Glycoside Hydrolase Family 93 - Revision history

Harry Brumer: /* Three-dimensional structures */

2019-03-05T16:17:42Z

Three-dimensional structures

Harry Brumer: /* Catalytic Residues */

2019-03-05T16:15:19Z

Catalytic Residues

Harry Brumer: /* Kinetics and Mechanism */

2019-03-05T16:14:54Z

Kinetics and Mechanism

Harry Brumer: GoddardBorger2011 pmid now working

2019-03-05T16:12:49Z

GoddardBorger2011 pmid now working

Harry Brumer: fixed some formatting issues

2019-03-05T16:08:52Z

fixed some formatting issues

Annabelle Varrot: /* Three-dimensional structures */

2019-03-05T14:47:00Z

Three-dimensional structures

Annabelle Varrot: /* Kinetics and Mechanism */

2019-03-05T14:45:56Z

Kinetics and Mechanism

Annabelle Varrot: /* Kinetics and Mechanism */

2019-03-05T14:44:50Z

Kinetics and Mechanism

Annabelle Varrot: /* Three-dimensional structures */

2019-03-05T14:43:27Z

Three-dimensional structures

Annabelle Varrot: /* Kinetics and Mechanism */

2019-03-05T14:43:00Z

Kinetics and Mechanism

@@ Line 38: / Line 38: @@
 [[File:62 araf chembiochem-17.jpg|thumb|right|300px|'''Figure 3. Electron density for hydroximolactone inhibitor bound to the active site of Arb93A (PDB ID [{{PDBlink}}5m1z 5M1Z].<cite>Coyle2017</cite>''']]
-The crystal structure of  Arb93A reveals a six-bladed &beta;-propeller fold characteristic of sialidases of [[clan]] GH-E (Fig. 3). <cite>Carapito2009 Sogabe2011</cite>,  The catalytic machinery is however very different from that of sialidases. <cite>Gaskell1995</cite> The wild-type structure was solved at 2.05 angstrom resolution in complex with arabinobiose . The active site is located in a deep acidic L-shaped crevice at the center of the beta-propeller (Fig. 1). Structures of the wild-type or E242A mutant enzyme in complex with iminoarabinobiose were solved at 1.6 and 1.85 angstrom resolution respectively as well as a complex with a shape mimic inhibitor and demonstrated ring distorsion (Fig. 2-3). <cite>GoddardBorger2011 Coyle2017</cite>
+The crystal structure of  Arb93A reveals a six-bladed &beta;-propeller fold characteristic of [[GH33]], [[GH34]], and [[GH83]] sialidases, which are also members of [[clan]] GH-E (Fig. 3) <cite>Carapito2009 Sogabe2011</cite>. The catalytic machinery is however very different from that of sialidases <cite>Gaskell1995</cite>. The wild-type structure was solved at 2.05 angstrom resolution in complex with arabinobiose . The active site is located in a deep acidic L-shaped crevice at the center of the beta-propeller (Fig. 1). Structures of the wild-type or E242A mutant enzyme in complex with iminoarabinobiose were solved at 1.6 and 1.85 angstrom resolution respectively as well as a complex with a shape mimic inhibitor and demonstrated ring distorsion (Fig. 2-3) <cite>GoddardBorger2011 Coyle2017</cite>.
 == Family Firsts ==

@@ Line 32: / Line 32: @@
 == Catalytic Residues ==
-From the crystal structure of  Arb93A, Glu170 and Glu242 are proposed to act as [[catalytic nucleophile]] and [[general acid/base]] respectively. Mutagenesis experiment support their role in catalysis and they are strictly conserved among the family members. <cite>Carapito2009</cite> Recent structures and mutagenesis studies for the arabinanase Abnx from ''Penicillium chrysogenum 31B'' strengthened this assignment. Mutations to alanine or glutamine of their equivalent Glu174 and Glu246 lead to inactive enzyme. <cite>Sogabe2011</cite>
+From the crystal structure of  Arb93A, Glu170 and Glu242 are proposed to act as [[catalytic nucleophile]] and [[general acid/base]] respectively. Mutagenesis experiment support their role in catalysis and they are strictly conserved among the family members <cite>Carapito2009</cite>. Recent structures and mutagenesis studies for the arabinanase Abnx from ''Penicillium chrysogenum 31B'' strengthened this assignment. Mutations to alanine or glutamine of their equivalent Glu174 and Glu246 lead to inactive enzyme <cite>Sogabe2011</cite>.
 == Three-dimensional structures ==

