CAZypedia - User contributions [en-ca]

User:Gabriela Persinoti

2023-07-11T17:06:34Z

Gabriela Persinoti:

[[File:Gabriela persinoti.jpeg|200px|right]]

Gabriela Persinoti is the head of Integrative Omics team of the Brazilian Biorenewables National Laboratory [https://lnbr.cnpem.br/en/ LNBR], from Brazilian National Center for Research in Energy and Materials [https://cnpem.br/en/ CNPEM]. She obtained her B.Sc. in Biomedical Informatics from the University of São Paulo (2006) and completed her PhD in Genetics (2012) at the Medical School of Ribeirão Preto (University of São Paulo). Her research interests are focused on the invetigation of microbiomes from diverse environments for the discovery of novel enzymes.

She has contributed to the investigation of CAZymes from families GH26 <cite>Mandelli2020</cite>, GH39 <cite>Morais2020</cite> GH128 <cite>Santos2020</cite>, the xyloglucan depolyemerization locus from ''Xanthomonas citri'' <cite>Vieira2021</cite> and the N-glycan depolymerization loci from ''Bifidobacterium longum'' the <cite>Cordeiro2023</cite>.

Particular notable work include the investigation of the gut microbiome of the largest living roedent Capybara <cite>Cabral2022</cite> that led to the discovery of [[Carbohydrate Binding Module Family 89|CBM89]], and [[GH173]] novel CAZy families and GH5_57 subfamily <cite>Martins2022</cite>.

----

<biblio>
#Mandelli2020 pmid=32139511
#Morais2020 pmid=32500063

#Santos2020 pmid=32451508
#Vieira2021 pmid=34193873
#Cabral2022 pmid=35110564
#Martins2022 pmid=36322419
#Cordeiro2023 pmid=36443572

</biblio>


[[Category:Contributors|Persinoti,Gabriela]]

File:Gabriela persinoti.jpeg

2023-07-11T17:02:38Z

Gabriela Persinoti:

User:Gabriela Persinoti

2023-07-11T16:44:36Z

Gabriela Persinoti:

[[Image:Blank_user-200px.png|200px|right]]

Gabriela Persinoti is the head of Integrative Omics team of the Brazilian Biorenewables National Laboratory [https://lnbr.cnpem.br/en/ LNBR], from Brazilian National Center for Research in Energy and Materials [https://cnpem.br/en/ CNPEM]. She obtained her B.Sc. in Biomedical Informatics from the University of São Paulo (2006) and completed her PhD in Genetics (2012) at the Medical School of Ribeirão Preto (University of São Paulo). Her research interests are focused on the invetigation of microbiomes from diverse environments for the discovery of novel enzymes.

She has contributed to the investigation of CAZymes from families GH26 <cite>Mandelli2020</cite>, GH39 <cite>Morais2020</cite> GH128 <cite>Santos2020</cite>, the xyloglucan depolyemerization locus from ''Xanthomonas citri'' <cite>Vieira2021</cite> and the N-glycan depolymerization loci from ''Bifidobacterium longum'' the <cite>Cordeiro2023</cite>.

Particular notable work include the investigation of the gut microbiome of the largest living roedent Capybara <cite>Cabral2022</cite> that led to the discovery of [[Carbohydrate Binding Module Family 89|CBM89]], and [[GH173]] novel CAZy families and GH5_57 subfamily <cite>Martins2022</cite>.

----

<biblio>
#Mandelli2020 pmid=32139511
#Morais2020 pmid=32500063

#Santos2020 pmid=32451508
#Vieira2021 pmid=34193873
#Cabral2022 pmid=35110564
#Martins2022 pmid=36322419
#Cordeiro2023 pmid=36443572

</biblio>


[[Category:Contributors|Persinoti,Gabriela]]

User:Gabriela Persinoti

2023-07-07T19:31:26Z

Gabriela Persinoti:

[[Image:Blank_user-200px.png|200px|right]]

Gabriela Persinoti is the head of Integrative Omics team of the Brazilian Biorenewables National Laboratory [[LNBR]], from Brazilian National Center for Research in Energy and Materials [[CNPEM]]. She obtained her B.Sc. in Biomedical Informatics from the University of São Paulo (2006) and completed her PhD in Genetics (2012) at the Medical School of Ribeirão Preto (University of São Paulo). Her research interests are focused on the invetigation of microbiomes from diverse environments for the discovery of novel enzymes.

She has contributed to the investigation of CAZymes from families GH26 <cite>Mandelli2020</cite>, GH39 <cite>Morais2020</cite> GH128 <cite>Santos2020</cite>, the xyloglucan depolyemerization locus from ''Xanthomonas citri'' <cite>Vieira2021</cite> and the N-glycan depolymerization loci from ''Bifidobacterium longum'' the <cite>Cordeiro2023</cite>.

Particular notable work include the investigation of the gut microbiome of the largest living roedent Capybara <cite>Cabral2022</cite> that led to the discovery of [[Carbohydrate Binding Module Family 89|CBM89]], and [[GH173]] novel CAZy families and GH5_57 subfamily <cite>Martins2022</cite>.

