Glycoside Hydrolase Family 117 - Revision history

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

2021-12-18T21:14:24Z

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

Harry Brumer: removed old biblio references

2013-06-04T15:36:02Z

removed old biblio references

Jan-Hendrik Hehemann at 05:19, 4 July 2012

2012-07-04T05:19:42Z

Jan-Hendrik Hehemann at 05:19, 4 July 2012

2012-07-04T05:19:21Z

Jan-Hendrik Hehemann at 22:10, 2 July 2012

2012-07-02T22:10:31Z

Harry Brumer: /* Kinetics and Mechanism */

2012-06-28T22:54:39Z

Kinetics and Mechanism

Etienne Rebuffet: /* Kinetics and Mechanism */

2012-06-26T09:06:04Z

Kinetics and Mechanism

Etienne Rebuffet at 09:04, 26 June 2012

2012-06-26T09:04:48Z

Etienne Rebuffet: /* References */

2012-06-26T08:58:51Z

References

Etienne Rebuffet: /* Kinetics and Mechanism */

2012-06-26T08:56:55Z

Kinetics and Mechanism

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
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-* [[Author]]: ^^^Etienne Rebuffet^^^
+* [[Author]]: [[User:Etienne Rebuffet|Etienne Rebuffet]]
-* [[Responsible Curator]]:  ^^^Mirjam Czjzek^^^
+* [[Responsible Curator]]:  [[User:Mirjam Czjzek|Mirjam Czjzek]]
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 #Hehemann2012 pmid=22393053
 </biblio>
 [[Category:Glycoside Hydrolase Families|GH117]]

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 == Three-dimensional structures ==
-Three crystal structures of GH117 family have been reported. Two are enzymes from marine bacteria, one from ''Saccharophagus degradans''  (PDB: [{{PDBlink}}3r4y 3R4Y]) <cite>Ha2011</cite> and one from ''Zobellia galactanivorans'' (PDB: [{{PDBlink}}3p2n 3P2N]) <cite>Rebuffet2011</cite>, the third one is from the human gut bacterium''Bacteroidetes plebeius''  (PDB: [{{PDBlink}}4ak5 4AK5]) <cite>Hehemann2012</cite>.
+Three crystal structures of GH117 family have been reported. Two are enzymes from marine bacteria, one from ''Saccharophagus degradans''  (PDB: [{{PDBlink}}3r4y 3R4Y]) <cite>Ha2011</cite> and one from ''Zobellia galactanivorans'' (PDB: [{{PDBlink}}3p2n 3P2N]) <cite>Rebuffet2011</cite>, the third one is from the human gut bacterium ''Bacteroidetes plebeius''  (PDB: [{{PDBlink}}4ak5 4AK5]) <cite>Hehemann2012</cite>.
 GH117 adopts a five-bladed β-propeller fold and forms a dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 3) <cite>Rebuffet2011</cite>. Interestingly, previous sequences reported from ''Vibrio sp.'' JT0107 and ''Bacillus sp.'' MK03 contain the conserved domain-swapping signature SxAxxR in the HTH domain. Consistently, these proteins were reported to form multimers (a dimer and an octamer respectively), based on calibrated gel filtration estimations <cite>Sugano1994 Suzuki2002 </cite>. In contrast, RB13146 (Clade B) lacks the domain-swapping signature, in which the crucial residues are missing. This enzyme from ''R. baltica'' thus likely occurs as a monomer and may represent an ‘ancestral’ form of the GH117 family, which would be limited to the catalytic β-propeller domain <cite>Rebuffet2011</cite>.
 Structure of ''Sd''NABH and ''Bp''GH117 possess a ordered C terminus part which also interact with the adjacent monomer <cite>Ha2011 Hehemann2012</cite>. Moreover in the case of ''Bp''GH117, His-392 from the C terminus of the monomer A participate in the substrate binding in the binding pocket of monomer B, and aims versa <cite>Hehemann2012</cite>.

