CAZypedia - User contributions [en-ca]

Auxiliary Activity Family 14

2019-07-02T08:48:33Z

Marie Couturier:

{{UnderConstruction}}
* [[Author]]: ^^^Marie Couturier^^^ and ^^^Jean-Guy Berrin^^^
* [[Responsible Curator]]: ^^^Jean-Guy Berrin^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Auxiliary Activity Family AA14'''
|-
|'''Clan'''
|Structurally related to [[AA9]]
|-
|'''Mechanism'''
|lytic oxidase
|-
|'''Active site residues'''
|mononuclear copper ion
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}AA14.html
|}
</div>


== Discovery of AA14 LPMOs ==

The gene encoding the first AA14 family member was identified by analysing transcriptomic and proteomic data from the white-rot basidiomycete ''Pycnoporus coccineus'' <cite>Couturier2015</cite>. This gene was highly upregulated when the fungus was grown on pine or poplar. The corresponding protein (GenBank ID [https://www.ncbi.nlm.nih.gov/nuccore/KY769370 KY769370]) was secreted only during growth on pine and poplar, suggesting a role in wood decay. AA14 modules never occur with CBMs, [[carbohydrate-binding modules]] which explains why the family could not be discovered by the module-walking approach, as were [[AA11]] and [[AA13]].

== Substrate specificities ==

The only two AA14 characterized so far were tested for copper-dependent oxidase activity on a range of polysaccharides. No activity could be detected on any substrate tested, including cellulose and xylans. However, addition of either of the AA14 enzymes to a ''Trichoderma reesei'' cocktail mainly composed of cellulases and xylanases led to a boost of glucose release from poplar and pine . This improvement in glucose release was dose dependent, yielding up to ~100% increase on pretreated softwood. AA14 enzymes also showed synergystic action on wood with [[AA9]] LPMOs. Finally, activity was detected on xylan adsorbed onto cellulose chains, using solid state 13C CP/MAS NMR and mass spectrometry. The observed products were C1-oxidized species with an aldonic acid at the reducing end.

== Kinetics and Mechanism ==

As all LPMOs, AA14s are copper-dependent mono-oxygenases and accordingly, mass spectrometry analyses revealed that PcAA14A and PcAA14B contained ∼1 copper atom per protein molecule. Additionally, RPE analysis revealed spin-Hamiltonian parameters similar to those obtained for AA9 LPMOs, confirming the presence of the copper(II) ion within the histidine brace coordination environment. However, as for the other LPMOs, the chemical mechanism by which the enzymes perform the reaction is still a matter of debate <cite>Hedegard2018,Bertini2018,Bissaro2017</cite>. Although the natural electron donor for AA14s is unknown, PcAA14A and PcAA14B were both able to produce hydrogen peroxide in the presence of ascorbate, cysteine or gallate as electron donors. They were also active on micronized wood without addition of electron donor, suggesting that wood components such as lignin may act as electron donors <cite>Westereng2015</cite>. N-terminal histidine in AA14s is methylated in vivo as seen for all other fungal LPMOs, but the effect on the reaction performed by the enzyme is not established yet.

== Catalytic and other important Residues ==
AA14s exhibit the canonical LPMO histidine brace coordinating the copper ion, which is exposed at the surface. In PcAA14B this histidine brace is constituted by His1, His99 and Tyr176. Interestingly, PcAA14B possesses an equally conserved tyrosine residue, Tyr240, at the edge of the substrate-binding surface, albeit located on a different loop region, which could potentially make substrate interactions. This tyrosine residue is also conserved in AA9 LPMOs <cite>Frandsen2016</cite>

== Three-dimensional structures ==
The structure of PcAA14B was solved by multiple-wavelength anomalous dispersion data recorded at the gadolinium edge, and refined at 3.0 Å resolution <cite>Couturier2018</cite>. The core of PcAA14B structure folds into a largely antiparallel immunoglobulin-like β-sandwich, a fold globally similar to those seen in LPMOs from other families <cite>Tandrup2018</cite>. However, in contrast to the flat substrate-binding surfaces observed in AA9 LPMOs, the surface of PcAA14B has a rippled shape with a clamp formed by two prominent surface loops located at the N-terminal half of the enzyme. It is interesting to note that these loops are equivalent to the L2 and L3 loop regions in AA9 LPMOs which have been shown to be involved in LPMO-substrate interactions <cite>Vaaje-Kolstadt2017</cite>.

