CAZypedia - User contributions [en-ca]

Glycoside Hydrolase Family 117

2012-06-26T09:06:04Z

Etienne Rebuffet: /* Kinetics and Mechanism */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Ha2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific
<cite>Rebuffet2011</cite>.
[[Image:GH117_Phylogeny.png|thumb|left|150px|Figure 1: Phylogeny of GH117 family (''click to enlarge''). From <cite>Rebuffet2011</cite>.]]
<br style="clear: both" />

== 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. The Asp-His dyad was already reported in the retaining mechanism of the [[GH3]] family <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>]]
<br style="clear: both" />
Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind divalent cation, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be Asp-90 as the base and His-302 as the acid ''Bp''GH117 numbering) <cite>Hehemann2012</cite>.

== 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>.
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>.
[[Image:Agha_structure.png|thumb|left|600px|Figure 3: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.]]
<br style="clear: both" />

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Litzinger2010 pmid=20826810
#Rebuffet2011 pmid=21332624
#Ha2011 pmid=21810409
#Hehemann2012 pmid=22393053
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-26T09:04:48Z

Etienne Rebuffet:

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Ha2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific
<cite>Rebuffet2011</cite>.
[[Image:GH117_Phylogeny.png|thumb|left|150px|Figure 1: Phylogeny of GH117 family (''click to enlarge''). From <cite>Rebuffet2011</cite>.]]
<br style="clear: both" />

== 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. The Asp-His dyad was already reported in the retaining mechanism of the ([[GH3]]) family <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>]]
<br style="clear: both" />
Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind divalent cation, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be Asp-90 as the base and His-302 as the acid ''Bp''GH117 numbering) <cite>Hehemann2012</cite>.

== 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>.
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>.
[[Image:Agha_structure.png|thumb|left|600px|Figure 3: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.]]
<br style="clear: both" />

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Litzinger2010 pmid=20826810
#Rebuffet2011 pmid=21332624
#Ha2011 pmid=21810409
#Hehemann2012 pmid=22393053
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-26T08:58:51Z

Etienne Rebuffet: /* References */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Ha2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific
<cite>Rebuffet2011</cite>.
[[Image:GH117_Phylogeny.png|thumb|left|150px|Figure 1: Phylogeny of GH117 family (''click to enlarge''). From <cite>Rebuffet2011</cite>.]]
<br style="clear: both" />

== 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. The Asp-His dyad was already reported in the retaining mechanism of the GH3 family <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>]]
<br style="clear: both" />
Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind divalent cation, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be Asp-90 as the base and His-302 as the acid ''Bp''GH117 numbering) <cite>Hehemann2012</cite>.

== 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>.
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>.
[[Image:Agha_structure.png|thumb|left|600px|Figure 3: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.]]
<br style="clear: both" />

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Litzinger2010 pmid=20826810
#Rebuffet2011 pmid=21332624
#Ha2011 pmid=21810409
#Hehemann2012 pmid=22393053
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-26T08:56:55Z

Etienne Rebuffet: /* Kinetics and Mechanism */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Ha2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific
<cite>Rebuffet2011</cite>.
[[Image:GH117_Phylogeny.png|thumb|left|150px|Figure 1: Phylogeny of GH117 family (''click to enlarge''). From <cite>Rebuffet2011</cite>.]]
<br style="clear: both" />

== 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. The Asp-His dyad was already reported in the retaining mechanism of the GH3 family <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>]]
<br style="clear: both" />
Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind divalent cation, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be Asp-90 as the base and His-302 as the acid ''Bp''GH117 numbering) <cite>Hehemann2012</cite>.

== 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>.
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>.
[[Image:Agha_structure.png|thumb|left|600px|Figure 3: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.]]
<br style="clear: both" />

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Ha2011 pmid=21810409
#Hehemann2012 pmid=22393053
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-25T12:25:28Z

Etienne Rebuffet: /* Three-dimensional structures */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Ha2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== 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.

[[File:gh117mechajan2012.jpg|800x200px|frame|none|alt=alt text|Figure 2: Proposed mechanism of α-1,3-L-(3,6-anhydro)-galactosidase. From <cite>Hehemann2012</cite>]]

Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind divalent cation, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be Asp-90 as the base and His-302 as the acid ''Bp''GH117 numbering) <cite>Hehemann2012</cite>.

== 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>.
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>.
[[Image:Agha_structure.png|thumb|Figure 3: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Ha2011 pmid=21810409
#Hehemann2012 pmid=22393053
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-25T12:23:25Z

Etienne Rebuffet: /* Kinetics and Mechanism */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Ha2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== 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.

[[File:gh117mechajan2012.jpg|800x200px|frame|none|alt=alt text|Figure 2: Proposed mechanism of α-1,3-L-(3,6-anhydro)-galactosidase. From <cite>Hehemann2012</cite>]]

Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind divalent cation, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be Asp-90 as the base and His-302 as the acid ''Bp''GH117 numbering) <cite>Hehemann2012</cite>.

== 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>.
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>.
[[Image:Agha_structure.png|thumb|Figure 3: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Ha2011 pmid=21810409
#Hehemann2012 pmid=22393053
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-25T11:00:19Z

Etienne Rebuffet: /* Kinetics and Mechanism */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Ha2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== 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 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.

[[File:gh117mechajan2012.jpg|800x200px|frame|none|alt=alt text|Figure 2: Proposed mechanism of α-1,3-L-(3,6-anhydro)-galactosidase. From <cite>Hehemann2012</cite>]]

Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind divalent cation, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be Asp-90 as the base and His-302 as the acid ''Bp''GH117 numbering) <cite>Hehemann2012</cite>.

== 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>.
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>.
[[Image:Agha_structure.png|thumb|Figure 3: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Ha2011 pmid=21810409
#Hehemann2012 pmid=22393053
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-25T10:57:24Z

Etienne Rebuffet: /* Three-dimensional structures */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Ha2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== 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 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.

[[File:gh117mechajan2012.jpg|800x200px|frame|none|alt=alt text|Figure 2: Proposed mechanism of α-1,3-L-(3,6-anhydro)-galactosidase. From <cite>Hehemann2012</cite>]]

Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind divalent cation, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be Asp-90 as the base and His-302 as the acid ''Bp''GH117 numbering) <cite>Hehemann2012</cite>.

== 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>.
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>.
[[Image:Agha_structure.png|thumb|Figure 3: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Ha2011 pmid=21810409
#Hehemann2012 pmid=22393053
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-25T10:53:55Z

Etienne Rebuffet: /* Three-dimensional structures */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Ha2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== 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 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.

[[File:gh117mechajan2012.jpg|800x200px|frame|none|alt=alt text|Figure 2: Proposed mechanism of α-1,3-L-(3,6-anhydro)-galactosidase. From <cite>Hehemann2012</cite>]]

Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind divalent cation, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be Asp-90 as the base and His-302 as the acid ''Bp''GH117 numbering) <cite>Hehemann2012</cite>.

== 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>.
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 posse 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 monomer A participate in the substrate binding in the binding pocket of monomer B <cite>Hehemann2012</cite>.
[[Image:Agha_structure.png|thumb|Figure 3: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Ha2011 pmid=21810409
#Hehemann2012 pmid=22393053
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-25T10:31:38Z

Etienne Rebuffet: /* Catalytic Residues */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Ha2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== 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 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.

[[File:gh117mechajan2012.jpg|800x200px|frame|none|alt=alt text|Figure 2: Proposed mechanism of α-1,3-L-(3,6-anhydro)-galactosidase. From <cite>Hehemann2012</cite>]]

Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind divalent cation, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be Asp-90 as the base and His-302 as the acid ''Bp''GH117 numbering) <cite>Hehemann2012</cite>.

== 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>.
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>.
[[Image:Agha_structure.png|thumb|Figure 3: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Ha2011 pmid=21810409
#Hehemann2012 pmid=22393053
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-25T10:30:19Z

Etienne Rebuffet: /* Catalytic Residues */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Ha2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== 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 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.

[[File:gh117mechajan2012.jpg|800x200px|frame|none|alt=alt text|Figure 2: Proposed mechanism of α-1,3-L-(3,6-anhydro)-galactosidase. From <cite>Hehemann2012</cite>]]

Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind divalent cation, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be Asp-90 as the base and His-302 as the acid ("Bp"GH117 numbering) <cite>Hehemann2012</cite>.

== 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>.
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>.
[[Image:Agha_structure.png|thumb|Figure 3: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Ha2011 pmid=21810409
#Hehemann2012 pmid=22393053
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-25T10:29:45Z

Etienne Rebuffet: /* Three-dimensional structures */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Ha2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== 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 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.

[[File:gh117mechajan2012.jpg|800x200px|frame|none|alt=alt text|Figure 2: Proposed mechanism of α-1,3-L-(3,6-anhydro)-galactosidase. From <cite>Hehemann2012</cite>]]

Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind divalent cation, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be Asp-90 as the base and His-302 as the acid (BpGH117 numbering) <cite>Hehemann2012</cite>.

