Glycoside Hydrolase Family 173 - Revision history

Harry Brumer at 22:01, 5 July 2023

2023-07-05T22:01:23Z

Mario Murakami at 23:47, 25 June 2023

2023-06-25T23:47:25Z

Harry Brumer: added intrawiki GH family links

2023-06-25T19:34:23Z

added intrawiki GH family links

Mario Murakami at 12:59, 21 June 2023

2023-06-21T12:59:11Z

Clelton Santos at 12:57, 21 June 2023

2023-06-21T12:57:06Z

Mario Murakami at 12:41, 21 June 2023

2023-06-21T12:41:00Z

Mario Murakami at 12:40, 21 June 2023

2023-06-21T12:40:34Z

Clelton Santos at 13:36, 16 June 2023

2023-06-16T13:36:44Z

Clelton Santos at 13:31, 16 June 2023

2023-06-16T13:31:41Z

Clelton Santos at 13:28, 16 June 2023

2023-06-16T13:28:39Z

@@ Line 29: / Line 29: @@
 == Substrate specificities ==
-The GH173 family comprises so far members with β-galactosidase activity <cite>Cabral2022</cite>. The founding member of the GH173 family named herein as CapGH173 ([https://www.ncbi.nlm.nih.gov/nuccore/2205462651 PBMDCECB_44807]), was identified in a metagenome-assembled genome (''Bacteroidales bacterium'' MAG42) recovered from capybara gut microbiota, which potentially represents a novel genus from the UBA932 family. The enzyme CapGH173 was found in a Polysaccharide Utilization Loci (PUL) that includes enzymes from the families [[GH2]] and [[GH78]], remaining yet unclear the target carbohydrate. GH173 members often exhibit a modular architecture including a [[GH36]] domain. Substrate kinetics characterization of CapGH173 was demonstrated on synthetic substrate ''p''-nitrophenyl-β-D-galactopyranoside (pNP-β-D-Gal). Phylogenetic analysis showed that this family belongs to the GH-A clan, being remotely related to the families [[GH30]] and [[GH5]] <cite>Cabral2022</cite>.
+The GH173 family comprises so far members with β-galactosidase activity <cite>Cabral2022</cite>. The founding member of the GH173 family named herein as CapGH173 ([https://www.ncbi.nlm.nih.gov/nuccore/2205462651 PBMDCECB_44807]), was identified in a metagenome-assembled genome (''Bacteroidales bacterium'' MAG42) recovered from capybara gut microbiota, which potentially represents a novel genus from the UBA932 family. The enzyme CapGH173 was found in a Polysaccharide Utilization Loci (PUL) that includes enzymes from the families [[GH2]] and [[GH78]], yet the target carbohydrate remains unclear. GH173 members often exhibit a modular architecture including a [[GH36]] domain. Substrate kinetics characterization of CapGH173 was demonstrated on synthetic substrate ''p''-nitrophenyl-β-D-galactopyranoside (pNP-β-D-Gal). Phylogenetic analysis showed that this family belongs to the GH-A clan, being remotely related to the families [[GH30]] and [[GH5]] <cite>Cabral2022</cite>.
 == Kinetics and Mechanism ==

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
-{{UnderConstruction}}
+{{CuratorApproved}}
 * [[Author]]s: [[User:Clelton Santos|Clelton Aparecido dos Santos]] and [[User:Gabriela Persinoti|Gabriela Felix Persinoti]]
 * [[Responsible Curator]]: [[User:Mario Murakami|Mario Murakami]]

