SEA-PHAGES | Proposed function alpha-L-arabinofuranosidase

Link to this post \| posted 03 Dec, 2018 03:22
MSMC	This gene (Stop site 27488 in Gordonia phage Bradissa) was a point of discussion at the December 1st Hackathon at Nyack College. Below is the information supporting this gene functino as alpha-L-arabinofuranosidase. Any thoughts greatly appreciated! ————————— Gene 30 – Proposed function alpha-L-arabinofuranosidase. The top HHPRED result is PF09206.10 ArabFuran-catal ; Alpha-L-arabinofuranosidase B, catalytic - This has a 100% probability (4.9 e-35 E-value) with 49.8% coverage. The CDD has 10.7% identity to pfam02906 (E-value 1.14 e-7). The following is the description for this pfam: Alpha-L-arabinofuranosidase B, catalytic Members of this family, which are present in fungal alpha-L-arabinofuranosidase B, adopt a beta-sandwich fold similar to that of Concanavalin A-like lectins/glucanase. The beta-sandwich fold consists of two anti-parallel beta-sheets with seven and and six strands, respectively. In addition, there are four helices outside of the beta-strands. The beta-sandwich strands are closely packed and curved with a jelly roll topology, creating a small catalytic pocket. The domain catalyzes the hydrolysis of alpha-1,2-, alpha-1,3- and alpha-1,5-L-arabinofuranosidic bonds in L-arabinose-containing hemicelluloses such as arabinoxylan and L-arabinan. When the amino acid sequence was run on Phyre2, the following results were provided: Fold:Concanavalin A-like lectins/glucanases Superfamily:Concanavalin A-like lectins/glucanases Family:Alpha-L-arabinofuranosidase B, N-terminal domain 103 residues ( 33% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template There are three annotated phams (14992) for this gene. Lucky10 assigns a function of alpha-L-arabinofuranosidase. The other two phages (Pollux and Hedwig) with this pham do not assign a function. HHPRED analysis of this pham in these two phages give identical results to those seen with Bradissa (>99% probability of Alpha-L-arabinofuranosidase). The role of alpha-L-arabinofuranosidase is hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides. It has been annotated in Microbacterium testaceum (https://www.uniprot.org/uniprot/E8NDZ9).

Link to this post | posted 03 Dec, 2018 03:22

This gene (Stop site 27488 in Gordonia phage Bradissa) was a point of discussion at the December 1st Hackathon at Nyack College. Below is the information supporting this gene functino as alpha-L-arabinofuranosidase. Any thoughts greatly appreciated!

—————————

Gene 30 – Proposed function alpha-L-arabinofuranosidase.

The top HHPRED result is PF09206.10 ArabFuran-catal ; Alpha-L-arabinofuranosidase B, catalytic
- This has a 100% probability (4.9 e-35 E-value) with 49.8% coverage.

The CDD has 10.7% identity to pfam02906 (E-value 1.14 e-7). The following is the description for this pfam:
Alpha-L-arabinofuranosidase B, catalytic
Members of this family, which are present in fungal alpha-L-arabinofuranosidase B, adopt a beta-sandwich fold similar to that of Concanavalin A-like lectins/glucanase. The beta-sandwich fold consists of two anti-parallel beta-sheets with seven and and six strands, respectively. In addition, there are four helices outside of the beta-strands. The beta-sandwich strands are closely packed and curved with a jelly roll topology, creating a small catalytic pocket. The domain catalyzes the hydrolysis of alpha-1,2-, alpha-1,3- and alpha-1,5-L-arabinofuranosidic bonds in L-arabinose-containing hemicelluloses such as arabinoxylan and L-arabinan.

When the amino acid sequence was run on Phyre2, the following results were provided:
Fold:Concanavalin A-like lectins/glucanases
Superfamily:Concanavalin A-like lectins/glucanases
Family:Alpha-L-arabinofuranosidase B, N-terminal domain
103 residues ( 33% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template

There are three annotated phams (14992) for this gene. Lucky10 assigns a function of alpha-L-arabinofuranosidase. The other two phages (Pollux and Hedwig) with this pham do not assign a function. HHPRED analysis of this pham in these two phages give identical results to those seen with Bradissa (>99% probability of Alpha-L-arabinofuranosidase).

The role of alpha-L-arabinofuranosidase is hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides. It has been annotated in Microbacterium testaceum (https://www.uniprot.org/uniprot/E8NDZ9).

Link to this post \| posted 03 Dec, 2018 13:12
welkin	Hi Evan, So here's some questions: How big are these types of enzymes in general? Does the phage gene encompass the entire enzyme or just the N-terminal domain? Is the N-terminal domain where the catalytic activity is, or is it just a binding region? Best, Welkin

Link to this post \| posted 03 Dec, 2018 13:46
MSMC	Welkin Pope Hi Evan, So here's some questions: How big are these types of enzymes in general? Does the phage gene encompass the entire enzyme or just the N-terminal domain? Is the N-terminal domain where the catalytic activity is, or is it just a binding region? Best, Welkin The median size of these proteins is 512 a.a. (with a SD of 173 a.a.) according to OrthoDB (2287 genes in 1175 species). This putative phage gene consists of 309 amino acids. Therefore it appears that the phage gene aligns with the N-terminus of this protein but not the C-terminus. HHPRED indicates positions 27-181 of the phage gene align with positions 4-177 of the target gene. Alpha-L-arabinofuranosidase B comprises two domains: a catalytic domain and an arabinose-binding domain (ABD). The catalytic domain appears to be in the N-terminus of the protein, while the ABD appears to be in the C-terminus. The alignment in this case is with the N-terminal catalytic domain region. I am currently looking for better resolution of how much of this domain is likely aligned in this instance.

Link to this post | posted 03 Dec, 2018 13:46

MSMC

Welkin Pope
Hi Evan,
So here's some questions:
How big are these types of enzymes in general? Does the phage gene encompass the entire enzyme or just the N-terminal domain? Is the N-terminal domain where the catalytic activity is, or is it just a binding region?

Best,
Welkin

The median size of these proteins is 512 a.a. (with a SD of 173 a.a.) according to OrthoDB (2287 genes in 1175 species). This putative phage gene consists of 309 amino acids. Therefore it appears that the phage gene aligns with the N-terminus of this protein but not the C-terminus. HHPRED indicates positions 27-181 of the phage gene align with positions 4-177 of the target gene.

Alpha-L-arabinofuranosidase B comprises two domains: a catalytic domain and an arabinose-binding domain (ABD). The catalytic domain appears to be in the N-terminus of the protein, while the ABD appears to be in the C-terminus. The alignment in this case is with the N-terminal catalytic domain region. I am currently looking for better resolution of how much of this domain is likely aligned in this instance.

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Proposed function alpha-L-arabinofuranosidase