== 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>.
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>.
[[Image:Agha_structure.png|thumb|Figure 3: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Ha2011 pmid=21810409
#Hehemann2012 pmid=22393053
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-25T10:22:36Z

Etienne Rebuffet: /* Three-dimensional structures */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Ha2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== 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 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.

[[File:gh117mechajan2012.jpg|800x200px|frame|none|alt=alt text|Figure 2: Proposed mechanism of α-1,3-L-(3,6-anhydro)-galactosidase. From <cite>Hehemann2012</cite>]]

Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind divalent cation, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be Asp-90 as the base and His-302 as the acid (BpGH117 numbering) <cite>Hehemann2012</cite>.

== 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>.
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 2) <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>.
[[Image:Agha_structure.png|thumb|Figure 2: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Ha2011 pmid=21810409
#Hehemann2012 pmid=22393053
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-25T10:17:49Z

Etienne Rebuffet: /* Three-dimensional structures */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Ha2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== 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 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.

[[File:gh117mechajan2012.jpg|800x200px|frame|none|alt=alt text|Figure 2: Proposed mechanism of α-1,3-L-(3,6-anhydro)-galactosidase. From <cite>Hehemann2012</cite>]]

Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind divalent cation, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be Asp-90 as the base and His-302 as the acid (BpGH117 numbering) <cite>Hehemann2012</cite>.

== Three-dimensional structures ==
At the moment 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>.
AhgA adopts a five-bladed β-propeller fold and forms a dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 2) <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>.
[[Image:Agha_structure.png|thumb|Figure 2: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Ha2011 pmid=21810409
#Hehemann2012 pmid=22393053
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-25T10:16:23Z

Etienne Rebuffet: /* Three-dimensional structures */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Ha2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== 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 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.

[[File:gh117mechajan2012.jpg|800x200px|frame|none|alt=alt text|Figure 2: Proposed mechanism of α-1,3-L-(3,6-anhydro)-galactosidase. From <cite>Hehemann2012</cite>]]

Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind divalent cation, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be Asp-90 as the base and His-302 as the acid (BpGH117 numbering) <cite>Hehemann2012</cite>.

== Three-dimensional structures ==
At the moment 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>.
AhgA adopts a five-bladed β-propeller fold and forms a dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 2) <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>.
[[Image:Agha_structure.png|thumb|Figure 2: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Ha2011 pmid=21810409
#Hehemann2012 pmid=22393053
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-25T10:00:35Z

Etienne Rebuffet: /* Kinetics and Mechanism */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Ha2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== 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 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.

[[File:gh117mechajan2012.jpg|800x200px|frame|none|alt=alt text|Figure 2: Proposed mechanism of α-1,3-L-(3,6-anhydro)-galactosidase. From <cite>Hehemann2012</cite>]]

Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind divalent cation, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be Asp-90 as the base and His-302 as the acid (BpGH117 numbering) <cite>Hehemann2012</cite>.

== Three-dimensional structures ==
At the moment three structures of GH117 family have been solved. Two are enzymes from marine bacteria, one from ''Saccharophagus degradans'' <cite>Ha2011</cite> and one from ''Zobellia galactanivorans'' <cite>Rebuffet2011</cite>, the third one is from the human gut bacteria ''Bacteroidetes plebeius''<cite>Hehemann2012</cite>. A crystal structure has only been reported for the α-1,3-L-(3,6-anhydro)-galactosidase (AhgA, Zg4663) from ''Z. galactanivorans'' (PDB: [{{PDBlink}}3p2n 3p2n]) <cite>Rebuffet2011</cite>.
AhgA adopts a five-bladed β-propeller fold and forms a dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 2) <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>.
[[Image:Agha_structure.png|thumb|Figure 2: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Ha2011 pmid=21810409
#Hehemann2012 pmid=22393053
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-25T09:46:14Z

Etienne Rebuffet: /* References */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Ha2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== 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 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.

[[File:gh117mechajan2012.jpg|800x200px|frame|none|alt=alt text|Figure 2: Proposed mechanism of α-1,3-L-(3,6-anhydro)-galactosidase. From <cite>Hehemann2012</cite>]]

Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind zinc ions, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be Asp-90 as the base and His-302 as the acid (BpGH117 numbering) <cite>Hehemann2012</cite>.

== Three-dimensional structures ==
At the moment three structures of GH117 family have been solved. Two are enzymes from marine bacteria, one from ''Saccharophagus degradans'' <cite>Ha2011</cite> and one from ''Zobellia galactanivorans'' <cite>Rebuffet2011</cite>, the third one is from the human gut bacteria ''Bacteroidetes plebeius''<cite>Hehemann2012</cite>. A crystal structure has only been reported for the α-1,3-L-(3,6-anhydro)-galactosidase (AhgA, Zg4663) from ''Z. galactanivorans'' (PDB: [{{PDBlink}}3p2n 3p2n]) <cite>Rebuffet2011</cite>.
AhgA adopts a five-bladed β-propeller fold and forms a dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 2) <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>.
[[Image:Agha_structure.png|thumb|Figure 2: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Ha2011 pmid=21810409
#Hehemann2012 pmid=22393053
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-25T09:42:17Z

Etienne Rebuffet: /* Three-dimensional structures */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Ha2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== 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 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.

[[File:gh117mechajan2012.jpg|800x200px|frame|none|alt=alt text|Figure 2: Proposed mechanism of α-1,3-L-(3,6-anhydro)-galactosidase. From <cite>Hehemann2012</cite>]]

Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind zinc ions, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be Asp-90 as the base and His-302 as the acid (BpGH117 numbering) <cite>Hehemann2012</cite>.

== Three-dimensional structures ==
At the moment three structures of GH117 family have been solved. Two are enzymes from marine bacteria, one from ''Saccharophagus degradans'' <cite>Ha2011</cite> and one from ''Zobellia galactanivorans'' <cite>Rebuffet2011</cite>, the third one is from the human gut bacteria ''Bacteroidetes plebeius''<cite>Hehemann2012</cite>. A crystal structure has only been reported for the α-1,3-L-(3,6-anhydro)-galactosidase (AhgA, Zg4663) from ''Z. galactanivorans'' (PDB: [{{PDBlink}}3p2n 3p2n]) <cite>Rebuffet2011</cite>.
AhgA adopts a five-bladed β-propeller fold and forms a dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 2) <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>.
[[Image:Agha_structure.png|thumb|Figure 2: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Lee2009 pmid=20054134
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-25T09:31:25Z

Etienne Rebuffet: /* Kinetics and Mechanism */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Ha2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== 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 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.

[[File:gh117mechajan2012.jpg|800x200px|frame|none|alt=alt text|Figure 2: Proposed mechanism of α-1,3-L-(3,6-anhydro)-galactosidase. From <cite>Hehemann2012</cite>]]

Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind zinc ions, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be Asp-90 as the base and His-302 as the acid (BpGH117 numbering) <cite>Hehemann2012</cite>.

== Three-dimensional structures ==
At the moment two members of GH117 family have been crystallized. Both are enzymes from marine bacteria, one from ''Saccharophagus degradans'' <cite>Lee2009</cite> and one from ''Zobellia galactanivorans'' <cite>Rebuffet2011</cite>. A crystal structure has only been reported for the α-1,3-L-(3,6-anhydro)-galactosidase (AhgA, Zg4663) from ''Z. galactanivorans'' (PDB: [{{PDBlink}}3p2n 3p2n]) <cite>Rebuffet2011</cite>.
AhgA adopts a five-bladed β-propeller fold and forms a dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 2) <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>.
[[Image:Agha_structure.png|thumb|Figure 2: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Lee2009 pmid=20054134
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-25T09:30:39Z

Etienne Rebuffet: /* Catalytic Residues */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Ha2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== 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 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.

[[File:gh117mechajan2012.jpg|800x200px|frame|none|alt=alt text|Proposed mechanism of α-1,3-L-(3,6-anhydro)-galactosidase. From <cite>Hehemann2012</cite>]]

Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind zinc ions, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be Asp-90 as the base and His-302 as the acid (BpGH117 numbering) <cite>Hehemann2012</cite>.

== Three-dimensional structures ==
At the moment two members of GH117 family have been crystallized. Both are enzymes from marine bacteria, one from ''Saccharophagus degradans'' <cite>Lee2009</cite> and one from ''Zobellia galactanivorans'' <cite>Rebuffet2011</cite>. A crystal structure has only been reported for the α-1,3-L-(3,6-anhydro)-galactosidase (AhgA, Zg4663) from ''Z. galactanivorans'' (PDB: [{{PDBlink}}3p2n 3p2n]) <cite>Rebuffet2011</cite>.
AhgA adopts a five-bladed β-propeller fold and forms a dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 2) <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>.
[[Image:Agha_structure.png|thumb|Figure 2: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Lee2009 pmid=20054134
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-25T09:28:06Z

Etienne Rebuffet: /* Substrate specificities */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Ha2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== 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 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.