== Family Firsts ==
;First family member identified: AA14 from ''Pycnoporus coccineus'' <cite>Couturier2018</cite>.
;First demonstration of oxidative cleavage: ''Pc''AA114A and ''Pc''AA114AB were shown to oxidatively cleave xylan chains bound to cellulose <cite>Couturier2018</cite>.
;First 3-D structure: ''Pc''AA14B from ''P. coccineus'' [{{PDBlink}}5no7 5NO7] <cite>Couturier2018</cite>

== References ==
<biblio>
#Couturier2015 pmid=26692083
#Couturier2018 pmid=29377002
#Bissaro2017 pmid=28846668
#Westereng2015 pmid=26686263
#Tandrup2018 pmid=30381341
#Frandsen2016 pmid=26928935
#Vaaje-Kolstadt2017 pmid=28086105
#Hedegard2018 pmid=29780519
#Bertini2018 pmid=29232119
</biblio>

[[Category:Auxiliary Activity Families|AA014]]

Auxiliary Activity Family 14

2019-07-02T08:46:02Z

Marie Couturier:

{{UnderConstruction}}
* [[Author]]: ^^^Marie Couturier^^^ and ^^^Jean-Guy Berrin^^^
* [[Responsible Curator]]: ^^^Jean-Guy Berrin^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Auxiliary Activity Family AA14'''
|-
|'''Clan'''
|Structurally related to [[AA9]]
|-
|'''Mechanism'''
|lytic oxidase
|-
|'''Active site residues'''
|mononuclear copper ion
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}AA14.html
|}
</div>


== Discovery of AA14 LPMOs ==

The gene encoding the first AA14 family member was identified by analysing transcriptomic and proteomic data from the white-rot basidiomycete ''Pycnoporus coccineus'' <cite>Couturier2015</cite>. This gene was highly upregulated when the fungus was grown on pine or poplar. The corresponding protein (GenBank ID [https://www.ncbi.nlm.nih.gov/nuccore/KY769370 KY769370]) was secreted only during growth on pine and poplar, suggesting a role in wood decay. AA14 modules never occur with CBMs, [[carbohydrate-binding modules]] which explains why the family could not be discovered by the module-walking approach, as were [[AA11]] and [[AA13]].

== Substrate specificities ==

The only two AA14 characterized so far were tested for copper-dependent oxidase activity on a range of polysaccharides. No activity could be detected on any substrate tested, including cellulose and xylans. However, addition of either of the AA14 enzymes to a ''Trichoderma reesei'' cocktail mainly composed of cellulases and xylanases led to a boost of glucose release from poplar and pine . This improvement in glucose release was dose dependent, yielding up to ~100% increase on pretreated softwood. AA14 enzymes also showed synergystic action on wood with [[AA9]] LPMOs. Finally, activity was detected on xylan adsorbed onto cellulose chains, using solid state 13C CP/MAS NMR and mass spectrometry. The observed products were C1-oxidized species with an aldonic acid at the reducing end.

