Glycoside Hydrolase Family 55 - Revision history

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

2021-12-18T21:15:44Z

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

Harry Brumer: /* Three-dimensional structures */

2016-12-27T02:20:54Z

Three-dimensional structures

Harry Brumer: /* Catalytic Residues */

2016-12-27T02:18:40Z

Catalytic Residues

Harry Brumer: /* Catalytic Residues */

2016-12-27T02:17:35Z

Catalytic Residues

Harry Brumer: /* Kinetics and Mechanism */

2016-12-27T02:08:51Z

Kinetics and Mechanism

Harry Brumer: /* Substrate specificities */ Extensively revised substrate specificity section

2016-12-27T02:08:23Z

Substrate specificities: Extensively revised substrate specificity section

Harry Brumer: /* Three-dimensional structures */ Added surface binding site link

2016-12-27T01:55:20Z

Three-dimensional structures: Added surface binding site link

Harry Brumer: removed extra line breaks introduced during last edits

2016-12-27T01:52:09Z

removed extra line breaks introduced during last edits

Takuya Ishida at 02:26, 21 December 2016

2016-12-21T02:26:46Z

Takuya Ishida at 10:55, 20 December 2016

2016-12-20T10:55:08Z

Show changes

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 {{CuratorApproved}}
-* [[Author]]s: ^^^Takuya Ishida^^^ and ^^^Kiyohiko Igarashi^^^
+* [[Author]]s: [[User:Takuya Ishida|Takuya Ishida]] and [[User:Kiyohiko Igarashi|Kiyohiko Igarashi]]
-* [[Responsible Curator]]:  ^^^Shinya Fushinobu^^^
+* [[Responsible Curator]]:  [[User:Shinya Fushinobu|Shinya Fushinobu]]
 ----

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 The first solved 3-D structure was Lam55A from ''P. chrysosporium'' <cite>Ishida2009</cite>. In this structure, two tandem &beta;-helix domains are positioned side-by-side to form a rib cage-like structure. The active site is located between the two &beta;-helix domains. A duplicated motif had been found in the primary sequence of EXG1 from ''Cochliobolus carbonum'' <cite>Nikolskaya1998</cite>, predicting the presence of two structurally similar domains in this family.
-SacteLam55A E502A structure complexed with laminarioligosaccharides revealed binding of scissile ligand and conformation of proposed catalytic residues. The structure also shows a solvent-exposed [[Surface Binding Site]] <CITE>Bianchetti2015</CITE>.
+The SacteLam55A E502A structure complexed with laminarioligosaccharides revealed the positioning of the substrate in the active site and the conformation of the proposed catalytic residues. The structure also shows a solvent-exposed [[Surface Binding Site]] <CITE>Bianchetti2015</CITE>.
 == Family Firsts ==

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 A crystal structure of [[exo]]-&beta;-1,3-glucanase Lam55A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5306 ''Phanerochaete chrysospoirum''] K-3 (PcLam55A) complexed with gluconolactone (PDB ID [{{PDBlink}}3eqo 3eqo]) suggested that Glu633 is the [[general acid]]. A candidate nucleophilic water was found near the C-1 atom of gluconolactone. A crystal structure of the bacterial enzyme SacteLam55A complexed with laminarihexaose (PDB ID [{{PDBlink}}4pf0 4pf0]), together with kinetic analysis of site-directed mutants, revealed that corresponding glutamic acid (Glu502 in SacteLam55A) also functions as the [[general acid]] in bacterial enzymes.
-The identification of the [[general base]] in this family is less clear, as is common with several other inverting GH families. In the crystal structures of both PcLam55A and SacteLam55A, the candidate nucleophilic water has no direct interaction with a sidechain carboxylate, but rather with a highly conserved glutamine residue that is, in turn, hydrogen-bonded to a conserved glutamic acid (Glu480 in SacteLam55A). Mutations (E480Q and E480A of SacteLam55A) significantly reduce catalytic activity.  Based on these kinetic and structural observations, a proton relay system for the activation of water has been proposed <CITE>Bianchetti2015</CITE>.
+The identification of the [[general base]] in this family is less clear, as is common with several other inverting GH families. In the crystal structures of both PcLam55A and SacteLam55A, the candidate nucleophilic water has no direct interaction with a sidechain carboxylate, but rather with a highly conserved glutamine residue that is, in turn, hydrogen-bonded to a conserved glutamic acid (Glu480 in SacteLam55A). Mutations of this glutamic acid (E480Q and E480A of SacteLam55A) significantly reduce catalytic activity.  Based on these kinetic and structural observations, a proton relay system for the activation of water has been proposed <CITE>Bianchetti2015</CITE>.
 In classical studies of a [[exo]]-&beta;-1,3-glucanase from ''Sporotrichum dimorphosporum'' (formerly known as ''Basidiomycete'' QM-806), Jeffcoat and Kirkwood reported that chemical modification of histidine residues in the catalytic site of the enzyme caused irreversible loss of activity, suggesting a crucial role for this residue <CITE>Jeffcoat1987</CITE>.