[[File:gh117mechajan2012.jpg|800x200px|frame|none|alt=alt text|Proposed mechanism of α-1,3-L-(3,6-anhydro)-galactosidase. From <cite>Hehemann2012</cite>]]

Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind zinc ions, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be two of the three acidic residues Asp-97, Asp-252 and Glu-310 (Zg4663 numbering) <cite>Rebuffet2011</cite>.

== Three-dimensional structures ==
At the moment two members of GH117 family have been crystallized. Both are enzymes from marine bacteria, one from ''Saccharophagus degradans'' <cite>Lee2009</cite> and one from ''Zobellia galactanivorans'' <cite>Rebuffet2011</cite>. A crystal structure has only been reported for the α-1,3-L-(3,6-anhydro)-galactosidase (AhgA, Zg4663) from ''Z. galactanivorans'' (PDB: [{{PDBlink}}3p2n 3p2n]) <cite>Rebuffet2011</cite>.
AhgA adopts a five-bladed β-propeller fold and forms a dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 2) <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>.
[[Image:Agha_structure.png|thumb|Figure 2: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Lee2009 pmid=20054134
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-25T09:14:28Z

Etienne Rebuffet: /* Kinetics and Mechanism */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== 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 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.

[[File:gh117mechajan2012.jpg|800x200px|frame|none|alt=alt text|Proposed mechanism of α-1,3-L-(3,6-anhydro)-galactosidase. From <cite>Hehemann2012</cite>]]

Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind zinc ions, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be two of the three acidic residues Asp-97, Asp-252 and Glu-310 (Zg4663 numbering) <cite>Rebuffet2011</cite>.

== Three-dimensional structures ==
At the moment two members of GH117 family have been crystallized. Both are enzymes from marine bacteria, one from ''Saccharophagus degradans'' <cite>Lee2009</cite> and one from ''Zobellia galactanivorans'' <cite>Rebuffet2011</cite>. A crystal structure has only been reported for the α-1,3-L-(3,6-anhydro)-galactosidase (AhgA, Zg4663) from ''Z. galactanivorans'' (PDB: [{{PDBlink}}3p2n 3p2n]) <cite>Rebuffet2011</cite>.
AhgA adopts a five-bladed β-propeller fold and forms a dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 2) <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>.
[[Image:Agha_structure.png|thumb|Figure 2: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Lee2009 pmid=20054134
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-25T09:13:17Z

Etienne Rebuffet: /* Kinetics and Mechanism */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== 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 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.

[[File:gh117mechajan2012.jpg|800x200px|border|text|Proposed mechanism of α-1,3-L-(3,6-anhydro)-galactosidase. From <cite>Hehemann2012</cite>]]

Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind zinc ions, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be two of the three acidic residues Asp-97, Asp-252 and Glu-310 (Zg4663 numbering) <cite>Rebuffet2011</cite>.

== Three-dimensional structures ==
At the moment two members of GH117 family have been crystallized. Both are enzymes from marine bacteria, one from ''Saccharophagus degradans'' <cite>Lee2009</cite> and one from ''Zobellia galactanivorans'' <cite>Rebuffet2011</cite>. A crystal structure has only been reported for the α-1,3-L-(3,6-anhydro)-galactosidase (AhgA, Zg4663) from ''Z. galactanivorans'' (PDB: [{{PDBlink}}3p2n 3p2n]) <cite>Rebuffet2011</cite>.
AhgA adopts a five-bladed β-propeller fold and forms a dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 2) <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>.
[[Image:Agha_structure.png|thumb|Figure 2: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Lee2009 pmid=20054134
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-25T09:09:54Z

Etienne Rebuffet: /* Kinetics and Mechanism */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== 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 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.

[[File:gh117mechajan2012.jpg|800x200px|text|Proposed mechanism of α-1,3-L-(3,6-anhydro)-galactosidase. From <cite>Hehemann2012</cite>]]

Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind zinc ions, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be two of the three acidic residues Asp-97, Asp-252 and Glu-310 (Zg4663 numbering) <cite>Rebuffet2011</cite>.

== Three-dimensional structures ==
At the moment two members of GH117 family have been crystallized. Both are enzymes from marine bacteria, one from ''Saccharophagus degradans'' <cite>Lee2009</cite> and one from ''Zobellia galactanivorans'' <cite>Rebuffet2011</cite>. A crystal structure has only been reported for the α-1,3-L-(3,6-anhydro)-galactosidase (AhgA, Zg4663) from ''Z. galactanivorans'' (PDB: [{{PDBlink}}3p2n 3p2n]) <cite>Rebuffet2011</cite>.
AhgA adopts a five-bladed β-propeller fold and forms a dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 2) <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>.
[[Image:Agha_structure.png|thumb|Figure 2: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Lee2009 pmid=20054134
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-25T09:08:20Z

Etienne Rebuffet: /* Kinetics and Mechanism */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== 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 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.

[[File:gh117mechajan2012.jpg|800x200px|Proposed mechanism of α-1,3-L-(3,6-anhydro)-galactosidase. From <cite>Hehemann2012</cite>]]

Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind zinc ions, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be two of the three acidic residues Asp-97, Asp-252 and Glu-310 (Zg4663 numbering) <cite>Rebuffet2011</cite>.

== Three-dimensional structures ==
At the moment two members of GH117 family have been crystallized. Both are enzymes from marine bacteria, one from ''Saccharophagus degradans'' <cite>Lee2009</cite> and one from ''Zobellia galactanivorans'' <cite>Rebuffet2011</cite>. A crystal structure has only been reported for the α-1,3-L-(3,6-anhydro)-galactosidase (AhgA, Zg4663) from ''Z. galactanivorans'' (PDB: [{{PDBlink}}3p2n 3p2n]) <cite>Rebuffet2011</cite>.
AhgA adopts a five-bladed β-propeller fold and forms a dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 2) <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>.
[[Image:Agha_structure.png|thumb|Figure 2: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Lee2009 pmid=20054134
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-25T09:05:03Z

Etienne Rebuffet: /* Kinetics and Mechanism */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== 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 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.

[[File:gh117mechajan2012.jpg|800x200px|thumb|Proposed mechanism of α-1,3-L-(3,6-anhydro)-galactosidase. From <cite>Hehemann2012</cite>]]

Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind zinc ions, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be two of the three acidic residues Asp-97, Asp-252 and Glu-310 (Zg4663 numbering) <cite>Rebuffet2011</cite>.

== Three-dimensional structures ==
At the moment two members of GH117 family have been crystallized. Both are enzymes from marine bacteria, one from ''Saccharophagus degradans'' <cite>Lee2009</cite> and one from ''Zobellia galactanivorans'' <cite>Rebuffet2011</cite>. A crystal structure has only been reported for the α-1,3-L-(3,6-anhydro)-galactosidase (AhgA, Zg4663) from ''Z. galactanivorans'' (PDB: [{{PDBlink}}3p2n 3p2n]) <cite>Rebuffet2011</cite>.
AhgA adopts a five-bladed β-propeller fold and forms a dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 2) <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>.
[[Image:Agha_structure.png|thumb|Figure 2: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Lee2009 pmid=20054134
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-25T09:01:07Z

Etienne Rebuffet: /* Kinetics and Mechanism */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== 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 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.

[[File:gh117mechajan2012.jpg|800x200px|Proposed mechanism of α-1,3-L-(3,6-anhydro)-galactosidase. From <cite>Hehemann2012</cite>]]

Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind zinc ions, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be two of the three acidic residues Asp-97, Asp-252 and Glu-310 (Zg4663 numbering) <cite>Rebuffet2011</cite>.

== Three-dimensional structures ==
At the moment two members of GH117 family have been crystallized. Both are enzymes from marine bacteria, one from ''Saccharophagus degradans'' <cite>Lee2009</cite> and one from ''Zobellia galactanivorans'' <cite>Rebuffet2011</cite>. A crystal structure has only been reported for the α-1,3-L-(3,6-anhydro)-galactosidase (AhgA, Zg4663) from ''Z. galactanivorans'' (PDB: [{{PDBlink}}3p2n 3p2n]) <cite>Rebuffet2011</cite>.
AhgA adopts a five-bladed β-propeller fold and forms a dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 2) <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>.
[[Image:Agha_structure.png|thumb|Figure 2: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Lee2009 pmid=20054134
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-25T09:00:28Z

Etienne Rebuffet: /* Kinetics and Mechanism */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== 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 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.
[[File:gh117mechajan2012.jpg|800x200px|Proposed mechanism of α-1,3-L-(3,6-anhydro)-galactosidase. From <cite>Hehemann2012</cite>]]
Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind zinc ions, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be two of the three acidic residues Asp-97, Asp-252 and Glu-310 (Zg4663 numbering) <cite>Rebuffet2011</cite>.