== Kinetics and Mechanism ==

As all LPMOs, AA14s are copper-dependent mono-oxygenases and accordingly, mass spectrometry analyses revealed that PcAA14A and PcAA14B contained ∼1 copper atom per protein molecule. Additionally, RPE analysis revealed spin-Hamiltonian parameters similar to those obtained for AA9 LPMOs, confirming the presence of the copper(II) ion within the histidine brace coordination environment. However, as for the other LPMOs, the chemical mechanism by which the enzymes perform the reaction is still a matter of debate <cite>Hedegard2018,Bertini2018,Bissaro2017</cite>. Although the natural electron donor for AA14s is unknown, PcAA14A and PcAA14B were both able to produce hydrogen peroxide in the presence of ascorbate, cysteine or gallate as electron donors. They were also active on micronized wood without addition of electron donor, suggesting that wood components such as lignin may act as electron donors <cite>Westereng2015</cite>. N-terminal histidine in AA14s is methylated as seen for all other fungal LPMOs, but the effect on the reaction performed by the enzyme is not established yet.

== Catalytic and other important Residues ==
AA14s exhibit the canonical histidine brace, exposed at the surface, that coordinates the copper ion. In PcAA14B this histidine brace is constituted by His1, His99 and Tyr176. Interestingly, PcAA14B possesses an equally conserved tyrosine residue, Tyr240, at the edge of the substrate-binding surface, albeit located on a different loop region, which could potentially make substrate interactions. This tyrosine residue is also conserved in AA9 <cite>Frandsen2016</cite>

== Three-dimensional structures ==
The structure of PcAA14B was solved by multiple-wavelength anomalous dispersion data recorded at the gadolinium edge, and refined at 3.0 Å resolution <cite>Couturier2018</cite>. The core of PcAA14B structure folds into a largely antiparallel immunoglobulin-like β-sandwich, a fold globally similar to those seen in LPMOs from other families <cite>Tandrup2018</cite>. However, in contrast to the flat substrate-binding surfaces observed in AA9 LPMOs, the surface of PcAA14B has a rippled shape with a clamp formed by two prominent surface loops located at the N-terminal half of the enzyme. It is interesting to note that these loops are equivalent to the L2 and L3 loop regions in AA9 LPMOs which have been shown to be involved in LPMO-substrate interactions <cite>Vaaje-Kolstadt2017</cite>.

== Family Firsts ==
;First family member identified: AA14 from ''Pycnoporus coccineus'' <cite>Couturier2018</cite>.
;First demonstration of oxidative cleavage: ''Pc''AA114A and ''Pc''AA114AB were shown to oxidatively cleave xylan chains bound to cellulose <cite>Couturier2018</cite>.
;First 3-D structure: ''Pc''AA14B from ''P. coccineus'' [{{PDBlink}}5no7 5NO7] <cite>Couturier2018</cite>

== References ==
<biblio>
#Couturier2015 pmid=26692083
#Couturier2018 pmid=29377002
#Bissaro2017 pmid=28846668
#Westereng2015 pmid=26686263
#Tandrup2018 pmid=30381341
#Frandsen2016 pmid=26928935
#Vaaje-Kolstadt2017 pmid=28086105
#Hedegard2018 pmid=29780519
#Bertini2018 pmid=29232119
</biblio>

[[Category:Auxiliary Activity Families|AA014]]

Auxiliary Activity Family 14

2019-07-01T14:34:53Z

Marie Couturier:

{{UnderConstruction}}
* [[Author]]: ^^^Marie Couturier^^^ and ^^^Jean-Guy Berrin^^^
* [[Responsible Curator]]: ^^^Jean-Guy Berrin^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Auxiliary Activity Family AA14'''
|-
|'''Clan'''
|Structurally related to [[AA9]]
|-
|'''Mechanism'''
|lytic oxidase
|-
|'''Active site residues'''
|mononuclear copper ion
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}AA14.html
|}
</div>


== Substrate specificities ==
The gene encoding the first AA14 family member was identified by analysing transcriptomic and proteomic data from the white-rot basidiomycete ''Pycnoporus coccineus'' <cite>Couturier2015</cite>. This gene was highly upregulated when the fungus was grown on pine or poplar. The corresponding protein (GenBank ID [https://www.ncbi.nlm.nih.gov/nuccore/KY769370 KY769370]) was secreted only during growth on pine and poplar, suggesting a role in wood decay. AA14 modules never occur with CBMs, [[carbohydrate-binding modules]] which explains why the family could not be discovered by the module-walking approach, as were [[AA11]] and [[AA13]].

