Glycoside Hydrolase Family 47 - Revision history

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

2021-12-18T21:15:10Z

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

Mslwebmin at 19:54, 7 May 2015

2015-05-07T19:54:05Z

Mslwebmin at 19:53, 7 May 2015

2015-05-07T19:53:52Z

Spencer Williams: /* Kinetics and Mechanism */

2013-06-27T05:50:27Z

Kinetics and Mechanism

Harry Brumer at 18:28, 17 January 2013

2013-01-17T18:28:02Z

Harry Brumer: fixed spacing

2013-01-17T01:38:33Z

fixed spacing

Spencer Williams at 01:28, 17 January 2013

2013-01-17T01:28:28Z

Spencer Williams at 01:02, 17 January 2013

2013-01-17T01:02:13Z

Spencer Williams at 01:01, 17 January 2013

2013-01-17T01:01:02Z

Spencer Williams at 00:58, 17 January 2013

2013-01-17T00:58:43Z

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 {{CuratorApproved}}
-* [[Author]]: ^^^Rohan Williams^^^
+* [[Author]]: [[User:Rohan Williams|Rohan Williams]]
-* [[Responsible Curator]]:  ^^^Spencer Williams^^^
+* [[Responsible Curator]]:  [[User:Spencer Williams|Spencer Williams]]
 ----

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−	~~TEST TEST TEST~~
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 GH47 enzymes are Ca<sup>2+</sup>-dependent, as demonstrated by loss of activity upon addition of the metal binding ligand EDTA, and restoration of activity through subsequent addition of Ca<sup>2+</sup> <cite>Herscovics1988</cite>. ''Exo''-&alpha;-mannosidases from [[GH38]] and [[GH92]] also require a metal ion for catalysis.
-GH47 mannosidases operate through an unusual <sup>3,O</sup>''B''/<sup>3</sup>''S''<sub>1</sub>&rarr;<sup>3</sup>''H''<sub>4</sub><sup>‡</sup>&rarr;<sup>1</sup>''C''<sub>4</sub> conformational itinerary. Structural studies employing unhydrolysable S-linked substrate analogues have examined the [[Michaelis complex]], with the ligands found to bind in <sup>3</sup>''S''<sub>1</sub> <cite>Moremen2005</cite> and <sup>3,O</sup>''B''/<sup>3</sup>''S''<sub>1</sub> conformations <cite>Davies2012</cite>. Mannoimidazole, whose binding to other mannosidases has been shown to be consistent with good transition state mimicry <cite>Davies2008</cite>, binds GH47 in a <sup>3</sup>''H''<sub>4</sub> conformation <cite>Davies2012</cite>. Noeuromycin <cite>Davies2012</cite>, kifunensine <cite>HowellJBC2000</cite> and 1-deoxymannojirimycin <cite>HowellJBC2000</cite> all bind in a <sup>1</sup>''C''<sub>4</sub> conformation, analogous to enzyme-product complexes. Computational studies also support a <sup>3,O</sup>''B''/<sup>3</sup>''S''<sub>1</sub>&rarr;<sup>3</sup>''H''<sub>4</sub><sup>‡</sup>&rarr;<sup>1</sup>''C''<sub>4</sub> conformational itinerary <cite>Reilly2006 Reilly2007 Davies2012</cite>. Quantum mechanical/molecular modelling calculations have found that the free energy landscape of &alpha;-D-mannopyranose is perturbed on-enzyme such that the accessible conformations of the ligand are altered to those that correlate well with a <sup>3,O</sup>''B''/<sup>3</sup>''S''<sub>1</sub>&rarr;<sup>3</sup>''H''<sub>4</sub><sup>‡</sup>&rarr;<sup>1</sup>''C''<sub>4</sub> conformational itinerary <cite>Davies2012</cite>.
+GH47 mannosidases operate through an unusual <sup>3,O</sup>''B''/<sup>3</sup>''S''<sub>1</sub>&rarr;<sup>3</sup>''H''<sub>4</sub><sup>‡</sup>&rarr;<sup>1</sup>''C''<sub>4</sub> conformational itinerary. Structural studies employing unhydrolysable S-linked substrate analogues have examined the Michaelis complex, with the ligands found to bind in <sup>3</sup>''S''<sub>1</sub> <cite>Moremen2005</cite> and <sup>3,O</sup>''B''/<sup>3</sup>''S''<sub>1</sub> conformations <cite>Davies2012</cite>. Mannoimidazole, whose binding to other mannosidases has been shown to be consistent with good transition state mimicry <cite>Davies2008</cite>, binds GH47 in a <sup>3</sup>''H''<sub>4</sub> conformation <cite>Davies2012</cite>. Noeuromycin <cite>Davies2012</cite>, kifunensine <cite>HowellJBC2000</cite> and 1-deoxymannojirimycin <cite>HowellJBC2000</cite> all bind in a <sup>1</sup>''C''<sub>4</sub> conformation, analogous to enzyme-product complexes. Computational studies also support a <sup>3,O</sup>''B''/<sup>3</sup>''S''<sub>1</sub>&rarr;<sup>3</sup>''H''<sub>4</sub><sup>‡</sup>&rarr;<sup>1</sup>''C''<sub>4</sub> conformational itinerary <cite>Reilly2006 Reilly2007 Davies2012</cite>. Quantum mechanical/molecular modelling calculations have found that the free energy landscape of &alpha;-D-mannopyranose is perturbed on-enzyme such that the accessible conformations of the ligand are altered to those that correlate well with a <sup>3,O</sup>''B''/<sup>3</sup>''S''<sub>1</sub>&rarr;<sup>3</sup>''H''<sub>4</sub><sup>‡</sup>&rarr;<sup>1</sup>''C''<sub>4</sub> conformational itinerary <cite>Davies2012</cite>.
 == Catalytic Residues ==