== Three-dimensional structures ==
At the moment two members of GH117 family have been crystallized. Both are enzymes from marine bacteria, one from ''Saccharophagus degradans'' <cite>Lee2009</cite> and one from ''Zobellia galactanivorans'' <cite>Rebuffet2011</cite>. A crystal structure has only been reported for the α-1,3-L-(3,6-anhydro)-galactosidase (AhgA, Zg4663) from ''Z. galactanivorans'' (PDB: [{{PDBlink}}3p2n 3p2n]) <cite>Rebuffet2011</cite>.
AhgA adopts a five-bladed β-propeller fold and forms a dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 2) <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>.
[[Image:Agha_structure.png|thumb|Figure 2: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Lee2009 pmid=20054134
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-25T08:59:17Z

Etienne Rebuffet: /* Kinetics and Mechanism */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== 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 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.
[[File:gh117mechajan2012.jpg|upright=0.5|Proposed mechanism of α-1,3-L-(3,6-anhydro)-galactosidase. From <cite>Hehemann2012</cite>]]
Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind zinc ions, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be two of the three acidic residues Asp-97, Asp-252 and Glu-310 (Zg4663 numbering) <cite>Rebuffet2011</cite>.

== Three-dimensional structures ==
At the moment two members of GH117 family have been crystallized. Both are enzymes from marine bacteria, one from ''Saccharophagus degradans'' <cite>Lee2009</cite> and one from ''Zobellia galactanivorans'' <cite>Rebuffet2011</cite>. A crystal structure has only been reported for the α-1,3-L-(3,6-anhydro)-galactosidase (AhgA, Zg4663) from ''Z. galactanivorans'' (PDB: [{{PDBlink}}3p2n 3p2n]) <cite>Rebuffet2011</cite>.
AhgA adopts a five-bladed β-propeller fold and forms a dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 2) <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>.
[[Image:Agha_structure.png|thumb|Figure 2: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Lee2009 pmid=20054134
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

File:Gh117mechajan2012.jpg

2012-06-25T08:51:05Z

Etienne Rebuffet:

Glycoside Hydrolase Family 117

2012-06-25T08:40:07Z

Etienne Rebuffet: /* Kinetics and Mechanism */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== 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 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.
[[File:gh117mechajan2012.jpg]]
Two of the three 3D structures revealed the presence of a divalent cation, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011 Hehemann2012</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind zinc ions, which could be related to their difference in substrate specificity <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be two of the three acidic residues Asp-97, Asp-252 and Glu-310 (Zg4663 numbering) <cite>Rebuffet2011</cite>.

== Three-dimensional structures ==
At the moment two members of GH117 family have been crystallized. Both are enzymes from marine bacteria, one from ''Saccharophagus degradans'' <cite>Lee2009</cite> and one from ''Zobellia galactanivorans'' <cite>Rebuffet2011</cite>. A crystal structure has only been reported for the α-1,3-L-(3,6-anhydro)-galactosidase (AhgA, Zg4663) from ''Z. galactanivorans'' (PDB: [{{PDBlink}}3p2n 3p2n]) <cite>Rebuffet2011</cite>.
AhgA adopts a five-bladed β-propeller fold and forms a dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 2) <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>.
[[Image:Agha_structure.png|thumb|Figure 2: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Lee2009 pmid=20054134
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2012-06-25T08:15:10Z

Etienne Rebuffet: /* Substrate specificities */

{{CuratorApproved}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of [[glycoside hydrolases]] is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011 Hehemann2012</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== Kinetics and Mechanism ==
The stereochemical outcome of members of glycoside hydrolase family GH117 is still unknown. The first 3D structure revealed the presence of a zinc ion, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind zinc ions, which could be related to their difference in substrate specificity.

== Catalytic Residues ==
From structural analysis and sequence alignments the catalytic residues have been predicted to be two of the three acidic residues Asp-97, Asp-252 and Glu-310 (Zg4663 numbering) <cite>Rebuffet2011</cite>.

== Three-dimensional structures ==
At the moment two members of GH117 family have been crystallized. Both are enzymes from marine bacteria, one from ''Saccharophagus degradans'' <cite>Lee2009</cite> and one from ''Zobellia galactanivorans'' <cite>Rebuffet2011</cite>. A crystal structure has only been reported for the α-1,3-L-(3,6-anhydro)-galactosidase (AhgA, Zg4663) from ''Z. galactanivorans'' (PDB: [{{PDBlink}}3p2n 3p2n]) <cite>Rebuffet2011</cite>.
AhgA adopts a five-bladed β-propeller fold and forms a dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 2) <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>.
[[Image:Agha_structure.png|thumb|Figure 2: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [{{PDBlink}}3p2n 3p2n] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Lee2009 pmid=20054134
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 82

2011-05-06T12:09:42Z

Etienne Rebuffet:

{{CuratorApproved}}
* [[Author]]s: ^^^Mirjam Czjzek^^^, ^^^Gurvan Michel^^^, and ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----

<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH82'''
|-
|'''Clan'''
|none
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH82.html
|}
</div>

== Substrate specificities ==
At the moment, all characterised members of [[glycoside hydrolase]] family 82 enzymes cleave the β-1,4 galactosidic bond of the marine algal polysaccharide iota-carrageenan <cite>Barbeyron2000 Rebuffet2010 Hatada2010</cite> yielding products of the neocarrabiose series.

== Kinetics and Mechanism ==
Family 82 enzymes are [[inverting]] enzymes, as first shown by NMR <cite>Barbeyron2000</cite> on the iota-carrageenase from ''Alteromonas fortis''. The reaction seems to involve a chloride ion which through the Glu222 participated in the polarisation of the catalytic water molecule <cite>Rebuffet2010</cite>.

== Catalytic Residues ==
From structural analysis the catalytic residues have been predicted to be two out of the three candidate amino acids Glu245, Asp247 or Glu310 in the ''A. fortis'' iota-carrageenase <cite>Michel2001</cite>. A study in 2010, which utilized site directed mutagenesis, has confirmed that Glu245 plays the role of the [[general acid]] residue in this [[inverting]] enzyme, while Asp247 is the [[general base]] activating the nucleophilic water molecule <cite>Rebuffet2010</cite>. However, intriguingly the position of equivalent residues to Asp247 in other iota-carrageenase sequences are not strictly conserved <cite>Rebuffet2010 Hatada2010</cite>.

== Three-dimensional structures ==
[[Image:gh82_domA.gif|'''Figure 1:''' Movement of domain A induced by substrate binding. <span style="color:#0000ff"> The β-helix is in blue </span>, <span style="color:#ff0000"> the domain A is in red </span> and <span style="color:#00ff00"> the domain B is in green </span>.|frame|right]]
A crystal structure has only been determined for the iota-carrageenase from ''A. fortis'' and the protein folds into a right-handed parallel β-helix of 10 complete turns with two additional C-terminal domains (A and B) <cite>Michel2001</cite>. The crystal structure of a product complex has shed light on the existence of domain movement of domain A that is closed around the oligo-carrageenan in the complexed form and open in the uncomplexed enzyme ('''Figure 1''') <cite>Michel2003</cite>. Recent discovering of shorter sequences shows the existence of enzymes devoid of the C-terminal domain A or both domains A and B <cite>Rebuffet2010</cite>.

== Family Firsts ==
;First sequence identification and family creation: iota-carrageenase sequences have been first reported for enzymes from ''A. fortis'' and ''Z. galactanivorans'' <cite>Barbeyron2000</cite>.
;First sterochemistry determination: GH82 enzymes are inverting as shown by NMR <cite>Barbeyron2000</cite>.
;First general acid residue identification: Glu245 <cite>Rebuffet2010</cite>
;First general base residue identification: Asp247 <cite>Rebuffet2010</cite>.
;First 3-D structure: iota-carrageenase from ''A. fortis'' <cite>Michel2001</cite>. The structure belongs to the β-helix fold ([{{PDBlink}}1h80 PDB 1h80] and [{{PDBlink}}1ktw PDB 1ktw]).

== References ==
<biblio>
#Barbeyron2000 pmid=10934194
#Michel2001 pmid=11493601
#Rebuffet2010 pmid=20681629
#Hatada2010 pmid=20686828
#Michel2003 pmid=14623184
</biblio>

[[Category:Glycoside Hydrolase Families|GH082]]

Glycoside Hydrolase Family 82

2011-05-06T12:07:50Z

Etienne Rebuffet:

{{CuratorApproved}}
* [[Author]]s: ^^^Mirjam Czjzek^^^, ^^^Gurvan Michel^^^, and ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----

<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH82'''
|-
|'''Clan'''
|none
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH82.html
|}
</div>

== Substrate specificities ==
At the moment, all characterised members of [[glycoside hydrolase]] family 82 enzymes cleave the β-1,4 galactosidic bond of the marine algal polysaccharide iota-carrageenan <cite>Barbeyron2000 Rebuffet2010 Hatada2010</cite> yielding products of the neocarrabiose series.

== Kinetics and Mechanism ==
Family 82 enzymes are [[inverting]] enzymes, as first shown by NMR <cite>Barbeyron2000</cite> on the iota-carrageenase from ''Alteromonas fortis''. The reaction seems to involve a chloride ion which through the Glu222 participated in the polarisation of the catalytic water molecule <cite>Rebuffet2010</cite>.