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 == Catalytic Residues ==
-Crystal structure of [[exo]]-&beta;-1,3-glucanase Lam55A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5306 ''Phanerochaete chrysospoirum''] K-3 (PcLam55A) complexed with gluconolactone (PDB ID [{{PDBlink}}3eqo 3eqo]) suggests that Glu633 is the [[general acid]]. A candidate nucleophilic water was found near the C-1 atom of gluconolactone. Crystal structure of bacterial enzyme SacteLam55A complexed with laminarihexaose (PDB ID [{{PDBlink}}4pf0 4pf0]) and kinetic analysis on its mutants revealed that corresponding glutamic acid (Glu502 in SacteLam55A) is functioning as [[general acid]] in bacterial enzymes.
+A crystal structure of [[exo]]-&beta;-1,3-glucanase Lam55A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5306 ''Phanerochaete chrysospoirum''] K-3 (PcLam55A) complexed with gluconolactone (PDB ID [{{PDBlink}}3eqo 3eqo]) suggested that Glu633 is the [[general acid]]. A candidate nucleophilic water was found near the C-1 atom of gluconolactone. A crystal structure of the bacterial enzyme SacteLam55A complexed with laminarihexaose (PDB ID [{{PDBlink}}4pf0 4pf0]), together with kinetic analysis of site-directed mutants, revealed that corresponding glutamic acid (Glu502 in SacteLam55A) also functions as the [[general acid]] in bacterial enzymes.
-[[General base]] identification for this family is less clear compared to [[general acid]] as well as several inverting GH families. In crystal structure of both PcLam55A and SacteLam55A, the candidate nucleophilic water have no direct interaction with acidic residue but with highly conserved glutamine residue which is h-bonded by conserved glutamic acid (Glu480 in SacteLam55A). The mutation on the corresponding glutamic acid (E480Q and E480A) of SacteLam55A is crucial for catalytic activity, based on which along with active site structure, proton relay system for activation of the water has been proposed <CITE>Bianchetti2015</CITE>.
+The identification of the [[general base]] in this family is less clear, as is common with several other inverting GH families. In the crystal structures of both PcLam55A and SacteLam55A, the candidate nucleophilic water has no direct interaction with a sidechain carboxylate, but rather with a highly conserved glutamine residue that is, in turn, hydrogen-bonded to a conserved glutamic acid (Glu480 in SacteLam55A). Mutations (E480Q and E480A of SacteLam55A) significantly reduce catalytic activity.  Based on these kinetic and structural observations, a proton relay system for the activation of water has been proposed <CITE>Bianchetti2015</CITE>.
-In classical studies of a [[exo]]-&beta;-1,3-glucanase from ''Sporotrichum dimorphosporum'' (formerly known as ''Basidiomycete'' QM-806), Jeffcoat and Kirkwood reported that chemical modification of histidine residues in the catalytic site of the enzyme caused irreversible loss of activity, suggesting a crucial role of a histidine residue <CITE>Jeffcoat1987</CITE>.
+In classical studies of a [[exo]]-&beta;-1,3-glucanase from ''Sporotrichum dimorphosporum'' (formerly known as ''Basidiomycete'' QM-806), Jeffcoat and Kirkwood reported that chemical modification of histidine residues in the catalytic site of the enzyme caused irreversible loss of activity, suggesting a crucial role for this residue <CITE>Jeffcoat1987</CITE>.
 == Three-dimensional structures ==