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 == Three-dimensional structures ==
-Three crystal structures of GH117 family have been reported. Two are enzymes from marine bacteria, one from ''Saccharophagus degradans''  (PDB: [{{PDBlink}}3r4y 3R4Y]) <cite>Ha2011</cite> and one from ''Zobellia galactanivorans'' (PDB: [{{PDBlink}}3p2n 3P2N]) <cite>Rebuffet2011</cite>, the third one is from the human gut bacteria ''Bacteroidetes plebeius''  (PDB: [{{PDBlink}}4ak5 4AK5]) <cite>Hehemann2012</cite>.
+Three crystal structures of GH117 family have been reported. Two are enzymes from marine bacteria, one from ''Saccharophagus degradans''  (PDB: [{{PDBlink}}3r4y 3R4Y]) <cite>Ha2011</cite> and one from ''Zobellia galactanivorans'' (PDB: [{{PDBlink}}3p2n 3P2N]) <cite>Rebuffet2011</cite>, the third one is from the human gut bacterium''Bacteroidetes plebeius''  (PDB: [{{PDBlink}}4ak5 4AK5]) <cite>Hehemann2012</cite>.
 GH117 adopts a five-bladed β-propeller fold and forms a dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 3) <cite>Rebuffet2011</cite>. Interestingly, previous sequences reported from ''Vibrio sp.'' JT0107 and ''Bacillus sp.'' MK03 contain the conserved domain-swapping signature SxAxxR in the HTH domain. Consistently, these proteins were reported to form multimers (a dimer and an octamer respectively), based on calibrated gel filtration estimations <cite>Sugano1994 Suzuki2002 </cite>. In contrast, RB13146 (Clade B) lacks the domain-swapping signature, in which the crucial residues are missing. This enzyme from ''R. baltica'' thus likely occurs as a monomer and may represent an ‘ancestral’ form of the GH117 family, which would be limited to the catalytic β-propeller domain <cite>Rebuffet2011</cite>.
 Structure of ''Sd''NABH and ''Bp''GH117 possess a ordered C terminus part which also interact with the adjacent monomer <cite>Ha2011 Hehemann2012</cite>. Moreover in the case of ''Bp''GH117, His-392 from the C terminus of the monomer A participate in the substrate binding in the binding pocket of monomer B, and aims versa <cite>Hehemann2012</cite>.

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 == Kinetics and Mechanism ==
-The stereochemical outcome of members of glycoside hydrolase family GH117 is still not determined experimentally. Nevertheless a mechanism based on the structure of an inactive mutant (''Bp''GH117 E303Q) complexed to a neoagarobiose have been proposed <cite>Hehemann2012</cite> (Figure 2). In this unusual inverting catalytic mechanism an aspartic acid acting as the base and a histidine acting as the acid.  An analogous Asp-His dyad has been similarly reported to act as the general base catalyst in the retaining mechanism of select [[GH3]] members <cite>Litzinger2010</cite>.
+The stereochemical outcome of members of glycoside hydrolase family GH117 is still not determined experimentally. Nevertheless a mechanism based on the structure of an inactive mutant (''Bp''GH117 E303Q) complexed to a neoagarobiose has been proposed <cite>Hehemann2012</cite> (Figure 2). In this unusual inverting catalytic mechanism an aspartic acid acting as the base and a histidine acting as the acid.  An analogous Asp-His dyad has been similarly reported to act as the general base catalyst in the retaining mechanism of select [[GH3]] members <cite>Litzinger2010</cite>.
 [[File:gh117mechajan2012.jpg|thumb|left|800px|Figure 2: Proposed mechanism of α-1,3-L-(3,6-anhydro)-galactosidase. From <cite>Hehemann2012</cite>]]
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 #Sugano1994 pmid=7961439
 #Suzuki2002 pmid=16233232
 #Rebuffet2011 pmid=21332624
 #Ha2011 pmid=21810409