@@ Line 29: / Line 29: @@
 == Substrate specificities ==
-The GH173 family comprises so far members with β-galactosidase activity <cite>Cabral2022</cite>. The founding member of the GH173 family named herein as CapGH173 ([https://www.ncbi.nlm.nih.gov/nuccore/2205462651 PBMDCECB_44807]), was identified in a metagenome-assembled genome (''Bacteroidales bacterium'' MAG42) recovered from capybara gut microbiota, which potentially represents a novel genus from the UBA932 family. The enzyme CapGH173 was found in a Polysaccharide Utilization Loci (PUL) that includes enzymes from the families GH2 and GH78, remaining yet unclear the target carbohydrate. GH173 members often exhibit a modular architecture including a GH36 domain. Substrate kinetics characterization of CapGH173 was demonstrated on synthetic substrate ''p''-nitrophenyl-β-D-galactopyranoside (pNP-β-D-Gal). Phylogenetic analysis showed that this family belongs to the GH-A clan, being remotely related to the families GH30 and GH5 <cite>Cabral2022</cite>.
+The GH173 family comprises so far members with β-galactosidase activity <cite>Cabral2022</cite>. The founding member of the GH173 family named herein as CapGH173 ([https://www.ncbi.nlm.nih.gov/nuccore/2205462651 PBMDCECB_44807]), was identified in a metagenome-assembled genome (''Bacteroidales bacterium'' MAG42) recovered from capybara gut microbiota, which potentially represents a novel genus from the UBA932 family. The enzyme CapGH173 was found in a Polysaccharide Utilization Loci (PUL) that includes enzymes from the families [[GH2]] and [[GH78]], remaining yet unclear the target carbohydrate. GH173 members often exhibit a modular architecture including a [[GH36]] domain. Substrate kinetics characterization of CapGH173 was demonstrated on synthetic substrate ''p''-nitrophenyl-β-D-galactopyranoside (pNP-β-D-Gal). Phylogenetic analysis showed that this family belongs to the GH-A clan, being remotely related to the families [[GH30]] and [[GH5]] <cite>Cabral2022</cite>.
 == Kinetics and Mechanism ==
@@ Line 38: / Line 38: @@
 == Three-dimensional structures ==
-Protein modeling and threading performed using AlphaFold and PDBsum, respectively, suggest that CapGH173 consists of an (α/β)<sub>8</sub>-barrel structure, which is an archetypal scaffold of the clan GH-A. According to structural predictions, CapGH173 exhibits a two-domain architecture including an appended β-sandwich domain, which is a similar structural organization found in the GH30 family. Except for the residues defining the clan GH-A, sequence alignment with GH5 and GH30 members revealed very low sequence conservation, below the criterium for significant similarity detection (using an e-value < 0.05), demonstrating that although the domains in the tertiary structure can be similar, the sequences between these families are remarkably diverse <cite>Cabral2022</cite>.
+Protein modeling and threading performed using AlphaFold and PDBsum, respectively, suggest that CapGH173 consists of an (α/β)<sub>8</sub>-barrel structure, which is an archetypal scaffold of the clan GH-A. According to structural predictions, CapGH173 exhibits a two-domain architecture including an appended β-sandwich domain, which is a similar structural organization found in the [[GH30]] family. Except for the residues defining the clan GH-A, sequence alignment with [[GH5]] and [[GH30]] members revealed very low sequence conservation, below the criterium for significant similarity detection (using an e-value < 0.05), demonstrating that although the domains in the tertiary structure can be similar, the sequences between these families are remarkably diverse <cite>Cabral2022</cite>.
 == Family Firsts ==

@@ Line 35: / Line 35: @@
 == Catalytic Residues ==
-The residues E305 and E207 was inferred to correspond to the nucleophile and acid/base, respectively, based on the structural analysis of AlphaFold models <cite>Cabral2022</cite>.
+The residues E305 and E207 (sequence numbering based on the founding member, CapGH173) was inferred to correspond to the nucleophile and acid/base, respectively, based on the structural analysis of AlphaFold models <cite>Cabral2022</cite>.
 == Three-dimensional structures ==

@@ Line 29: / Line 29: @@
 == Substrate specificities ==
-The GH173 family comprises so far members with β-galactosidase activity <cite>Cabral2022</cite>. The founding member of the GH173 family named herein as CapGH173 ([https://www.ncbi.nlm.nih.gov/nuccore/2205462651 PBMDCECB_44807]), was identified in a metagenome-assembled genome (''Bacteroidales bacterium'' MAG42) recovered from capybara microbiota, which potentially represents a novel genus from the UBA932 family. The enzyme CapGH173 was found in a Polysaccharide Utilization Loci (PUL) that includes enzymes from the families GH2 and GH78, remaining yet unclear the target carbohydrate. GH173 members often exhibit a modular architecture including a GH36 domain. Substrate kinetics characterization of CapGH173 was demonstrated on synthetic substrate ''p''-nitrophenyl-β-D-galactopyranoside (pNP-β-D-Gal). Phylogenetic analysis showed that this family belongs to the GH-A clan, being remotely related to the families GH30 and GH5 <cite>Cabral2022</cite>.
+The GH173 family comprises so far members with β-galactosidase activity <cite>Cabral2022</cite>. The founding member of the GH173 family named herein as CapGH173 ([https://www.ncbi.nlm.nih.gov/nuccore/2205462651 PBMDCECB_44807]), was identified in a metagenome-assembled genome (''Bacteroidales bacterium'' MAG42) recovered from capybara gut microbiota, which potentially represents a novel genus from the UBA932 family. The enzyme CapGH173 was found in a Polysaccharide Utilization Loci (PUL) that includes enzymes from the families GH2 and GH78, remaining yet unclear the target carbohydrate. GH173 members often exhibit a modular architecture including a GH36 domain. Substrate kinetics characterization of CapGH173 was demonstrated on synthetic substrate ''p''-nitrophenyl-β-D-galactopyranoside (pNP-β-D-Gal). Phylogenetic analysis showed that this family belongs to the GH-A clan, being remotely related to the families GH30 and GH5 <cite>Cabral2022</cite>.
 == Kinetics and Mechanism ==