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 == Kinetics and Mechanism ==
-Family 55 enzymes are [[inverting]] enzymes, as shown by <sup>1</sup>NMR analysis on ExgS from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5063 ''Aspergillus phoenicis''] (formerly known as ''Aspergillus saitoi'') <CITE>Kasahara1992</CITE>. Release of &alpha;-glucose was subsequently confirmed by polarimetric analysis on family 55 enzymes from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5051 ''Acremonium persicinum'']<CITE>Pitson1995</CITE>.  These results are consistent with many classical reports on gentiobiose-producing exo-&beta;-1,3-glucanases from fungi <CITE>Nelson1970 Nagasaki1977</CITE>, although the genes for these enzymes have not yet been described.
+Family 55 enzymes are [[inverting]] enzymes, as shown by <sup>1</sup>NMR analysis on ExgS from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5063 ''Aspergillus phoenicis''] (formerly known as ''Aspergillus saitoi'') <CITE>Kasahara1992</CITE>. Release of &alpha;-glucose was subsequently confirmed by polarimetric analysis on family 55 enzymes from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5051 ''Acremonium persicinum''] <CITE>Pitson1995</CITE>.  These results are consistent with many classical reports on gentiobiose-producing exo-&beta;-1,3-glucanases from fungi <CITE>Nelson1970 Nagasaki1977</CITE>, although the genes for these enzymes have not yet been described.
 == Catalytic Residues ==

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 == Substrate specificities ==
-[[Glycoside Hydrolases|Glycoside Hydrolase]] family 55 consists exclusively of &beta;-1,3-glucanases, including both [[exo]]- and [[endo]]-enzymes. All biochemically characterized members of this family had been limited to fungal enzymes until the extensive work by Bianchetti and Takasuka et al. reporting crystallography of [[exo]]-&beta;-1,3-glucanase SacteLam55A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=862751 ''Streptmyces'' sp. SirexAA-E] ([http://www.uniprot.org/uniprot/G2NFJ9 Uniprot G2NFJ9]) together with characterization of many other bacterial enzymes <CITE>Bianchetti2015</CITE>.
+[[Glycoside Hydrolases|Glycoside Hydrolase]] family 55 consists exclusively of &beta;-1,3-glucanases, including both [[exo]]- and [[endo]]-enzymes. All biochemically characterized members of this family had been limited to fungal enzymes until the extensive work by Bianchetti, Takasuka, et al., who reported the crystallography of [[exo]]-&beta;-1,3-glucanase SacteLam55A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=862751 ''Streptmyces'' sp. SirexAA-E] ([http://www.uniprot.org/uniprot/G2NFJ9 Uniprot G2NFJ9]), together with characterization of many other bacterial enzymes <CITE>Bianchetti2015</CITE>.
-The enzymes belonging to this family are generally called "laminarinases," because they hydrolyze laminarin from brown algae (&beta;-1,3-glucan having single &beta;-1,6-glucoside side chains: &beta;-1,3/1,6-glucan). However, the physiological substrate for the enzymes might be fungal cell wall, whose major component is also &beta;-1,3/1,6-glucan.
+The majority of the members in this family are [[exo]]-glucan-1,3-&beta;-glucosidases (EC [{{EClink}}3.2.1.58 3.2.1.58]), which cleave the terminal &beta;-1,3-glycosidic linkage at the non-reducing end of &beta;-1,3-glucans or &beta;-1,3/1,6-glucans (&beta;-1,3-glucan having single &beta;-1,6-glucoside side chains, also known as laminarin, from brown algae). Many produce gentiobiose (&beta;-D-glucopyranosyl-1,6-D-glucose) in addition to glucose during the degradation of &beta;-1,3/1,6-glucan <CITE>Pitson1995 Bara2003</CITE>.  Due to activity on laminarin, GH55 members may be referred to as "laminarinases." However, the physiological substrate for these enzymes might be fungal cell walls, whose major component is also &beta;-1,3/1,6-glucan.
 The majority of the members in this family are [[exo]]-glucan-1,3-&beta;-glucosidases (EC [{{EClink}}3.2.1.58 3.2.1.58]), which cleave the terminal &beta;-1,3-glycosidic linkage at the non-reducing end of &beta;-1,3-glucans or &beta;-1,3/1,6-glucans. Many produce gentiobiose (&beta;-D-glucopyranosyl-1,6-D-glucose) in addition to glucose during the degradation of &beta;-1,3/1,6-glucan <CITE>Pitson1995 Bara2003</CITE>.
-Bgn13.1 from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5544 ''Hypocrea lixii''] (formerly known as ''Trichoderma harzianum'') <CITE>delaCruz1995</CITE> and LamAI from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5547 ''Trichoderma viride''] <CITE>Nobe2003</CITE>were characterised as [[endo]]-acting enzymes (EC [{{EClink}}3.2.1.39 3.2.1.39]).
+Bgn13.1 from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5544 ''Hypocrea lixii''] (formerly known as ''Trichoderma harzianum'') <CITE>delaCruz1995</CITE> and LamAI from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5547 ''Trichoderma viride''] <CITE>Nobe2003</CITE> were characterised as [[endo]]-acting enzymes (EC [{{EClink}}3.2.1.39 3.2.1.39]).
 == Kinetics and Mechanism ==