The only two AA14 characterized so far were tested for copper dependant oxidase activity on a range of polysaccharides. No activity could be detected on any substrate tested, including cellulose and xylans. However, addition of either of the AA14 enzymes to a ''Trichoderma reesei'' cocktail composed of mainly cellulases and xylanases led to a boost of glucose release from poplar and pine . This improvement in glucose release was dose dependent, yielding up to ~100% increase on pretreated softwood. AA14 enzymes also showed synergystic action on wood with [[AA9]] LPMOs. Finally, activity was detected on xylan adsorbed onto cellulose chains, using solid state 13C CP/MAS NMR and mass spectrometry. The observed products were C1 oxidized species with an aldonic acid at the reducing end.

== Kinetics and Mechanism ==

As all LPMOs, AA14s are copper dependent mono-oxygenases and accordingly, mass spectrometry analyses revealed that PcAA14A and PcAA14B contained ∼1 copper atom per protein molecule. However, as for the other LPMOs, the chemical mechanism by which the enzymes perform the reaction is still a matter of debate <cite>Hedegard2018</cite>,<cite>Bertini2018</cite>. Although the natural electron donor for AA14s is unknown, PcAA14A and PcAA14B were both able to produce hydrogen peroxide in the presence of ascorbate, cysteine or gallate as electron donors. They were also active on micronized wood without addition of electron donor, suggesting that wood components such as lignin may act as electron donors (Enzymatic cellulose oxidation is linked to lignin by long-range electron transfer <cite>Westereng2015</cite>. N-terminal histidine in AA14s is methylated as seen for all other fungal LPMOs, but the effect on the reaction performed by the enzyme is not established yet.

== Catalytic and other important Residues ==
AA14s exhibit the canonical histidine brace, exposed at the surface, that coordinates the copper ion. In PcAA14B this histidine brace is constituted by His1, His99 and Tyr176. Interestingly, PcAA14B possesses an equally conserved tyrosine residue, Tyr240, at the edge of the substrate-binding surface, albeit located on a different loop region, which could potentially make substrate interactions. This tyrosine residue is also conserved in AA9 <cite>Frandsen2016</cite>

== Three-dimensional structures ==
The structure of PcAA14B was solved by multiple-wavelength anomalous dispersion data recorded at the gadolinium edge, and refined at 3.0 Å resolution <cite>Couturier2018</cite>. The core of PcAA14B structure folds into a largely antiparallel immunoglobulin-like β-sandwich, a fold globally similar to those seen in LPMOs from other families <cite>Vaaje-Kolstadt2017</cite>. However, in contrast to the flat substrate-binding surfaces observed in AA9 LPMOs, the surface of PcAA14B has a rippled shape with a clamp formed by two prominent surface loops located at the N-terminal half of the enzyme. It is interesting to note that these loops are equivalent to the L2 and L3 loop regions in AA9 LPMOs which have been shown to be involved in LPMO-substrate interactions <cite>Vaaje-Kolstadt2017</cite>.

