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Discovery and characterization of a new family of lytic polysaccharide monooxygenases.

Hemsworth GR, Henrissat B, Davies GJ, Walton PH - Nat. Chem. Biol. (2013)

Bottom Line: They are attracting considerable attention owing to their potential use in biomass conversion, notably in the production of biofuels.Previous studies have identified two discrete sequence-based families of these enzymes termed AA9 (formerly GH61) and AA10 (formerly CBM33).The newly characterized AA11 family expands the LPMO clan, potentially broadening both the range of potential substrates and the types of reactive copper-oxygen species formed at the active site of LPMOs.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, University of York, Heslington, York, UK.

ABSTRACT
Lytic polysaccharide monooxygenases (LPMOs) are a recently discovered class of enzymes capable of oxidizing recalcitrant polysaccharides. They are attracting considerable attention owing to their potential use in biomass conversion, notably in the production of biofuels. Previous studies have identified two discrete sequence-based families of these enzymes termed AA9 (formerly GH61) and AA10 (formerly CBM33). Here, we report the discovery of a third family of LPMOs. Using a chitin-degrading exemplar from Aspergillus oryzae, we show that the three-dimensional structure of the enzyme shares some features of the previous two classes of LPMOs, including a copper active center featuring the 'histidine brace' active site, but is distinct in terms of its active site details and its EPR spectroscopy. The newly characterized AA11 family expands the LPMO clan, potentially broadening both the range of potential substrates and the types of reactive copper-oxygen species formed at the active site of LPMOs.

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“Module walking” to discover new LPMOs.
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Figure 2: “Module walking” to discover new LPMOs.

Mentions: Analysis of the sequences in this candidate new LPMO family shows that these proteins exist either appended to X278 or as a single module, Fig. 2. The AA11 domain of BAE61530.1 was used as the query sequence for a BLAST search (23 September 2013) on the non-redundant protein sequence database of the NCBI, and this retrieved approximately 450 sequences of the putative AA11 family with e-values better than 4 × 10−4 (data not shown). Only three of the several hundred known AA9 sequences were found in the BLAST report, but with e-values worse than 10−3, the commonly accepted threshold of significance. Similarly a Pfam search on the server of the Sanger Institute (pfam.sanger.ac.uk) with the sequence of A. oryzae AA11 (GenBank BAE61530) failed to identify a significant hit with the profile “glyco_hydro_61” corresponding to family AA9, whereas a search conducted with the bona fide A. oryzae AA9 protein (GenBank BAE64395) gave a significant match (e-value of 3.9 × 10−80) with this profile. Collectively this indicates that AA11 defines a sequence family separate from AA9 and one which already contains several hundred fungal proteins (Supplementary Data Set). An alignment of thirty AA11 sequences derived from finished genomes is shown in Supplementary Fig. 2. Furthermore, we identified three metazoan AA11 genes in the recently published genome of the bdelloid rotifer Adineta vaga (PMID=23873043).18 The asexual reproductive biology of this organism has been shown to be accompanied by large amounts of horizontal gene transfers (HGT) from bacteria, plants and fungi.18 Notably all polysaccharide lyase and 40% of all glycoside hydrolase genes in A. vaga are from HGT. It is very likely therefore that the three AA11 genes in A. vaga have a fungal origin.


Discovery and characterization of a new family of lytic polysaccharide monooxygenases.

Hemsworth GR, Henrissat B, Davies GJ, Walton PH - Nat. Chem. Biol. (2013)

“Module walking” to discover new LPMOs.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4274766&req=5

Figure 2: “Module walking” to discover new LPMOs.
Mentions: Analysis of the sequences in this candidate new LPMO family shows that these proteins exist either appended to X278 or as a single module, Fig. 2. The AA11 domain of BAE61530.1 was used as the query sequence for a BLAST search (23 September 2013) on the non-redundant protein sequence database of the NCBI, and this retrieved approximately 450 sequences of the putative AA11 family with e-values better than 4 × 10−4 (data not shown). Only three of the several hundred known AA9 sequences were found in the BLAST report, but with e-values worse than 10−3, the commonly accepted threshold of significance. Similarly a Pfam search on the server of the Sanger Institute (pfam.sanger.ac.uk) with the sequence of A. oryzae AA11 (GenBank BAE61530) failed to identify a significant hit with the profile “glyco_hydro_61” corresponding to family AA9, whereas a search conducted with the bona fide A. oryzae AA9 protein (GenBank BAE64395) gave a significant match (e-value of 3.9 × 10−80) with this profile. Collectively this indicates that AA11 defines a sequence family separate from AA9 and one which already contains several hundred fungal proteins (Supplementary Data Set). An alignment of thirty AA11 sequences derived from finished genomes is shown in Supplementary Fig. 2. Furthermore, we identified three metazoan AA11 genes in the recently published genome of the bdelloid rotifer Adineta vaga (PMID=23873043).18 The asexual reproductive biology of this organism has been shown to be accompanied by large amounts of horizontal gene transfers (HGT) from bacteria, plants and fungi.18 Notably all polysaccharide lyase and 40% of all glycoside hydrolase genes in A. vaga are from HGT. It is very likely therefore that the three AA11 genes in A. vaga have a fungal origin.

Bottom Line: They are attracting considerable attention owing to their potential use in biomass conversion, notably in the production of biofuels.Previous studies have identified two discrete sequence-based families of these enzymes termed AA9 (formerly GH61) and AA10 (formerly CBM33).The newly characterized AA11 family expands the LPMO clan, potentially broadening both the range of potential substrates and the types of reactive copper-oxygen species formed at the active site of LPMOs.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, University of York, Heslington, York, UK.

ABSTRACT
Lytic polysaccharide monooxygenases (LPMOs) are a recently discovered class of enzymes capable of oxidizing recalcitrant polysaccharides. They are attracting considerable attention owing to their potential use in biomass conversion, notably in the production of biofuels. Previous studies have identified two discrete sequence-based families of these enzymes termed AA9 (formerly GH61) and AA10 (formerly CBM33). Here, we report the discovery of a third family of LPMOs. Using a chitin-degrading exemplar from Aspergillus oryzae, we show that the three-dimensional structure of the enzyme shares some features of the previous two classes of LPMOs, including a copper active center featuring the 'histidine brace' active site, but is distinct in terms of its active site details and its EPR spectroscopy. The newly characterized AA11 family expands the LPMO clan, potentially broadening both the range of potential substrates and the types of reactive copper-oxygen species formed at the active site of LPMOs.

Show MeSH
Related in: MedlinePlus