== Catalytic Residues ==
From structural analysis the catalytic residues have been predicted to be two out of the three candidate amino acids Glu245, Asp247 or Glu310 in the ''A. fortis'' iota-carrageenase <cite>Michel2001</cite>. A study in 2010, which utilized site directed mutagenesis, has confirmed that Glu245 plays the role of the [[general acid]] residue in this [[inverting]] enzyme, while Asp247 is the [[general base]] activating the nucleophilic water molecule <cite>Rebuffet2010</cite>. However, intriguingly the position of equivalent residues to Asp247 in other iota-carrageenase sequences are not strictly conserved <cite>Rebuffet2010 Hatada2010</cite>.

== Three-dimensional structures ==
[[Image:gh82_domA.gif|'''Figure 1:''' Movement of domain A induced by substrate binding. <span style="color:#0000ff"> The β-helix is in blue </span>, <span style="color:#ff0000"> the domain A is in red </span> and <span style="color:#00ff00"> the domain B is in green </span>.|frame|right]]
A crystal structure has only been determined for the iota-carrageenase from ''A. fortis'' and the protein folds into a right-handed parallel β-helix of 10 complete turns with two additional C-terminal domains (A and B) <cite>Michel2001</cite>. The crystal structure of a product complex has shed light on the existence of domain movement of domain A that is closed around the oligo-carrageenan in the complexed form and open in the uncomplexed enzyme ('''Figure 1''') <cite>Michel2003</cite>. Recent discovering of shorter sequences show the existence of enzymes devoid of the C-terminal domain A or both domains A and B <cite>Rebuffet2010</cite>.

== Family Firsts ==
;First sequence identification and family creation: iota-carrageenase sequences have been first reported for enzymes from ''A. fortis'' and ''Z. galactanivorans'' <cite>Barbeyron2000</cite>.
;First sterochemistry determination: GH82 enzymes are inverting as shown by NMR <cite>Barbeyron2000</cite>.
;First general acid residue identification: Glu245 <cite>Rebuffet2010</cite>
;First general base residue identification: Asp247 <cite>Rebuffet2010</cite>.
;First 3-D structure: iota-carrageenase from ''A. fortis'' <cite>Michel2001</cite>. The structure belongs to the β-helix fold ([{{PDBlink}}1h80 PDB 1h80] and [{{PDBlink}}1ktw PDB 1ktw]).

== References ==
<biblio>
#Barbeyron2000 pmid=10934194
#Michel2001 pmid=11493601
#Rebuffet2010 pmid=20681629
#Hatada2010 pmid=20686828
#Michel2003 pmid=14623184
</biblio>

[[Category:Glycoside Hydrolase Families|GH082]]

Glycoside Hydrolase Family 82

2011-05-06T12:02:56Z

Etienne Rebuffet:

{{CuratorApproved}}
* [[Author]]s: ^^^Mirjam Czjzek^^^, ^^^Gurvan Michel^^^, and ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----

<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH82'''
|-
|'''Clan'''
|none
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH82.html
|}
</div>

== Substrate specificities ==
At the moment, all characterised members of [[glycoside hydrolase]] family 82 enzymes cleave the β-1,4 galactosidic bond of the marine algal polysaccharide iota-carrageenan <cite>Barbeyron2000 Rebuffet2010 Hatada2010</cite> yielding products of the neocarrabiose series.

== Kinetics and Mechanism ==
Family 82 enzymes are [[inverting]] enzymes, as first shown by NMR <cite>Barbeyron2000</cite> on the iota-carrageenase from ''Alteromonas fortis''. The reaction seems to involve a chloride ion which through the Glu222 participated in the polarisation of the catalytic water molecule <cite>Rebuffet2010</cite>.

== Catalytic Residues ==
From structural analysis the catalytic residues have been predicted to be two out of the three candidate amino acids Glu245, Asp247 or Glu310 in the ''A. fortis'' iota-carrageenase <cite>Michel2001</cite>. A study in 2010, which utilized site directed mutagenesis, has confirmed that Glu245 plays the role of the [[general acid]] residue in this [[inverting]] enzyme, while Asp247 is the [[general base]] activating the nucleophilic water molecule <cite>Rebuffet2010</cite>. However, intriguingly the position of equivalent residues to Asp247 in other iota-carrageenase sequences are not strictly conserved <cite>Rebuffet2010 Hatada2010</cite>.

== Three-dimensional structures ==
[[Image:gh82_domA.gif|Figure 1: Movement of domain A induced by substrate binding. <span style="color:#0000ff"> The β-helix is in blue </span>, <span style="color:#ff0000"> the domain A is in red </span> and <span style="color:#00ff00"> the domain B is in green </span>.|frame|right]]
A crystal structure has only been determined for the iota-carrageenase from ''A. fortis'' and the protein folds into a right-handed parallel β-helix of 10 complete turns with two additional C-terminal domains <cite>Michel2001</cite>. The crystal structure of a product complex has shed light on the existence of domain movement of domain A that is closed around the oligo-carrageenan in the complexed form and open in the uncomplexed enzyme (Figure 1) <cite>Michel2003</cite>. Recent discovering of shorter sequences show the existence of enzymes devoid of one or two additional domain <cite>Rebuffet2010</cite>.

== Family Firsts ==
;First sequence identification and family creation: iota-carrageenase sequences have been first reported for enzymes from ''A. fortis'' and ''Z. galactanivorans'' <cite>Barbeyron2000</cite>.
;First sterochemistry determination: GH82 enzymes are inverting as shown by NMR <cite>Barbeyron2000</cite>.
;First general acid residue identification: Glu245 <cite>Rebuffet2010</cite>
;First general base residue identification: Asp247 <cite>Rebuffet2010</cite>.
;First 3-D structure: iota-carrageenase from ''A. fortis'' <cite>Michel2001</cite>. The structure belongs to the β-helix fold ([{{PDBlink}}1h80 PDB 1h80] and [{{PDBlink}}1ktw PDB 1ktw]).

== References ==
<biblio>
#Barbeyron2000 pmid=10934194
#Michel2001 pmid=11493601
#Rebuffet2010 pmid=20681629
#Hatada2010 pmid=20686828
#Michel2003 pmid=14623184
</biblio>

[[Category:Glycoside Hydrolase Families|GH082]]

User:Etienne Rebuffet

2011-05-06T08:57:38Z

Etienne Rebuffet:

[[Image:etienne-rebuffet.png|thumb|250px|right]]
I'm biochemist and crystallographer and I started working on glycoside hydrolases during my PhD at the [http://www3.sb-roscoff.fr/ Station Biologique de Roscoff] (France) in the group [http://www3.sb-roscoff.fr/en/glycobiology-marine-algae.html marine glycobiology] and under the supervision of [http://www.cazypedia.org/index.php/User:Mirjam_Czjzek Dr. Mirjam Czjzek] and [http://www.cazypedia.org/index.php/User:Gurvan_Michel Dr. Gurvan Michel]. My work focused on iota-carrageenase ([[GH82]]) and α-1,3-L-(3,6-anhydro)-galactosidase ([[GH117]]). Since June 2010, I am post-doctor at the university of Gothenburg in the Biochemistry and Biophysics group. I am now working on uncoupling proteins, a subject which does not concern CAZymes.

Glycoside Hydrolase Family 117

2011-05-06T08:54:02Z

Etienne Rebuffet:

{{UnderConstruction}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far characterized within this recently discovered family of glycoside hydrolases is that of α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011</cite>. Nevertheless phylogenetic analyses (Figure 1) of this family together with activity tests for another member, Zg3597 (Clade C), show that the family GH117 most probably is polyspecific <cite>Rebuffet2011</cite>.

== Kinetics and Mechanism ==
The catalytic mechanism of members of glycoside hydrolase family GH117 is still unknown. The first 3D structure revealed the presence of a zinc ion, directly coordinated only by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction <cite>Rebuffet2011</cite>. Sequence alignments suggest that the enzymes of clades B and C do not bind zinc ions, which could be related to their difference in substrate specificity.

== Catalytic Residues ==
From structural analysis and sequences alignments the catalytic residues have been predicted to be two out of the three acidic residues Asp-97, Asp-252 and Glu-310 (Zg4663 numbering) <cite>Rebuffet2011</cite>.