@@ Line 2: / Line 2: @@
 * [[Author]]s: ^^^Takuya Ishida^^^ and ^^^Kiyohiko Igarashi^^^
 * [[Responsible Curator]]:  ^^^Shinya Fushinobu^^^
 ----
 <div style="float:right">
 {| {{Prettytable}}
 |-
 |{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family 55'''
 |-
 |'''Clan'''
 |none
 |-
 |'''Mechanism'''
 |inverting
 |-
 |'''Active site residues'''
 |not known
 |-
 |{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 |-
 | colspan="2" |{{CAZyDBlink}}GH55.html
 |}
 == Substrate specificities ==
 [[Glycoside Hydrolases|Glycoside Hydrolase]] family 55 consists exclusively of &beta;-1,3-glucanases, including both [[exo]]- and [[endo]]-enzymes. All biochemically characterized members of this family had been limited to fungal enzymes until the extensive work by Bianchetti and Takasuka et al. reporting crystallography of [[exo]]-&beta;-1,3-glucanase SacteLam55A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=862751 ''Streptmyces'' sp. SirexAA-E] ([http://www.uniprot.org/uniprot/G2NFJ9 Uniprot G2NFJ9]) together with characterization of many other bacterial enzymes <CITE>Bianchetti2015</CITE>.
@@ Line 52: / Line 33: @@
 == Kinetics and Mechanism ==
 Family 55 enzymes are [[inverting]] enzymes, as shown by <sup>1</sup>NMR analysis on ExgS from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5063 ''Aspergillus phoenicis''] (formerly known as ''Aspergillus saitoi'') <CITE>Kasahara1992</CITE>. Release of &alpha;-glucose was subsequently confirmed by polarimetric analysis on family 55 enzymes from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5051 ''Acremonium persicinum'']<CITE>Pitson1995</CITE>.  These results are consistent with many classical reports on gentiobiose-producing exo-&beta;-1,3-glucanases from fungi <CITE>Nelson1970 Nagasaki1977</CITE>, although the genes for these enzymes have not yet been described.
 == Catalytic Residues ==
 Crystal structure of [[exo]]-&beta;-1,3-glucanase Lam55A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5306 ''Phanerochaete chrysospoirum''] K-3 (PcLam55A) complexed with gluconolactone (PDB ID [{{PDBlink}}3eqo 3eqo]) suggests that Glu633 is the [[general acid]]. A candidate nucleophilic water was found near the C-1 atom of gluconolactone. Crystal structure of bacterial enzyme SacteLam55A complexed with laminarihexaose (PDB ID [{{PDBlink}}4pf0 4pf0]) and kinetic analysis on its mutants revealed that corresponding glutamic acid (Glu502 in SacteLam55A) is functioning as [[general acid]] in bacterial enzymes.
@@ Line 64: / Line 43: @@