@@ Line 29: / Line 29: @@
 [[Image:overallsurf.png|thumb|300px|right|'''Figure 1. Cartoon representation of the overall structure of Arb93A''' (PDB ID [{{PDBlink}}2w5o 2W5O] <cite>Carapito2009</cite>.The propeller is colored blue to red from the N- to C-terminus and arabinobiose is depicted as balls and sticks.]]
-GH93 enzymes are [[exo]]-acting enzymes that only release arabinobiose from the non-reducing end of α-1,5-L-arabinan. These enzymes are proposed to be [[retaining]] enzymes based on the net retention of the configuration of the anomeric carbon is proposed from the products of the transglycosylation activity of the protein Abnx from ''Penicillium chrysogenum'' <cite>Sakamoto2004</cite>. This proposal obtained support from the crystal structures  of the Arb93A enzyme from ''Fusarium graminearum'' and Abnx both in complex with arabinobiose (Fig. 1) <cite>Carapito2009 Sogabe2011</cite>. α-L-Arabinofuranosylated pyrrolidines were shown to be good inhibitors of Arb93A. The Arb93A complex structure with a deoxyiminosugar equivalent of arabinobiose revealed a <sup>4</sup>T<sub>N</sub> twist conformation expected for the Michaelis complex, as seen for several retaining GH51 α-L-arabinofuranosidases (Fig. 2).  <cite>GoddardBorger2011</cite> Potent shape mimic inhibitors exploiting sp<sup>2</sup> hybridization at the anomeric carbon have been recently synthetized as well as a chromogenic substrate (Fig. 3). They are useful tools to assist further biochemical studies on L-arabinanases.  <cite>Coyle2017</cite>
+GH93 enzymes are [[exo]]-acting enzymes that only release arabinobiose from the non-reducing end of α-1,5-L-arabinan. These enzymes are proposed to be [[retaining]] enzymes based on the net retention of the configuration of the anomeric carbon is proposed from the products of the transglycosylation activity of the protein Abnx from ''Penicillium chrysogenum'' <cite>Sakamoto2004</cite>. This proposal obtained support from the crystal structures  of the Arb93A enzyme from ''Fusarium graminearum'' and Abnx both in complex with arabinobiose (Fig. 1) <cite>Carapito2009 Sogabe2011</cite>. α-L-Arabinofuranosylated pyrrolidines were shown to be good inhibitors of Arb93A. The Arb93A complex structure with a deoxyiminosugar equivalent of arabinobiose revealed a <sup>4</sup>T<sub>N</sub> twist conformation expected for the Michaelis complex, as seen for several retaining GH51 α-L-arabinofuranosidases (Fig. 2) <cite>GoddardBorger2011</cite>. Potent shape mimic inhibitors exploiting sp<sup>2</sup> hybridization at the anomeric carbon have been recently synthetized as well as a chromogenic substrate (Fig. 3). They are useful tools to assist further biochemical studies on L-arabinanases <cite>Coyle2017</cite>.
 == Catalytic Residues ==

@@ Line 53: / Line 53: @@
 #Sakamoto2004 pmid=15342117
 #Sogabe2011 pmid=21543843
-#GoddardBorger2011 Goddard-Borger ED, Carapito R, Jeltsch JM, Phalip V, Stick RV, Varrot A. ''α-L-Arabinofuranosylated pyrrolidines as arabinanase inhibitors''. Chem Commun 2011 Sep 14;47(34):9684-9686.  //''Note: Due to a problem with PubMed data, this reference is not automatically formatted.  Please see these links out:'' [http://dx.doi.org/10.1039/C1CC13675E DOI:10.1039/C1CC13675E] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21773614 PMID: 21773614]
+#GoddardBorger2011 pmid=21773614
 #Coyle2017 pmid=28266777
 #Gaskell1995 pmid=8591030