== Three-dimensional structures ==
At the moment two members of GH117 family have been crystallized. Both are enzymes from marine bacteria, one from ''Saccharophagus degradans'' <cite>Lee2009</cite> and one from ''Zobelia galactanivorans'' <cite>Rebuffet2011</cite>. A crystal structure has only been reported for the α-1,3-L-(3,6-anhydro)-galactosidase (AhgA, Zg4663) from ''Z. galactanivorans'' (PDB: [http://www.pdb.org/pdb/explore/explore.do?structureId=3p2n 3P2N]) <cite>Rebuffet2011</cite>.
AhgA adopts a five-bladed β-propeller fold and forms a dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 2) <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>.
[[Image:Agha_structure.png|thumb|Figure 2: Structure of the dimer of AghA. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: not determined yet.
;First catalytic nucleophile identification: not determined yet.
;First general acid/base residue identification: not determined yet.
;First 3-D structure: The first 3D structure was reported in 2011 for an α-1,3-L-(3,6-anhydro)-galactosidase (AhgA or Zg4663) from the marine bacteria ''Zobellia galactanivorans'', PDB: [http://www.pdb.org/pdb/explore/explore.do?structureId=3p2n 3P2N] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Lee2009 pmid=20054134
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

File:Gh82 domA.gif

2011-05-05T15:19:11Z

Etienne Rebuffet: uploaded a new version of "File:Gh82 domA.gif"

File:Gh82 domA.gif

2011-05-05T15:17:30Z

Etienne Rebuffet: uploaded a new version of "File:Gh82 domA.gif"

Glycoside Hydrolase Family 82

2011-05-05T14:20:13Z

Etienne Rebuffet:

{{CuratorApproved}}
* [[Author]]s: ^^^Mirjam Czjzek^^^, ^^^Gurvan Michel^^^, and ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----

<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH82'''
|-
|'''Clan'''
|none
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH82.html
|}
</div>

== Substrate specificities ==
The two known members of [[glycoside hydrolase]] family 82 enzymes cleave the β-1,4 galactosidic bond of the marine algal polysaccharide iota-carrageenan <cite>Barbeyron2000</cite> yielding products of the neocarrabiose series.

== Kinetics and Mechanism ==
Family 82 enzymes are [[inverting]] enzymes, as first shown by NMR <cite>Barbeyron2000</cite> on the iota-carrageenase from ''Alteromonas fortis''.

== Catalytic Residues ==
From structural analysis the catalytic residues have been predicted to be two out of the three candidate amino acids Glu245, Asp247 or Glu310 in the ''A. fortis'' iota-carrageenase <cite>Michel2001</cite>. A study in 2010, which utilized site directed mutagenesis, has confirmed that Glu245 plays the role of the [[general acid]] residue in this [[inverting]] enzyme, while Asp247 is the [[general base]] activating the nucleophilic water molecule <cite>Rebuffet2010</cite>. However, intriguingly the position of equivalent residues to Asp247 in other iota-carrageenase sequences are not strictly conserved <cite>Rebuffet2010 Hatada2010</cite>.

== Three-dimensional structures ==
[[Image:gh82_domA.gif|Figure 1: Movement of domain A induced by substrate binding. <span style="color:#0000ff"> The β-helix is in blue </span>, <span style="color:#ff0000"> the domain A is in red </span> and <span style="color:#00ff00"> the domain B is in green </span>.|frame|right]]
A crystal structure has only been determined for the iota-carrageenase from ''A. fortis'' <cite></cite>Michel2001. The crystal structure of a product complex has shed light on the existance of domain movement of domain A that is closed around the oligo-carrageenan in the complexed form and open in the uncomplexed enzyme (Figure 1) <cite>Michel2003</cite>.

== Family Firsts ==
;First sequence identification and family creation: iota-carrageenase sequences have been first reported for enzymes from ''A. fortis'' and ''Z. galactanivorans'' <cite>Barbeyron2000</cite>.
;First sterochemistry determination: GH82 enzymes are inverting as shown by NMR <cite>Barbeyron2000</cite>.
;First general acid residue identification: Glu245 <cite>Rebuffet2010</cite>
;First general base residue identification: Asp247 <cite>Rebuffet2010</cite>.
;First 3-D structure: iota-carrageenase from ''A. fortis'' <cite>Michel2001</cite>. The structure belongs to the β-helix fold ([{{PDBlink}}1h80 PDB 1h80] and [{{PDBlink}}1ktw PDB 1ktw]).

== References ==
<biblio>
#Barbeyron2000 pmid=10934194
#Michel2001 pmid=11493601
#Rebuffet2010 pmid=20681629
#Hatada2010 pmid=20686828
#Michel2003 pmid=14623184
</biblio>

[[Category:Glycoside Hydrolase Families|GH082]]

Glycoside Hydrolase Family 82

2011-05-05T14:02:19Z

Etienne Rebuffet:

{{CuratorApproved}}
* [[Author]]s: ^^^Mirjam Czjzek^^^, ^^^Gurvan Michel^^^, and ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----

<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH82'''
|-
|'''Clan'''
|none
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH82.html
|}
</div>

== Substrate specificities ==
The two known members of [[glycoside hydrolase]] family 82 enzymes cleave the β-1,4 galactosidic bond of the marine algal polysaccharide iota-carrageenan <cite>Barbeyron2000</cite> yielding products of the neocarrabiose series.

== Kinetics and Mechanism ==
Family 82 enzymes are [[inverting]] enzymes, as first shown by NMR <cite>Barbeyron2000</cite> on the iota-carrageenase from ''Alteromonas fortis''.

== Catalytic Residues ==
From structural analysis the catalytic residues have been predicted to be two out of the three candidate amino acids Glu245, Asp247 or Glu310 in the ''A. fortis'' iota-carrageenase <cite>Michel2001</cite>. A study in 2010, which utilized site directed mutagenesis, has confirmed that Glu245 plays the role of the [[general acid]] residue in this [[inverting]] enzyme, while Asp247 is the [[general base]] activating the nucleophilic water molecule <cite>Rebuffet2010</cite>. However, intriguingly the position of equivalent residues to Asp247 in other iota-carrageenase sequences are not strictly conserved <cite>Rebuffet2010 Hatada2010</cite>.

== Three-dimensional structures ==
[[Image:gh82_domA.gif|Figure 1: Movement of domain A induced by substrate binding|frame|right]]
A crystal structure has only been determined for the iota-carrageenase from ''A. fortis'' <cite>2</cite>. The crystal structure of a product complex has shed light on the existance of domain movement of domain A that is closed around the oligo-carrageenan in the complexed form and open in the uncomplexed enzyme (Figure 1) <cite>Michel2003</cite>.

== Family Firsts ==
;First sequence identification and family creation: iota-carrageenase sequences have been first reported for enzymes from ''A. fortis'' and ''Z. galactanivorans'' <cite>Barbeyron2000</cite>.
;First sterochemistry determination: GH82 enzymes are inverting as shown by NMR <cite>Barbeyron2000</cite>.
;First general acid residue identification: Glu245 <cite>Rebuffet2010</cite>
;First general base residue identification: Asp247 <cite>Rebuffet2010</cite>.
;First 3-D structure: iota-carrageenase from ''A. fortis'' <cite>Michel2001</cite>. The structure belongs to the β-helix fold ([{{PDBlink}}1h80 PDB 1h80] and [{{PDBlink}}1ktw PDB 1ktw]).

== References ==
<biblio>
#Barbeyron2000 pmid=10934194
#Michel2001 pmid=11493601
#Rebuffet2010 pmid=20681629
#Hatada2010 pmid=20686828
#Michel2003 pmid=14623184
</biblio>

[[Category:Glycoside Hydrolase Families|GH082]]

File:Gh82 domA.gif

2011-05-05T13:57:55Z

Etienne Rebuffet:

Glycoside Hydrolase Family 82

2011-05-05T13:57:41Z

Etienne Rebuffet:

{{CuratorApproved}}
* [[Author]]s: ^^^Mirjam Czjzek^^^, ^^^Gurvan Michel^^^, and ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----

<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH82'''
|-
|'''Clan'''
|none
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH82.html
|}
</div>

== Substrate specificities ==
The two known members of [[glycoside hydrolase]] family 82 enzymes cleave the β-1,4 galactosidic bond of the marine algal polysaccharide iota-carrageenan <cite>Barbeyron2000</cite> yielding products of the neocarrabiose series.

== Kinetics and Mechanism ==
Family 82 enzymes are [[inverting]] enzymes, as first shown by NMR <cite>Barbeyron2000</cite> on the iota-carrageenase from ''Alteromonas fortis''.

== Catalytic Residues ==
From structural analysis the catalytic residues have been predicted to be two out of the three candidate amino acids Glu245, Asp247 or Glu310 in the ''A. fortis'' iota-carrageenase <cite>Michel2001</cite>. A study in 2010, which utilized site directed mutagenesis, has confirmed that Glu245 plays the role of the [[general acid]] residue in this [[inverting]] enzyme, while Asp247 is the [[general base]] activating the nucleophilic water molecule <cite>Rebuffet2010</cite>. However, intriguingly the position of equivalent residues to Asp247 in other iota-carrageenase sequences are not strictly conserved <cite>Rebuffet2010 Hatada2010</cite>.

== Three-dimensional structures ==
[[Image:gh82_domA.gif|thumb|200px|right]]
A crystal structure has only been determined for the iota-carrageenase from ''A. fortis'' <cite>2</cite>. The crystal structure of a product complex has shed light on the existance of domain movement of domain A that is closed around the oligo-carrageenan in the complexed form and open in the uncomplexed enzyme (Figure 1) <cite>Michel2003</cite>.