@@ Line 29: / Line 29: @@
 == Substrate specificities ==
-The GH173 family comprises members with β-galactosidase activity <cite>Cabral2022</cite>. The founding member of the GH173 family named herein as CapGH173 ([https://www.ncbi.nlm.nih.gov/nuccore/2205462651 PBMDCECB_44807]), was identified in a novel metagenome-assembled genome (MAG) recovered from the ''Bacteroidales bacterium'' MAG42, a novel genus among the Uncultivated Bacteria and Archaea family (UBA932). CapGH173 was found in a Polysaccharide Utilization Loci (PUL) that includes enzymes from families GH2 and GH78; however, a multidomain protein organization was also predicted among GH173 members, having an additional GH36 domain. Biochemical characterization of CapGH173 showed it is active on ''p''-nitrophenyl-β-D-galactopyranoside (pNP-β-D-Gal) and kinetic parameters were determined from substrate saturation curves. Phylogenetic analysis showed that CapGH173 is remotely related to GH-A CAZy families, with GH30 and GH5 being the closest ones <cite>Cabral2022</cite>.
+The GH173 family comprises so far members with β-galactosidase activity <cite>Cabral2022</cite>. The founding member of the GH173 family named herein as CapGH173 ([https://www.ncbi.nlm.nih.gov/nuccore/2205462651 PBMDCECB_44807]), was identified in a metagenome-assembled genome (''Bacteroidales bacterium'' MAG42) recovered from capybara microbiota, which potentially represents a novel genus from the UBA932 family. The enzyme CapGH173 was found in a Polysaccharide Utilization Loci (PUL) that includes enzymes from the families GH2 and GH78, remaining yet unclear the target carbohydrate. GH173 members often exhibit a modular architecture including a GH36 domain. Substrate kinetics characterization of CapGH173 was demonstrated on synthetic substrate ''p''-nitrophenyl-β-D-galactopyranoside (pNP-β-D-Gal). Phylogenetic analysis showed that this family belongs to the GH-A clan, being remotely related to the families GH30 and GH5 <cite>Cabral2022</cite>.
 == Kinetics and Mechanism ==
-Family GH173 members are retaining enzymes (inferred <cite>Cabral2022</cite>).
+GH173 members are inferred to be retaining enzymes <cite>Cabral2022</cite>.
 == Catalytic Residues ==
-The residues E305 and E207 correspond to the nucleophile and acid/base, respectively (inferred by structural superposition) <cite>Cabral2022</cite>.
+The residues E305 and E207 was inferred to correspond to the nucleophile and acid/base, respectively, based on the structural analysis of AlphaFold models (<cite>Cabral2022</cite>).
 == Three-dimensional structures ==
-Protein modeling and threading performed using AlphaFold and PDBsum, respectively, revealed that CapGH173 consists of an (α/β)<sub>8</sub>-barrel structure, which is an archetypal scaffold of the clan GH-A. According to structural predictions, CapGH173 exhibits a two-domain architecture including an appended β-sandwich domain, which is a similar structural organization found in the GH30 family. Except for the residues defining the clan GH-A, sequence alignment with GH5 and GH30 members revealed a very low sequence conservation below the criterium for significant similarity detection (using an e-value < 0.05), demonstrating that although the domains in the tertiary structure can be similar, the sequences between these families are remarkably diverse <cite>Cabral2022</cite>.
+Protein modeling and threading performed using AlphaFold and PDBsum, respectively, suggest that CapGH173 consists of an (α/β)<sub>8</sub>-barrel structure, which is an archetypal scaffold of the clan GH-A. According to structural predictions, CapGH173 exhibits a two-domain architecture including an appended β-sandwich domain, which is a similar structural organization found in the GH30 family. Except for the residues defining the clan GH-A, sequence alignment with GH5 and GH30 members revealed very low sequence conservation, below the criterium for significant similarity detection (using an e-value < 0.05), demonstrating that although the domains in the tertiary structure can be similar, the sequences between these families are remarkably diverse <cite>Cabral2022</cite>.
 == Family Firsts ==
-;First stereochemistry determination: CpGH173 is shown to have an inferred retaining mechanism.
+;First stereochemistry determination: CapGH173 is inferred to operate by a retaining mechanism.
 ;First catalytic nucleophile identification: E305 (inferred).
 ;First general acid/base residue identification: E207 (inferred).