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 {| {{Prettytable}}
 |-
-|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GHnn'''
+|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH47'''
 |-
 |'''Clan'''

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 {{CuratorApproved}}
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 |}
 <br style="clear: both" />
 == Family Firsts ==
 ;First sterochemistry determination: ''Saccharomyces cerevisiae'' &alpha;-1,2-mannosidase was shown to be [[inverting]] by <sup>1</sup>H NMR <cite>Herscovics1995</cite>.

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 GH47 enzymes are Ca<sup>2+</sup>-dependent, as demonstrated by loss of activity upon addition of the metal binding ligand EDTA, and restoration of activity through subsequent addition of Ca<sup>2+</sup> <cite>Herscovics1988</cite>. ''Exo''-&alpha;-mannosidases from [[GH38]] and [[GH92]] also require a metal ion for catalysis.
-GH47 mannosidases operate through an unusual <sup>3,O</sup>''B''/<sup>3</sup>''S''<sub>1</sub>&rarr;<sup>3</sup>''H''<sub>4</sub>‡&rarr;<sup>1</sup>''C''<sub>4</sub> conformational itinerary. Structural studies employing unhydrolysable S-linked substrate analogues have examined the [[Michaelis complex]], with the ligands found to bind in <sup>3</sup>''S''<sub>1</sub> <cite>Moremen2005</cite> and <sup>3,O</sup>''B''/<sup>3</sup>''S''<sub>1</sub> conformations <cite>Davies2012</cite>. Mannoimidazole, whose binding to other mannosidases has been shown to be consistent with good transition state mimicry <cite>Davies2008</cite>, binds GH47 in a <sup>3</sup>''H''<sub>4</sub> conformation <cite>Davies2012</cite>. Noeuromycin <cite>Davies2012</cite>, kifunensine <cite>HowellJBC2000</cite> and 1-deoxymannojirimycin <cite>HowellJBC2000</cite> all bind in a <sup>1</sup>''C''<sub>4</sub> conformation, analogous to enzyme-product complexes. Computational studies also support a <sup>3,O</sup>''B''/<sup>3</sup>''S''<sub>1</sub>&rarr;<sup>3</sup>''H''<sub>4</sub>&rarr;<sup>1</sup>''C''<sub>4</sub> conformational itinerary <cite>Reilly2006 Reilly2007 Davies2012</cite>. Quantum mechanical/molecular modelling calculations have found that the free energy landscape of &alpha;-D-mannopyranose is perturbed on-enzyme such that the accessible conformations of the ligand are altered to those that correlate well with a <sup>3,O</sup>''B''/<sup>3</sup>''S''<sub>1</sub>&rarr;<sup>3</sup>''H''<sub>4</sub>‡&rarr;<sup>1</sup>''C''<sub>4</sub> conformational itinerary <cite>Davies2012</cite>.
+GH47 mannosidases operate through an unusual <sup>3,O</sup>''B''/<sup>3</sup>''S''<sub>1</sub>&rarr;<sup>3</sup>''H''<sub>4</sub><sup>‡</sup>&rarr;<sup>1</sup>''C''<sub>4</sub> conformational itinerary. Structural studies employing unhydrolysable S-linked substrate analogues have examined the [[Michaelis complex]], with the ligands found to bind in <sup>3</sup>''S''<sub>1</sub> <cite>Moremen2005</cite> and <sup>3,O</sup>''B''/<sup>3</sup>''S''<sub>1</sub> conformations <cite>Davies2012</cite>. Mannoimidazole, whose binding to other mannosidases has been shown to be consistent with good transition state mimicry <cite>Davies2008</cite>, binds GH47 in a <sup>3</sup>''H''<sub>4</sub> conformation <cite>Davies2012</cite>. Noeuromycin <cite>Davies2012</cite>, kifunensine <cite>HowellJBC2000</cite> and 1-deoxymannojirimycin <cite>HowellJBC2000</cite> all bind in a <sup>1</sup>''C''<sub>4</sub> conformation, analogous to enzyme-product complexes. Computational studies also support a <sup>3,O</sup>''B''/<sup>3</sup>''S''<sub>1</sub>&rarr;<sup>3</sup>''H''<sub>4</sub><sup>‡</sup>&rarr;<sup>1</sup>''C''<sub>4</sub> conformational itinerary <cite>Reilly2006 Reilly2007 Davies2012</cite>. Quantum mechanical/molecular modelling calculations have found that the free energy landscape of &alpha;-D-mannopyranose is perturbed on-enzyme such that the accessible conformations of the ligand are altered to those that correlate well with a <sup>3,O</sup>''B''/<sup>3</sup>''S''<sub>1</sub>&rarr;<sup>3</sup>''H''<sub>4</sub><sup>‡</sup>&rarr;<sup>1</sup>''C''<sub>4</sub> conformational itinerary <cite>Davies2012</cite>.
 == Catalytic Residues ==
-Unequivocal assignment of catalytic residues for GH47 &alpha;-mannosidases is complicated by the presence of 3 carboxylate-containing residues all approximately 9.5 &Aring; apart from one another in the active site. Each of these could plausibly fulfill roles as catalytic residues <cite>Howell2000</cite>. Furthermore, all of the plausible catalytic residues complex water, as would be expected of the general base residue. Thus, it appears that the general acid residue transmits a proton to the glycosidic oxygen atom through a water molecule. Site-directed mutagenesis of residues in the &alpha;-mannosidase I  of ''Aspergillus saitoi'' and ''Saccharomyces cerevisiae'' predated determination of a crystal structure but demonstrated that mutation of any of the three catalytic candidates led to total or near-total loss of activity <cite>Herscovics1999 Ischishima1997</cite>. Mutagenesis of residues in human  ER &alpha;-mannosidase I, informed by the determination of the crystal structure, could not unambiguously assign the role of catalytic residues <cite>Moremen2005</cite>. Glu132 (Glu330 in human ER &alpha;-mannosidase I) in ''Saccharomyces cerevisiae'' &alpha;-mannosidase I was initially thought to be most likely candidate as the general base residue <cite>Howell2000</cite>. Subsequent crystal structures of human ER &alpha;-mannosidase I in complex with kifunensine and 1-deoxymannojirimycin bound these ligands in an unusual <sup>1</sup>''C''<sub>4</sub> conformation <cite>HowellJBC2000</cite>. These complexes were interpreted as being representative of a <sup>1</sup>''C''<sub>4</sub> Michaelis complex, making Glu330 (Glu132 in ''Saccharomyces'') incompatible with a role acting as the general base in an inverting mechanism. Thus, the general base residue was reassigned as either Glu599 or Asp463 (Glu435 and Asp275 in ''Saccharomyces'', respectively). A computational docking study found Glu599 to be the most likely general base, with Ca<sup>2+</sup> also coordinated to the nucleophilic water molecule <cite>Reilly2002</cite>. However, complexes with S-linked substrate analogues implicate a <sup>3,O</sup>''B''/<sup>3</sup>''S''<sub>1</sub>&rarr;<sup>3</sup>''H''<sub>4</sub>‡&rarr;<sup>1</sup>''C''<sub>4</sub> conformational itinerary, the reverse of that used to preclude Glu330 (Glu132 in ''Saccharomyces'') as the general base residue <cite>Moremen2005 Davies2012</cite>. The position of Glu330 (Glu132 in ''Saccharomyces'') on the opposite face of the glycan ring to the putative general base residue, Glu599 in human ER &alpha;-mannosidase I (Glu435 in ''Saccharomyces''), is consistent with a role as the general acid <cite>HowellJBC2000</cite>. Arg334 is within ion-pairing distance to Glu330 and coordinates to the same water molecule, suggestive of a possible catalytic zwitterionic arginine-carboxylate dyad <cite>Moremen2005</cite>. However, a computational docking study found Asp463 (Asp275 in ''Saccharomyces'') to be the most likely general acid, based upon the assumption that GH47 mannosidases are ''anti''-protonators <cite>Reilly2008</cite>. The low nanomolar binding of mannoimidazole to ''Ck''GH47 is consistent with ''anti''-protonation <cite>Davies2012</cite>.