== Family Firsts ==
;First sequence identification and family creation: iota-carrageenase sequences have been first reported for enzymes from ''A. fortis'' and ''Z. galactanivorans'' <cite>Barbeyron2000</cite>.
;First sterochemistry determination: GH82 enzymes are inverting as shown by NMR <cite>Barbeyron2000</cite>.
;First general acid residue identification: Glu245 <cite>Rebuffet2010</cite>
;First general base residue identification: Asp247 <cite>Rebuffet2010</cite>.
;First 3-D structure: iota-carrageenase from ''A. fortis'' <cite>Michel2001</cite>. The structure belongs to the β-helix fold ([{{PDBlink}}1h80 PDB 1h80] and [{{PDBlink}}1ktw PDB 1ktw]).

== References ==
<biblio>
#Barbeyron2000 pmid=10934194
#Michel2001 pmid=11493601
#Rebuffet2010 pmid=20681629
#Hatada2010 pmid=20686828
#Michel2003 pmid=14623184
</biblio>

[[Category:Glycoside Hydrolase Families|GH082]]

Glycoside Hydrolase Family 117

2011-05-05T13:34:32Z

Etienne Rebuffet:

{{UnderConstruction}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far identified in this recently discovered family of glycoside hydrolases is that α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011</cite>. Nevertheless phylogenetic analysis (figure 1) of this family and activity test on Zg3597 (Clade C) show that the family GH117 is polyspecific <cite>Rebuffet2011</cite>.

== Kinetics and Mechanism ==
Mechanism of glycoside hydrolase family 117 is still unknown. But structural analyse revealed the presence of a zinc ion, only coordinated by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction to take place <cite>Rebuffet2011</cite>. Sequence alignment suggest that the enzymes of clades B and C do not bind zinc ions which could be related to the difference of substrate.

== Catalytic Residues ==
From structural analysis and sequences alignment the catalytic residues have been predicted to be two out of the three acidic residues Asp-97, Asp-252 and Glu-310 (Zg4663 numbering) <cite>Rebuffet2011</cite>.

== Three-dimensional structures ==
At the moment two members of GH117 family have been crystallized. Both are enzymes from marine bacteria, one from ''Saccharophagus degradans'' <cite>Lee2009</cite> and one from ''Zobelia galactanivorans'' <cite>Rebuffet2011</cite>. A crystal structure has only been reported for the α-1,3-L-(3,6-anhydro)-galactosidase (AhgA, Zg4663) from ''Z. galactanivorans'' (PDB: [http://www.pdb.org/pdb/explore/explore.do?structureId=3p2n 3P2N]) <cite>Rebuffet2011</cite>.
Zg4663 adopting the five-bladed β-propeller fold and form dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 2) <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) misses the domain-swapping signature, and the crucial residues are missing. This protein from R. baltica is thus likely a monomer and may represent an ‘ancestral’ form of the GH117 family which would be limited to the β-propeller, catalytic domain <cite>Rebuffet2011</cite>.
[[Image:Agha_structure.png|thumb|Figure 2: Structure of the dimer of Zg4663. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: -
;First catalytic nucleophile identification: -
;First general acid/base residue identification: -
;First 3-D structure: 2011: Zg4663, α-1,3-L-(3,6-anhydro)-galactosidase (AhgA), PDB: [http://www.pdb.org/pdb/explore/explore.do?structureId=3p2n 3P2N] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Lee2009 pmid=20054134
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2011-05-05T13:33:50Z

Etienne Rebuffet:

{{UnderConstruction}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far identified in this recently discovered family of glycoside hydrolases is that α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011</cite>. Nevertheless phylogenetic analysis (figure 1) of this family and activity test on Zg3597 (Clade C) show that the family GH117 is polyspecific <cite>Rebuffet2011</cite>.

== Kinetics and Mechanism ==
Mechanism of glycoside hydrolase family 117 is still unknown. But structural analyse revealed the presence of a zinc ion, only coordinated by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction to take place <cite>Rebuffet2011</cite>. Sequence alignment suggest that the enzymes of clades B and C do not bind zinc ions which could be related to the difference of substrate.

== Catalytic Residues ==
From structural analysis and sequences alignment the catalytic residues have been predicted to be two out of the three acidic residues Asp-97, Asp-252 and Glu-310 (Zg4663 numbering) <cite>Rebuffet2011</cite>.

== Three-dimensional structures ==
At the moment two members of GH117 family have been crystallized. Both are enzymes from marine bacteria, one from ''Saccharophagus degradans'' <cite>Lee2009</cite> and one from ''Zobelia galactanivorans'' <cite>Rebuffet2011</cite>. A crystal structure has only been reported for the α-1,3-L-(3,6-anhydro)-galactosidase (AhgA, Zg4663) from ''Z. galactanivorans'' (PDB: [http://www.pdb.org/pdb/explore/explore.do?structureId=3p2n 3P2N]) <cite>Rebuffet2011</cite>.
Zg4663 adopting the five-bladed β-propeller fold and form dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 2) <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) misses the domain-swapping signature, and the crucial residues are missing. This protein from R. baltica is thus likely a monomer and may represent an ‘ancestral’ form of the GH117 family which would be limited to the β-propeller, catalytic domain <cite>Rebuffet2011</cite>.
[[Image:Agha_structure.png|thumb|Figure 2: Structure of the dimer of Zg4663. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: -
;First catalytic nucleophile identification: -
;First general acid/base residue identification: -
;First 3-D structure: Zg4663, α-1,3-L-(3,6-anhydro)-galactosidase (AhgA), PDB: [http://www.pdb.org/pdb/explore/explore.do?structureId=3p2n 3P2N] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Lee2009 pmid=20054134
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2011-05-05T13:07:25Z

Etienne Rebuffet:

{{UnderConstruction}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far identified in this recently discovered family of glycoside hydrolases is that α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011</cite>. Nevertheless phylogenetic analysis (figure 1) of this family and activity test on Zg3597 (Clade C) show that the family GH117 is polyspecific <cite>Rebuffet2011</cite>.

== Kinetics and Mechanism ==
Mechanism of glycoside hydrolase family 117 is still unknown. But structural analyse revealed the presence of a zinc ion, only coordinated by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction to take place <cite>Rebuffet2011</cite>. Sequence alignment suggest that the enzymes of clades B and C do not bind zinc ions which could be related to the difference of substrate.

== Catalytic Residues ==
From structural analysis and sequences alignment the catalytic residues have been predicted to be two out of the three acidic residues Asp-97, Asp-252 and Glu-310 (Zg4663 numbering) <cite>Rebuffet2011</cite>.

== Three-dimensional structures ==
At the moment two members of GH117 family have been crystallized. Both are enzymes from marine bacteria, one from ''Saccharophagus degradans'' <cite>Lee2009</cite> and one from ''Zobelia galactanivorans'' <cite>Rebuffet2011</cite>. A crystal structure has only been reported for the α-1,3-L-(3,6-anhydro)-galactosidase (AhgA, Zg4663) from ''Z. galactanivorans'' (PDB: [http://www.pdb.org/pdb/explore/explore.do?structureId=3p2n 3P2N]) <cite>Rebuffet2011</cite>.
Zg4663 adopting the five-bladed β-propeller fold and form dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 2) <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) misses the domain-swapping signature, and the crucial residues are missing. This protein from R. baltica is thus likely a monomer and may represent an ‘ancestral’ form of the GH117 family which would be limited to the β-propeller, catalytic domain <cite>Rebuffet2011</cite>.
[[Image:Agha_structure.png|thumb|Figure 2: Structure of the dimer of Zg4663. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>Comfort2007</cite>.
;First catalytic nucleophile identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>Sinnott1990</cite>.
;First general acid/base residue identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>He1999</cite>.
;First 3-D structure: Zg4663, α-1,3-L-(3,6-anhydro)-galactosidase (AhgA), PDB: [http://www.pdb.org/pdb/explore/explore.do?structureId=3p2n 3P2N] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Lee2009 pmid=20054134
</biblio>



[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2011-05-05T13:04:06Z

Etienne Rebuffet:

{{UnderConstruction}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far identified in this recently discovered family of glycoside hydrolases is that α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011</cite>. Nevertheless phylogenetic analysis (figure 1) of this family and activity test on Zg3597 (Clade C) show that the family GH117 is polyspecific <cite>Rebuffet2011</cite>.

== Kinetics and Mechanism ==
Mechanism of glycoside hydrolase family 117 is still unknown. But structural analyse revealed the presence of a zinc ion, only coordinated by water molecules, close to the active site, which could activate the catalytic water molecule and provide the energy needed for the enzymatic reaction to take place <cite>Rebuffet2011</cite>. Sequence alignment suggest that the enzymes of clades B and C do not bind zinc ions which could be related to the difference of substrate.

== Catalytic Residues ==
From structural analysis and sequences alignment the catalytic residues have been predicted to be two out of the three acidic residues Asp-97, Asp-252 and Glu-310 (Zg4663 numbering) <cite>Rebuffet2011</cite>.