----

<biblio>
#Mandelli2020 pmid=32139511
#Morais2020 pmid=32500063

#Santos2020 pmid=32451508
#Vieira2021 pmid=34193873
#Cabral2022 pmid=35110564
#Martins2022 pmid=36322419
#Cordeiro2023 pmid=36443572

</biblio>


[[Category:Contributors|Persinoti,Gabriela]]

User:Gabriela Persinoti

2023-07-07T19:17:20Z

Gabriela Persinoti:

User:Gabriela Persinoti

2023-07-07T19:11:29Z

Gabriela Persinoti:

User:Gabriela Persinoti

2023-07-07T19:07:05Z

Gabriela Persinoti:

[[Image:Blank_user-200px.png|200px|right]]
'''This is an empty template to help you get started with composing your User page.'''

Gabriela Persinoti is the head of Integrative Omics team of the Brazilian Biorenewables National Laboratory [[LNBR]], from Brazilian National Center for Research in Energy and Materials [[CNPEM]] (since 2020). She obtained her B.Sc. in Biomedical Informatics from the University of São Paulo (2006) and completed her PhD in Genetics (2012) at the Medical School of Ribeirão Preto (University of São Paulo). Her research interests are focused on the invetigation of microbiomes from diverse environments for the discovery of novel enzymes.

She has contributed to the investigation of CAZymes from families GH26 and GH128.

* See [[User:Gerlind_Sulzenbacher]] for an example. You may copy text from this example by opening the page in another browser window and clicking the "Edit" tab.
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----

<biblio>
#Santos2020 pmid=32451508
#Cabral2022 pmid=35110564
#Cordeiro2023 pmid=36443572

</biblio>


[[Category:Contributors|Persinoti,Gabriela]]

Carbohydrate Binding Module Family 89

2023-06-22T12:58:17Z

Gabriela Persinoti:

{{UnderConstruction}}
* [[Author]]s: [[User:Mariana Morais|Mariana Abrahão Bueno de Morais]] and [[User:Gabriela Persinoti|Gabriela Felix Persinoti]]
* [[Responsible Curator]]: [[User:Mario Murakami|Mario Murakami]]
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}CBM89.html
|}
</div>


== Ligand specificities ==
The CBM89 family was created based on the discovery of an N-terminal domain appended to a GH10 xylanase recovered from a metagenome-assembled genome (MAG) of the capybara gut microbiota. The founding member, CapCBM89, was shown to interact with beechwood xylan and rye arabinoxylan according to affinity gel electrophoresis (AGE) <cite>Cabral2022</cite>. Although similar β-helix structural architectures have been found in the families GH28, GH91, PL6, and CE8, it was not observed any catalytic activity of the isolated CapCBM89 on the tested substrates <cite>Cabral2022</cite>.

== Structural Features ==

* '''Fold:''' The crystal structure of the founding member was solved at 1.85 Å resolution, which consists of 14 helical turns establishing a parallel β-helix fold <cite>Cabral2022</cite>..

* '''Features of ligand binding:''' A Ca<sup>2+</sup> was found in the structure, connecting the 11<sup>th</sup> and 12<sup>th</sup> helical turns (https://www.rcsb.org/structure/7JVI). The role of the ion seems to be only related to the domain stabilization, since a mutation in the Ca<sup>2+</sup> binding site (D344L) affected the protein stability but not its capacity to bind to arabinoxylan/xylan <cite>Cabral2022</cite>. In CapCBM89, mutants Y62A and E82A impaired the capacity to bind to arabinoxylan/xylan, indicating the importance of this motif for carbohydrate binding <cite>Cabral2022</cite> .

== Functionalities ==

* '''Functional role of CBM:''' In general, CBM89 members comprise approximately 600 to 1000 residues, which can be fused to GH domains. The founding member, [https://www.ncbi.nlm.nih.gov/protein/UMW87592.1 CapCBM89], was found appended to the N-terminus of a GH10 domain, which is clustered with CAZymes targeting arabinoxylans <cite>Cabral2022</cite>. This CAZyme cluster encodes the CapCBM89-GH10 and two exo-acting enzymes from [https://www.ncbi.nlm.nih.gov/protein/2205462650 GH43] and [https://www.ncbi.nlm.nih.gov/protein/2205462646 GH97] families <cite>Cabral2022</cite>. The GH10 domain is active on arabinoxylan and xylan, which is in agreement with the binding assays of CapCBM89, suggesting that CapCBM89 targets the GH10 domain to these substrates catalysis <cite>Cabral2022</cite>.

* '''Most Common Associated Modules:''' 1. Glycoside hydrolases from the GH10 family.

== Family Firsts ==

*'''First Identified:''' The first identified CBM89 member (CapCBM89) was from an uncultured Bacteroidaceae MAG57 recovered from the capybara gut microbiome <cite>Cabral2022</cite> .

*'''First Structural Characterization:''' The first CBM89 structure is the PDB ID 7JVI https://www.rcsb.org/structure/7JVI, retrieved from the capybara gut microbiome <cite>Cabral2022</cite> .

== References ==
<biblio>
#Cabral2022 pmid=35110564

</biblio>


[[Category:Carbohydrate Binding Module Families|CBM089]]