+Unequivocal assignment of catalytic residues for GH47 &alpha;-mannosidases is complicated by the presence of 3 carboxylate-containing residues all approximately 9.5 &Aring; apart from one another in the active site. Each of these could plausibly fulfill roles as catalytic residues <cite>Howell2000</cite>. Furthermore, all of the plausible catalytic residues complex water, as would be expected of the general base residue. Thus, it appears that the general acid residue transmits a proton to the glycosidic oxygen atom through a water molecule. Site-directed mutagenesis of residues in the &alpha;-mannosidase I  of ''Aspergillus saitoi'' and ''Saccharomyces cerevisiae'' predated determination of a crystal structure but demonstrated that mutation of any of the three catalytic candidates led to total or near-total loss of activity <cite>Herscovics1999 Ischishima1997</cite>. Mutagenesis of residues in human  ER &alpha;-mannosidase I, informed by the determination of the crystal structure, could not unambiguously assign the role of catalytic residues <cite>Moremen2005</cite>. Glu132 (Glu330 in human ER &alpha;-mannosidase I) in ''Saccharomyces cerevisiae'' &alpha;-mannosidase I was initially thought to be most likely candidate as the general base residue <cite>Howell2000</cite>. Subsequent crystal structures of human ER &alpha;-mannosidase I in complex with kifunensine and 1-deoxymannojirimycin bound these ligands in an unusual <sup>1</sup>''C''<sub>4</sub> conformation <cite>HowellJBC2000</cite>. These complexes were interpreted as being representative of a <sup>1</sup>''C''<sub>4</sub> Michaelis complex, making Glu330 (Glu132 in ''Saccharomyces'') incompatible with a role acting as the general base in an inverting mechanism. Thus, the general base residue was reassigned as either Glu599 or Asp463 (Glu435 and Asp275 in ''Saccharomyces'', respectively). A computational docking study found Glu599 to be the most likely general base, with Ca<sup>2+</sup> also coordinated to the nucleophilic water molecule <cite>Reilly2002</cite>. However, complexes with S-linked substrate analogues implicate a <sup>3,O</sup>''B''/<sup>3</sup>''S''<sub>1</sub>&rarr;<sup>3</sup>''H''<sub>4</sub><sup>‡</sup>&rarr;<sup>1</sup>''C''<sub>4</sub> conformational itinerary, the reverse of that used to preclude Glu330 (Glu132 in ''Saccharomyces'') as the general base residue <cite>Moremen2005 Davies2012</cite>. The position of Glu330 (Glu132 in ''Saccharomyces'') on the opposite face of the glycan ring to the putative general base residue, Glu599 in human ER &alpha;-mannosidase I (Glu435 in ''Saccharomyces''), is consistent with a role as the general acid <cite>HowellJBC2000</cite>. Arg334 is within ion-pairing distance to Glu330 and coordinates to the same water molecule, suggestive of a possible catalytic zwitterionic arginine-carboxylate dyad <cite>Moremen2005</cite>. However, a computational docking study found Asp463 (Asp275 in ''Saccharomyces'') to be the most likely general acid, based upon the assumption that GH47 mannosidases are ''anti''-protonators <cite>Reilly2008</cite>. The low nanomolar binding of mannoimidazole to ''Ck''GH47 is consistent with ''anti''-protonation <cite>Davies2012</cite>.