== Three-dimensional structures ==
At the moment two members of GH117 family have been crystallized. Both are enzymes from marine bacteria, one from ''Saccharophagus degradans'' <cite>Lee2009</cite> and one from ''Zobelia galactanivorans'' <cite>Rebuffet2011</cite>. A crystal structure has only been reported for the α-1,3-L-(3,6-anhydro)-galactosidase (AhgA, Zg4663) from ''Z. galactanivorans'' (PDB: [http://www.pdb.org/pdb/explore/explore.do?structureId=3p2n 3P2N]) <cite>Rebuffet2011</cite>.
Zg4663 adopting the five-bladed β-propeller fold and form dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 2) <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) misses the domain-swapping signature, and the crucial residues are missing. This protein from R. baltica is thus likely a monomer and may represent an ‘ancestral’ form of the GH117 family which would be limited to the β-propeller, catalytic domain <cite>Rebuffet2011</cite>.
[[Image:Agha_structure.png|thumb|Figure 2: Structure of the dimer of Zg4663. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>Comfort2007</cite>.
;First catalytic nucleophile identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>Sinnott1990</cite>.
;First general acid/base residue identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>He1999</cite>.
;First 3-D structure: Zg4663, α-1,3-L-(3,6-anhydro)-galactosidase (AhgA), PDB: [http://www.pdb.org/pdb/explore/explore.do?structureId=3p2n 3P2N] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Lee2009 pmid=20054134

#He1999 pmid=9312086
#StickWilliams isbn=978-0-240-52118-3
#Sinnott1990 Sinnott, M.L. (1990) Catalytic mechanisms of enzymic glycosyl transfer. Chem. Rev. 90, 1171-1202. [http://dx.doi.org/10.1021/cr00105a006 DOI: 10.1021/cr00105a006]
</biblio>

This is an example of how to make references to a journal article <cite>Comfort2007</cite>. (See the References section below). Multiple references can go in the same place like this <cite>Comfort2007 He1999</cite>. You can even cite books using just the ISBN <cite>StickWilliams</cite>. References that are not in PubMed can be typed in by hand <cite>Sinnott1990</cite>.

[[Category:Glycoside Hydrolase Families|GH117]]

Glycoside Hydrolase Family 117

2011-05-05T12:17:04Z

Etienne Rebuffet:

{{UnderConstruction}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far identified in this recently discovered family of glycoside hydrolases is that α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011</cite>. Nevertheless phylogenetic analysis (figure 1) of this family and activity test on Zg3597 (Clade C) show that the family GH117 is polyspecific <cite>Rebuffet2011</cite>.

== Kinetics and Mechanism ==
Mechanism of glycoside hydrolase family 117 is still unknown. But structural analyse revealed the presence of a zinc ion close to the active site which could be involved in the reaction mechanism <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequences alignment the catalytic residues have been predicted to be two out of the three acidic residues Asp-97, Asp-252 and Glu-310 (Zg4663 numbering) <cite>Rebuffet2011</cite>.

== Three-dimensional structures ==
At the moment two members of GH117 family have been crystallized. Both are enzymes from marine bacteria, one from ''Saccharophagus degradans'' <cite>Lee2009</cite> and one from ''Zobelia galactanivorans'' <cite>Rebuffet2011</cite>. A crystal structure has only been reported for the α-1,3-L-(3,6-anhydro)-galactosidase (AhgA, Zg4663) from ''Z. galactanivorans'' (PDB: [http://www.pdb.org/pdb/explore/explore.do?structureId=3p2n 3P2N]) <cite>Rebuffet2011</cite>.
Zg4663 adopting the five-bladed β-propeller fold and form dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 2) <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) misses the domain-swapping signature, and the crucial residues are missing. This protein from R. baltica is thus likely a monomer and may represent an ‘ancestral’ form of the GH117 family which would be limited to the β-propeller, catalytic domain <cite>Rebuffet2011</cite>.
[[Image:Agha_structure.png|thumb|Figure 2: Structure of the dimer of Zg4663. From <cite>Rebuffet2011</cite>.|600px|centre]]

== Family Firsts ==
;First stereochemistry determination: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>Comfort2007</cite>.
;First catalytic nucleophile identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>Sinnott1990</cite>.
;First general acid/base residue identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>He1999</cite>.
;First 3-D structure: Zg4663, α-1,3-L-(3,6-anhydro)-galactosidase (AhgA), PDB: [http://www.pdb.org/pdb/explore/explore.do?structureId=3p2n 3P2N] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Lee2009 pmid=20054134

#He1999 pmid=9312086
#StickWilliams isbn=978-0-240-52118-3
#Sinnott1990 Sinnott, M.L. (1990) Catalytic mechanisms of enzymic glycosyl transfer. Chem. Rev. 90, 1171-1202. [http://dx.doi.org/10.1021/cr00105a006 DOI: 10.1021/cr00105a006]
</biblio>

This is an example of how to make references to a journal article <cite>Comfort2007</cite>. (See the References section below). Multiple references can go in the same place like this <cite>Comfort2007 He1999</cite>. You can even cite books using just the ISBN <cite>StickWilliams</cite>. References that are not in PubMed can be typed in by hand <cite>Sinnott1990</cite>.

[[Category:Glycoside Hydrolase Families|GH117]]

File:Agha structure.png

2011-05-05T12:14:22Z

Etienne Rebuffet:

Glycoside Hydrolase Family 117

2011-05-05T12:10:33Z

Etienne Rebuffet:

{{UnderConstruction}}
* [[Author]]: ^^^Etienne Rebuffet^^^
* [[Responsible Curator]]: ^^^Mirjam Czjzek^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH117'''
|-
|'''Clan'''
|None
|-
|'''Mechanism'''
|Not known
|-
|'''Active site residues'''
|Not known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH117.html
|}
</div>


== Substrate specificities ==
[[Image:GH117_Phylogeny.png|thumb|Figure 1: Phylogeny of GH117 family. From <cite>Rebuffet2011</cite>.|400px|right]]
The only activity so far identified in this recently discovered family of glycoside hydrolases is that α-1,3-L-(3,6-anhydro)-galactosidase <cite>Sugano1994 Suzuki2002 Rebuffet2011</cite>. Nevertheless phylogenetic analysis (figure 1) of this family and activity test on Zg3597 (Clade C) show that the family GH117 is polyspecific <cite>Rebuffet2011</cite>.

== Kinetics and Mechanism ==
Mechanism of glycoside hydrolase family 117 is still unknown. But structural analyse revealed the presence of a zinc ion close to the active site which could be involved in the reaction mechanism <cite>Rebuffet2011</cite>.

== Catalytic Residues ==
From structural analysis and sequences alignment the catalytic residues have been predicted to be two out of the three acidic residues Asp-97, Asp-252 and Glu-310 (Zg4663 numbering) <cite>Rebuffet2011</cite>.

== Three-dimensional structures ==
At the moment two members of GH117 family have been crystallized. Both are enzymes from marine bacteria, one from ''Saccharophagus degradans'' <cite>Lee2009</cite> and one from ''Zobelia galactanivorans'' <cite>Rebuffet2011</cite>. A crystal structure has only been reported for the α-1,3-L-(3,6-anhydro)-galactosidase (AhgA, Zg4663) from ''Z. galactanivorans'' (PDB: [http://www.pdb.org/pdb/explore/explore.do?structureId=3p2n 3P2N]) <cite>Rebuffet2011</cite>.
Zg4663 adopting the five-bladed β-propeller fold and form dimer via domain-swapping of the N-terminal HTH (Helix-Turn-Helix) domain (Figure 2) <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) misses the domain-swapping signature, and the crucial residues are missing. This protein from R. baltica is thus likely a monomer and may represent an ‘ancestral’ form of the GH117 family which would be limited to the β-propeller, catalytic domain <cite>Rebuffet2011</cite>.
[[Image:Agha_structure.png|thumb|Figure 2: Structure of the dimer of AhgA. From <cite>Rebuffet2011</cite>.|400px|right]]

== Family Firsts ==
;First stereochemistry determination: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>Comfort2007</cite>.
;First catalytic nucleophile identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>Sinnott1990</cite>.
;First general acid/base residue identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>He1999</cite>.
;First 3-D structure: Zg4663, α-1,3-L-(3,6-anhydro)-galactosidase (AhgA), PDB: [http://www.pdb.org/pdb/explore/explore.do?structureId=3p2n 3P2N] <cite>Rebuffet2011</cite>.

== References ==
<biblio>
#Sugano1994 pmid=7961439
#Suzuki2002 pmid=16233232
#Rebuffet2011 pmid=21332624
#Lee2009 pmid=20054134

#He1999 pmid=9312086
#StickWilliams isbn=978-0-240-52118-3
#Sinnott1990 Sinnott, M.L. (1990) Catalytic mechanisms of enzymic glycosyl transfer. Chem. Rev. 90, 1171-1202. [http://dx.doi.org/10.1021/cr00105a006 DOI: 10.1021/cr00105a006]
</biblio>

This is an example of how to make references to a journal article <cite>Comfort2007</cite>. (See the References section below). Multiple references can go in the same place like this <cite>Comfort2007 He1999</cite>. You can even cite books using just the ISBN <cite>StickWilliams</cite>. References that are not in PubMed can be typed in by hand <cite>Sinnott1990</cite>.

[[Category:Glycoside Hydrolase Families|GH117]]