== Family Firsts ==
;First family member identified: AA14 from ''Pycnoporus coccineus'' <cite>Couturier2018</cite>.
;First demonstration of oxidative cleavage: ''Pc''AA114A and ''Pc''AA114AB were shown to oxidatively cleave xylan chains bound to cellulose <cite>Couturier2018</cite>.
;First 3-D structure: ''Pc''AA14B from ''P. coccineus'' [{{PDBlink}}5no7 5NO7] <cite>Couturier2018</cite>

== References ==
<biblio>
#Couturier2015 pmid=26692083
#Couturier2018 pmid=29377002

#Westereng2015 pmid=26686263

#Frandsen2016 pmid=26928935

#Vaaje-Kolstadt2017 pmid=28086105
#Hedegard2018 pmid=29780519

#Bertini2018 pmid=29232119
</biblio>

[[Category:Auxiliary Activity Families|AA014]]

Auxiliary Activity Family 14

2019-05-09T15:22:20Z

Marie Couturier:

Auxiliary Activity Family 14

2019-05-09T15:01:49Z

Marie Couturier:

Auxiliary Activity Family 14

2019-05-09T07:05:03Z

Marie Couturier:

User:Marie Couturier

2019-05-09T06:57:59Z

Marie Couturier:

Marie Couturier started working on carbohydrate-active enzymes in 2008 at INRA (Fungal Biodiversity and Biotechnology Lab, Marseilles, France), first as a research assistant and then as a PhD student supervised by ^^^Jean-Guy Berrin^^^. Her PhD studies focused on the characterization of a variety of fungal CAZymes ([[GH5]], [[GH26]], [[GH45]]) <cite>Couturier2011a Couturier2011b Couturier2013</cite>. In 2013 she obtained a Marie Curie fellowship to join Emma Master’s team at the University of Toronto (Bioproducts Lab, Toronto, Canada) where she was involved in metagenomic exploration of microflora originating from moose and beaver intestinal tracts <cite>Wong2017</cite>. She also studied there the enzymatic arsenal of ''Pycnoporus coccineus'' by means of transcriptomic, proteomic and functional analyses <cite>Couturier2015</cite>. This work led to the discovery of the LPMO family [[AA14]] and structure-function characterization of its first member <cite>Couturier2018</cite>. In 2017 she started a postdoctoral contract at CERMAV (Centre for Research on Plant Macromolecules, CNRS, Grenoble, France) with William Helbert where she studied several mannanase families ([[GH26]], [[GH113]]) as well as mannan degrading Polysaccharide Utilization Loci. She recently obtained a research scientist position at CERMAV to pursue her research on enzymes involved in the deconstruction of polysaccharides.

----

<biblio>
#Couturier2018 pmid=29377002
#Couturier2015 pmid=26692083
#Wong2017 pmid=29326667
#Couturier2013 pmid=23558681
#Couturier2011b pmid=22145993
#Couturier2011a pmid=21037302
</biblio>


[[Category:Contributors|Couturier,Marie]]

User:Marie Couturier

2019-05-07T15:41:40Z

Marie Couturier:

Marie Couturier started working on carbohydrate-active enzymes in 2008 at INRA (Fungal Biodiversity and Biotecjnology Lab, Marseilles, France), first as a research assistant and then as a PhD student supervised by Jean-Guy Berrin. Her PhD studies focused on the characterization of a variety of fungal CAZymes ([[GH5]], [[GH26]], [[GH45]]) <cite>Couturier2011a</cite>, <cite>Couturier2011b</cite>, <cite>Couturier2013</cite>. In 2013 she obtained a Marie Curie fellowship to join Emma Master’s team at the University of Toronto (Bioproducts Lab, Toronto, Canada) where she was involved in metagenomic exploration of microflora originating from moose and beaver intestinal tracts <cite>Wong2017</cite>. She also studied there the enzymatic arsenal of ''Pycnoporus coccineus'' by means of transcriptomic, proteomic and functional analyses <cite>Couturier2015</cite>. This work led to the discovery of the LPMO family AA14 and structure-function characterization of its first member <cite>Couturier2018</cite>. In 2017 she started a postdoctoral contract at CERMAV (Centre for Research on Plant Macromolecules, CNRS, Grenoble, France) with William Helbert where she studied several mannanase families ([[GH26]], [[GH113]]) as well as mannan degrading Polysaccharide Utilization Loci. She recently obtained a research scientist position at CERMAV to pursue her research on enzymes involved in the deconstruction of polysaccharides.