@@ Line 27: / Line 27: @@
 == Kinetics and Mechanism ==
-[[Image:overallsurf.png|thumb|250px|right|'''Figure 1. Cartoon representation of the overall structure of Arb93A''' (PDB ID [{{PDBlink}}2w5o 2W5O] <cite>Carapito2009</cite>.''' Propeller colored by from N to C-terminus (blue to red) and arabinobiose depicted as balls and sticks.]]
+[[Image:overallsurf.png|thumb|300px|right|'''Figure 1. Cartoon representation of the overall structure of Arb93A''' (PDB ID [{{PDBlink}}2w5o 2W5O] <cite>Carapito2009</cite>.The propeller is colored blue to red from the N- to C-terminus and arabinobiose is depicted as balls and sticks.]]
 GH93 enzymes are [[exo]]-acting enzymes that only release arabinobiose from the non-reducing end of α-1,5-L-arabinan. These enzymes are proposed to be [[retaining]] enzymes based on the net retention of the configuration of the anomeric carbon is proposed from the products of the transglycosylation activity of the protein Abnx from ''Penicillium chrysogenum'' <cite>Sakamoto2004</cite>. This proposal obtained support from the crystal structures  of the Arb93A enzyme from ''Fusarium graminearum'' and Abnx both in complex with arabinobiose (Fig. 1) <cite>Carapito2009 Sogabe2011</cite>. α-L-Arabinofuranosylated pyrrolidines were shown to be good inhibitors of Arb93A. The Arb93A complex structure with a deoxyiminosugar equivalent of arabinobiose revealed a <sup>4</sup>T<sub>N</sub> twist conformation expected for the Michaelis complex, as seen for several retaining GH51 α-L-arabinofuranosidases (Fig. 2).  <cite>GoddardBorger2011</cite> Potent shape mimic inhibitors exploiting sp<sup>2</sup> hybridization at the anomeric carbon have been recently synthetized as well as a chromogenic substrate (Fig. 3). They are useful tools to assist further biochemical studies on L-arabinanases.  <cite>Coyle2017</cite>
@@ Line 35: / Line 35: @@
 == Three-dimensional structures ==
-[[Image:242den.png|thumb|right|200px|'''Figure 2. Electron density for deoxyiminoarabinobiose bound to the active site of Arb93A (PDB ID [{{PDBlink}}2ydt 2YDT] <cite>GoddardBorger2011</cite>.''' Hydrogens bond are represented as dash lines.]]
+[[Image:242den.png|thumb|right|300px|'''Figure 2. Electron density for deoxyiminoarabinobiose bound to the active site of Arb93A (PDB ID [{{PDBlink}}2ydt 2YDT] <cite>GoddardBorger2011</cite>.''' Hydrogens bond are represented as dashed lines.]]
-[[File:62 araf chembiochem-17.jpg|thumb|right|200px|'''Figure 3. Electron density for hydroximolactone inhibitor bound to the active site of Arb93A (PDB ID [{{PDBlink}}5m1z 5M1Z].<cite>Coyle2017</cite>''']]
+[[File:62 araf chembiochem-17.jpg|thumb|right|300px|'''Figure 3. Electron density for hydroximolactone inhibitor bound to the active site of Arb93A (PDB ID [{{PDBlink}}5m1z 5M1Z].<cite>Coyle2017</cite>''']]
 The crystal structure of  Arb93A reveals a six-bladed &beta;-propeller fold characteristic of sialidases of [[clan]] GH-E (Fig. 3). <cite>Carapito2009 Sogabe2011</cite>,  The catalytic machinery is however very different from that of sialidases. <cite>Gaskell1995</cite> The wild-type structure was solved at 2.05 angstrom resolution in complex with arabinobiose . The active site is located in a deep acidic L-shaped crevice at the center of the beta-propeller (Fig. 1). Structures of the wild-type or E242A mutant enzyme in complex with iminoarabinobiose were solved at 1.6 and 1.85 angstrom resolution respectively as well as a complex with a shape mimic inhibitor and demonstrated ring distorsion (Fig. 2-3). <cite>GoddardBorger2011 Coyle2017</cite>
 == Family Firsts ==
-'''First sterochemistry determination'''
+;First sterochemistry determination: This was determined with the ''Penicillium chrysogenum'' Abxn enzyme using <sup>1</sup>H-NMR to identify the transglycosylation products <cite>Sakamoto2004</cite>
+;First [[catalytic nucleophile]] identification: This was proposed based on the structure of ''Fusarium graminearum'' Arb93A <cite>Carapito2009</cite>
-This was determined with the ''Penicillium chrysogenum'' Abxn enzyme using <sup>1</sup>H-NMR to identify the transglycosylation products <cite>Sakamoto2004</cite>
+;First [[general acid/base]] residue identification: This was proposed based on the structure of ''Fusarium graminearum'' Arb93A <cite>Carapito2009</cite>
+;First 3-D structure: Determined for ''Fusarium graminearum'' Arb93A by Carapito and co-workers <cite>Carapito2009</cite>
 == References ==