← Older revision		Revision as of 00:58, 17 January 2013
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	== Catalytic Residues ==		== Catalytic Residues ==
−	Unequivocal assignment of catalytic residues for GH47 α-mannosidases is complicated by the presence of 3 carboxylate-containing residues all approximately 9.5 Å apart from one another in the active site. Each of these could plausibly fulfill roles as catalytic residues <cite>Howell2000</cite>. Furthermore, all of the plausible catalytic residues complex water, as would be expected of the general base residue. Thus, it appears that the general acid residue transmits a proton to the glycosidic oxygen atom through a water molecule. Site directed mutagenesis of residues in the α-mannosidase I of ''Aspergillus saitoi'' and ''Saccharomyces cerevisiae'' predated determination of a crystal structure but demonstrated that mutation of any of the three catalytic candidates led to total or near-total loss of activity <cite>Herscovics1999 Ischishima1997</cite>. Mutagenesis of residues in human ER α-mannosidase I, informed by the determination of the crystal structure, could not unambiguously assign the role of catalytic residues <cite>Moremen2005</cite>. Glu132 (Glu330 in human ER α-mannosidase I) in ''Saccharomyces cerevisiae'' α-mannosidase I was initially thought to be most likely candidate as the general base residue <cite>Howell2000</cite>. Subsequent crystal structures of human ER α-mannosidase I in complex with kifunensine and 1-deoxymannojirimycin bound these ligands in an unusual <sup>1</sup>''C''<sub>4</sub> conformation <cite>HowellJBC2000</cite>. These complexes were interpreted as being representative of a <sup>1</sup>''C''<sub>4</sub> Michaelis complex, making Glu330 (Glu132 in ''Saccharomyces'') incompatible with a role acting as the general base in an inverting mechanism. Thus, the general base residue was reassigned as either Glu599 or Asp463 (Glu435 and Asp275 in ''Saccharomyces'', respectively). A computational docking study found Glu599 to be the most likely general base, with Ca<sup>2+</sup> also coordinated to the nucleophilic water molecule <cite>Reilly2002</cite>. However, complexes with S-linked substrate analogues implicate a <sup>3,O</sup>''B''/<sup>3</sup>''S''<sub>1</sub>→<sup>3</sup>''H''<sub>4</sub>→<sup>1</sup>''C''<sub>4</sub> conformational itinerary, the reverse of that used to preclude Glu330 (Glu132 in ''Saccharomyces'') as the general base residue <cite>Moremen2005 Davies2012</cite>. The position of Glu330 (Glu132 in ''Saccharomyces'') on the opposite face of the glycan ring to the putative general base residue, Glu599 in human ER α-mannosidase I (Glu435 in ''Saccharomyces''), is consistent with a role as the general acid <cite>HowellJBC2000</cite>. Arg334 is within ion-pairing distance to Glu330 and coordinates to the same water molecule, suggestive of a possible catalytic zwitterionic arginine-carboxylate dyad <cite>Moremen2005</cite>. However, a computational docking study found Asp463 (Asp275 in ''Saccharomyces'') to be the most likely general acid, based upon the assumption that GH47 mannosidases are ''anti''-protonators <cite>Reilly2008</cite>. The low nanomolar binding of mannoimidazole to ''Ck''GH47 is consistent with ''anti''-protonation <cite>Davies2012</cite>.	