 == Three-dimensional structures ==
 The first solved 3-D structure was Lam55A from ''P. chrysosporium'' <cite>Ishida2009</cite>. In this structure, two tandem &beta;-helix domains are positioned side-by-side to form a rib cage-like structure. The active site is located between the two &beta;-helix domains. A duplicated motif had been found in the primary sequence of EXG1 from ''Cochliobolus carbonum'' <cite>Nikolskaya1998</cite>, predicting the presence of two structurally similar domains in this family.
@@ Line 70: / Line 48: @@
 == Family Firsts ==
 ;First sterochemistry determination: Probably ExgS from ''A. saitoi'' by H-NMR analysis <CITE>Kasahara1992</CITE>. See [[#Kinetics and Mechanism|kinetics and mechanism]].
 ;First gene cloning: BGN13.1 from ''T. harzianum'' ([http://www.uniprot.org/uniprot/P53626 Uniprot P53626]) <cite>delaCruz1995</cite> and EXG1 from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5017 ''C. carbonum''] (partial gene coning and gene knockout) ([http://www.uniprot.org/uniprot/P49426 Uniprot P49426]) <cite>Schaeffer1994</cite>. First bacterial gene was cloned from ''Arthrobacter'' sp. NHB-10 ([http://www.uniprot.org/uniprot/A4PHQ5 Uniprot A4PHQ5]) <cite>Okazaki2007</cite>.
@@ Line 76: / Line 53: @@
 ;First [[general base]] residue identification: SacteLam55A from ''Streptmyces'' sp. SirexAA-E ([http://www.uniprot.org/uniprot/G2NFJ9 Uniprot G2NFJ9]) by crystal structure and kinetic analysis on mutants <cite>Bianchetti2015</cite>.
 ;First 3-D structure: Lam55A from ''P. chrysosporium'' by X-ray crystallography <cite>Ishida2009</cite>.
 == References ==
 <biblio>
 #Schaeffer1994 pmid=8135518
 #Ishida2009 pmid=19193645
 #Pitson1995 pmid=8948426
 #Bara2003 pmid=12594027
 #delaCruz1995 pmid=7592488
 #Nobe2003 pmid=12843664
 #Kasahara1992 Kasahara S, Nakajima T, Miyamoto C, Wada K, Furuichi Y, and Ichishima E. Characterization and mode of action of exo-1,3-&beta;-D-glucanase from ''Aspergillus saitoi''. J Ferment Bioeng 74 (4), 238-240 (1992).[http://dx.doi.org/10.1016/0922-338X(92)90118-E  DOI:10.1016/0922-338X(92)90118-E]
 #Nelson1970 pmid=5416668
 #Nagasaki1977 Nagasaki N, Saito K, and Yarnamoto S. Purification and characterization of an exo-&beta;-l,3-glucanase from a fungi imperfecti. Agric Biol Cbem 41, 493-502 (1977).[http://joi.jlc.jst.go.jp/JST.Journalarchive/bbb1961/41.493 JOI:JST.Journalarchive/bbb1961/41.493]
 #Jeffcoat1987 pmid=3100526
 #Nikolskaya1998 pmid=9838227
 #Bianchetti2015 pmid=25752603
 #Okazaki2007 pmid=17587693
 [[Category:Glycoside Hydrolase Families|GH055]]