beta sheet with both random coil and beta turns. A large cleft running across the face of the structure that harbours the active site and the catalytic residues Glu35 and Asp52. Four disulfide bonds are present in the structure: Cys6-Cys127, Cys30-Cys115, Cys64-Cys80, and Cys76-Cys94.
+[http://www.cazy.org/GH22_structure.html A large number] of structures is available for family GH22 members. The bulk of the discussion here will focus on hen egg white lysozyme (HEWL), as it was the first structure reported for a GH22 member <cite>Blake1962 Blake1965</cite>. In fact, HEWL has a distinguished history as the first enzyme for which atomic resolution X-ray data was reported, and has attracted great interest as it provided the first molecular view of enzyme catalysis, launching the field of structural enzymology. An extensive range of lysozyme structures have been determined, including hundreds of structures of mutants, such that lysozyme is the most commonly deposited protein in the Protein Databank <cite> Goodsell2000</cite>. Lysozyme adopts a compact globular structure comprised of just 127 amino acids. There are five helical regions comprising around 40% of the amino acids. There are also five regions of beta sheet with both random coil and beta turns. A large cleft running across the face of the structure that harbours the active site and the catalytic residues Glu35 and Asp52. Four disulfide bonds are present in the structure: Cys6-Cys127, Cys30-Cys115, Cys64-Cys80, and Cys76-Cys94.
 [http://www.cazy.org/GH22_structure.html A range of complexes] of peptidoglycan derived NAG-NAM oligosaccharides and chitooligosaccharides have been determined, spanning mostly the -4 to -2 (A-C subsites). NAM-NAG-NAM binds in the -3/-2/-1 (B/C/D) subsites and the -1 subsite NAM was described as adopting an envelope conformation <cite>Strynadka1991</cite>; however, interpretation of this complex suffers from considerable disorder manifested as high temperature factors associated with the sugar bound in the -1 subsite <cite>Davies2009</cite>. A complex with a chitotetraose-derived lactone, which was proposed to be a transition state analogue by viture of its tight binding, was interpreted to show the -1 subsite lactone residue in an ''E''<sub>3</sub> or ''B''<sub>3,O</sub> conformation <cite>Ford1974</cite>. On the basis of these early structures in combination with modeling, HEWL was proposed to bind its substrate in a distorted conformation in which the NAM residue binding in the -1 subsite adopted a boat-like conformation <cite>Ford1974</cite>. A product complex of chitopentaoside spanning the negative subsites up to -1, determined at low temperature, revealed the sugar residue in the -1 subsite to be in an undistorted <sup>4</sup>''C''<sub>1</sub> chair conformation <cite>Davies2009</cite>. More recently, complexes of HEWL with the modified substrate ''N''-acetylglucosaminyl-(1,4)-2-deoxy-2-fluoroglycosyl fluoride and the HEWL E35Q mutant revealed a covalent bond to the nucleophile Glu35, with the -1 subsite sugar in a <sup>4</sup>''C''<sub>1</sub> chair conformation <cite>Vocadlo2001</cite>. These structural data were collectively interpreted in light of kinetic studies to propose an electrophilic migration mechanism for HEWL in which the enzyme uses a <sup>1,4</sup>''B'' &rarr; ''E''<sub>3</sub> &rarr; <sup>4</sup>''C''<sub>1</sub>, or closely related, conformational itinerary <cite>Vocadlo2001</cite>.

@@ Line 31: / Line 31: @@
 [[Glycoside hydrolase]] family 22 contains proteins with two main functions: lysozymes and α-lactalbumin.
-Lysozymes are [[endo]]-acting enzymes that catalyse the hydrolysis of (1→4)-β-linkages between ''N''-acetylmuramic acid and ''N''-acetyl-D-glucosamine residues in peptidoglycan and between ''N''-acetyl-D-glucosamine residues in chitooligosaccharides. Lysozymes are also referred to as muramidases. Lysozymes from family GH22 are classified as c-type lysozymes (c = chicken), to distinguish them from lysozymes of family [[GH23]], which are sometimes referred to as g-type (g = goose) lysozymes. Lysozymes provide a range of functions that are related to their bacteriolytic action and are conserved in mammals. Found in secretions such as milk, saliva, mucus, and tears, and in egg-white, lysozymes protect against bacterial infection through their ability to degrade the bacterial cell wall. Lysozymes are also intestinal secretions in ruminants including cattle (''Bos taursu'') and leaf-eating monkeys, where it is proposed that they assist in  lysis of commensal gut bacteria, releasing their nutrients for the host <cite>Dobson1984 Mackie2002</cite>. Defects in the gene encoding human lysozyme can result in a rare hereditary condition, amyloidosis VIII, in which lysozyme deposits as a protein aggregate <cite>Jeyashekar2005</cite>.
+Lysozymes are [[endo]]-acting enzymes that catalyse the hydrolysis of (1→4)-β-linkages between ''N''-acetylmuramic acid and ''N''-acetyl-D-glucosamine residues in peptidoglycan and between ''N''-acetyl-D-glucosamine residues in chitooligosaccharides. Lysozymes are also referred to as muramidases. Lysozymes from family GH22 are classified as c-type lysozymes (c = chicken), to distinguish them from lysozymes of family [[GH23]], which are sometimes referred to as g-type (g = goose) lysozymes. Lysozymes provide a range of functions that are related to their bacteriolytic action and are conserved in mammals. Found in secretions such as milk, saliva, mucus, and tears, and in egg-white, lysozymes protect against bacterial infection through their ability to degrade the bacterial cell wall. Lysozymes are also intestinal secretions in the foregut of ruminants including cattle (''Bos taurus'') and leaf-eating monkeys (''e.g.'' langurs), where it is proposed that they assist in  lysis of commensal gut bacteria, releasing their nutrients for the host <cite>Dobson1984 Mackie2002</cite>. Defects in the gene encoding human lysozyme can result in a rare hereditary condition, amyloidosis VIII, in which lysozyme deposits as a protein aggregate <cite>Jeyashekar2005</cite>.
 α-Lactalbumins are auxiliary proteins that bind to and modify the substrate specificity of galactosyltransferase (a family [[GT7]] enzyme that in the absence of α-lactalbumin transfers glucose to ''N''-acetylglucosamine), converting it to the heterodimer lactose synthase, which catalyzes transfer to glucose. α-Lactalbumin expression is induced by prolactin, and occurs within the mammary glands. It is believed that α-lactalbumins evolved at the outset of mammalian evolution, after divergence of mammalian and avian lineages <cite>Prager1988 Qasba1997</cite>. α-Lactalbumins possess a conserved Ca<sup>2+</sup> binding site, with a high affinity for the cation of 3-5 nM <cite>Mitani1986</cite>. α-Lactalbumin possesses no meaningful catalytic activity against peptidoglycan, nor does it bind chitooligosaccharides.