+	Unequivocal assignment of catalytic residues for GH47 α-mannosidases is complicated by the presence of 3 carboxylate-containing residues all approximately 9.5 Å apart from one another in the active site. Each of these could plausibly fulfill roles as catalytic residues <cite>Howell2000</cite>. Furthermore, all of the plausible catalytic residues complex water, as would be expected of the general base residue. Thus, it appears that the general acid residue transmits a proton to the glycosidic oxygen atom through a water molecule. Site-directed mutagenesis of residues in the α-mannosidase I of ''Aspergillus saitoi'' and ''Saccharomyces cerevisiae'' predated determination of a crystal structure but demonstrated that mutation of any of the three catalytic candidates led to total or near-total loss of activity <cite>Herscovics1999 Ischishima1997</cite>. Mutagenesis of residues in human ER α-mannosidase I, informed by the determination of the crystal structure, could not unambiguously assign the role of catalytic residues <cite>Moremen2005</cite>. Glu132 (Glu330 in human ER α-mannosidase I) in ''Saccharomyces cerevisiae'' α-mannosidase I was initially thought to be most likely candidate as the general base residue <cite>Howell2000</cite>. Subsequent crystal structures of human ER α-mannosidase I in complex with kifunensine and 1-deoxymannojirimycin bound these ligands in an unusual <sup>1</sup>''C''<sub>4</sub> conformation <cite>HowellJBC2000</cite>. These complexes were interpreted as being representative of a <sup>1</sup>''C''<sub>4</sub> Michaelis complex, making Glu330 (Glu132 in ''Saccharomyces'') incompatible with a role acting as the general base in an inverting mechanism. Thus, the general base residue was reassigned as either Glu599 or Asp463 (Glu435 and Asp275 in ''Saccharomyces'', respectively). A computational docking study found Glu599 to be the most likely general base, with Ca<sup>2+</sup> also coordinated to the nucleophilic water molecule <cite>Reilly2002</cite>. However, complexes with S-linked substrate analogues implicate a <sup>3,O</sup>''B''/<sup>3</sup>''S''<sub>1</sub>→<sup>3</sup>''H''<sub>4</sub>→<sup>1</sup>''C''<sub>4</sub> conformational itinerary, the reverse of that used to preclude Glu330 (Glu132 in ''Saccharomyces'') as the general base residue <cite>Moremen2005 Davies2012</cite>. The position of Glu330 (Glu132 in ''Saccharomyces'') on the opposite face of the glycan ring to the putative general base residue, Glu599 in human ER α-mannosidase I (Glu435 in ''Saccharomyces''), is consistent with a role as the general acid <cite>HowellJBC2000</cite>. Arg334 is within ion-pairing distance to Glu330 and coordinates to the same water molecule, suggestive of a possible catalytic zwitterionic arginine-carboxylate dyad <cite>Moremen2005</cite>. However, a computational docking study found Asp463 (Asp275 in ''Saccharomyces'') to be the most likely general acid, based upon the assumption that GH47 mannosidases are ''anti''-protonators <cite>Reilly2008</cite>. The low nanomolar binding of mannoimidazole to ''Ck''GH47 is consistent with ''anti''-protonation <cite>Davies2012</cite>.