----

<biblio>
#Couturier2018 pmid=29377002
#Couturier2015 pmid=26692083
#Wong2017 pmid=29326667
#Couturier2013 pmid=23558681
#Couturier2011b pmid=22145993
#Couturier2011a pmid=21037302
</biblio>


[[Category:Contributors|Couturier,Marie]]

User:Marie Couturier

2019-05-07T15:38:54Z

Marie Couturier:

Marie Couturier started working on carbohydrate-active enzymes in 2008 at INRA (Fungal Biodiversity and Biotecjnology Lab, Marseilles, France), first as a research assistant and then as a PhD student supervised by Jean-Guy Berrin. Her PhD studies focused on the characterization of a variety of fungal CAZymes (GH5, GH26, GH45) <cite>Couturier2011a</cite>, <cite>Couturier2011b</cite>, <cite>Couturier2013</cite>. In 2013 she obtained a Marie Curie fellowship to join Emma Master’s team at the University of Toronto (Bioproducts Lab, Toronto, Canada) where she was involved in metagenomic exploration of microflora originating from moose and beaver intestinal tracts <cite>Wong2017</cite>. She also studied there the enzymatic arsenal of ''Pycnoporus coccineus'' by means of transcriptomic, proteomic and functional analyses <cite>Couturier2015</cite>. This work led to the discovery of the LPMO family AA14 and structure-function characterization of its first member <cite>Couturier2018</cite>. In 2017 she started a postdoctoral contract at CERMAV (Centre for Research on Plant Macromolecules, CNRS, Grenoble, France) with William Helbert where she studied several mannanase families (GH26, GH113, GH134) as well as mannan degrading Polysaccharide Utilization Loci. She recently obtained a research scientist position at CERMAV to pursue her research on enzymes involved in the deconstruction of polysaccharides.

----

<biblio>
#Couturier2018 pmid=29377002
#Couturier2015 pmid=26692083
#Wong2017 pmid=29326667
#Couturier2013 pmid=23558681
#Couturier2011b pmid=22145993
#Couturier2011a pmid=21037302
</biblio>


[[Category:Contributors|Couturier,Marie]]

User:Marie Couturier

2019-05-07T15:22:39Z

Marie Couturier:

Marie Couturier started working on carbohydrate-active enzymes in 2008 at INRA (BBF, Marseilles, France), first as a research assistant and then as a PhD student supervised by Jean-Guy Berrin. Her PhD studies focused on the characterization of a variety of fungal CAZymes (GH5, GH26, GH45) <cite>Couturier2011a</cite>, <cite>Couturier2011b</cite>, <cite>Couturier2013</cite>. In 2013 she obtained a Marie Curie fellowship to join Emma Master’s team at the University of Toronto (Bioproducts Lab, Toronto, Canada) where she was involved in metagenomic exploration of microflora originating from moose and beaver intestinal tracts <cite>Wong2017</cite>. She also studied there the enzymatic arsenal of ''Pycnoporus coccineus'' by means of transcriptomic, proteomic and functional analyses <cite>Couturier2015</cite>. This work led to the discovery of the LPMO family AA14 and structure-function characterization of its first member <cite>Couturier2018</cite>. In 2017 she started a postdoctoral contract at CERMAV (CNRS, Grenoble, France) with William Helbert where she studied several mannanase families (GH26, GH113, GH134) as well as mannan degrading Polysaccharide Utilization Loci. She recently obtained a research scientist position at CERMAV to pursue her research on enzymes involved in the deconstruction of polysaccharides.

----

<biblio>
#Couturier2018 pmid=29377002
#Couturier2015 pmid=26692083
#Wong2017 pmid=29326667
#Couturier2013 pmid=23558681
#Couturier2011b pmid=22145993
#Couturier2011a pmid=21037302
</biblio>


[[Category:Contributors|Couturier,Marie]]