<i>Ab initio</i> phasing of a nucleoside hydrolase‐related hypothetical protein from <i>Saccharophagus degradans</i> that is associated with carbohydrate metabolism

Hehemann, Jan‐Hendrik; Marsters, C.; Boraston, A.B.

doi:10.1002/prot.23126

Cited by 5 publications

(5 citation statements)

References 23 publications

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“…KMS12 and HTS10 clusters included An02g13630.Aspni5_37552, which is expressed under most conditions of lignocellulose degradation but only to ~30 FPKM. Its DUF159 domain is also found in a bacterial protein with multiple carbohydrate-binding modules, but while its structure suggests that it is a catalytic domain active on furanose sugars, no activity has been demonstrated so far [ 55 ]. Gene An02g11390.Aspni5_197780 (ILS14) was identified only in cluster ILS14, and high expression (to ~1100 FPKM) for all substrates was observed at the 3- and 6-h time point, but also on glucose at 3 h, suggesting a non-lignocellulose specific role.…”

Section: Resultsmentioning

confidence: 99%

Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments

Daly

Munster

Blythe

et al. 2017

Biotechnol Biofuels

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BackgroundThe capacity of fungi, such as Aspergillus niger, to degrade lignocellulose is harnessed in biotechnology to generate biofuels and high-value compounds from renewable feedstocks. Most feedstocks are currently pretreated to increase enzymatic digestibility: improving our understanding of the transcriptomic responses of fungi to pretreated lignocellulosic substrates could help to improve the mix of activities and reduce the production costs of commercial lignocellulose saccharifying cocktails.ResultsWe investigated the responses of A. niger to untreated, ionic liquid and hydrothermally pretreated wheat straw over a 5-day time course using RNA-seq and targeted proteomics. The ionic liquid pretreatment altered the cellulose crystallinity while retaining more of the hemicellulosic sugars than the hydrothermal pretreatment. Ionic liquid pretreatment of straw led to a dynamic induction and repression of genes, which was correlated with the higher levels of pentose sugars saccharified from the ionic liquid-pretreated straw. Hydrothermal pretreatment of straw led to reduced levels of transcripts of genes encoding carbohydrate-active enzymes as well as the derived proteins and enzyme activities. Both pretreatments abolished the expression of a large set of genes encoding pectinolytic enzymes. These reduced levels could be explained by the removal of parts of the lignocellulose by the hydrothermal pretreatment. The time course also facilitated identification of temporally limited gene induction patterns.ConclusionsThe presented transcriptomic and biochemical datasets demonstrate that pretreatments caused modifications of the lignocellulose, to both specific structural features as well as the organisation of the overall lignocellulosic structure, that determined A. niger transcript levels. The experimental setup allowed reliable detection of substrate-specific gene expression patterns as well as hitherto non-expressed genes. Our data suggest beneficial effects of using untreated and IL-pretreated straw, but not HT-pretreated straw, as feedstock for CAZyme production.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-017-0700-9) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments

Daly

Munster

Blythe

et al. 2017

Biotechnol Biofuels

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“…β-Sandwich 2 closely interacts with the core β-helix and β-barrel 1 domain (Figure 2C). A structural homology search using the DALI server 34) was performed with each β-sandwich domain, and the only two hits related to CAZymes activity were found with the β-sandwich 1 domain (Table S5): an uncharacterized domain of a carbohydrate-associated hypothetical protein from Saccharophagus degradans 2-40 (Z-score = 8.1) 35) and a Bacteroidetes-associated carbohydrate-binding often N-terminal (BACON) domain of a xyloglucanase from Bacteroides ovatus (Z-score = 8.1). 36)…”

Section: Resultsmentioning

confidence: 99%

Crystal structure ofBifidobacterium bifidumglycoside hydrolase family 110 α-galactosidase specific for blood group B antigen

Kashima,

Akama,

Wakinaka

et al. 2024

Preprint

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To overcome incompatibility issues and increase the possibility of blood transfusion, technologies that enable efficient conversion of A- and B-type red blood cells to the universal donor O-type is desirable. Although several blood type-converting enzymes have been identified, detailed understanding about their molecular functions is limited. α-Galactosidase fromBifidobacterium bifidumJCM 1254 (AgaBb), belonging to glycoside hydrolase (GH) 110 subfamily A, specifically acts on blood group B antigen. Here we present the crystal structure of AgaBb, including the catalytic GH110 domain and part of the C-terminal uncharacterized regions. Based on this structure, we deduced a possible binding mechanism of blood group B antigen to the active site. Site-directed mutagenesis confirmed that R270 and E380 recognize the fucose moiety in the B antigen. Thermal shift assay revealed that the C-terminal uncharacterized region significantly contributes to protein stability. This region is shared only among GH110 enzymes fromB. bifidumand someRuminococcusspecies. The elucidation of the molecular basis for the specific recognition of blood group B antigen is expected to lead to the practical application of blood group conversion enzymes in the future.

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“…The NH domain in the putative protein Sde_0182 follows three carbohydrate-binding domains and a beta-sandwich domain and is inactive toward purine and pyrimidine nucleosides. Thus, the current hypothesis is that the NH-like domain in this protein is employed as a furanose sugar-interacting module [ 53 ].…”

Section: Reviewmentioning

confidence: 99%

“…In the S. degradans Sde_0182 protein, the C-terminal domain adopts an NH-like fold with a preserved Ca 2+ ion and an additional β-sandwich domain that interacts with the region corresponding to the dimerization interface. Thus, the presence of an additional domain provides structural stabilization but prevents oligomerization of the NH domain of Sde_0182 [ 53 ]. This protein is also catalytically inactive while retaining the ribofuranose-binding capability, and further reinforces the concept that the assembly of dimers or tetramers in NHs is a primary means to achieve a catalytically competent active site to achieve N-glycosidic bond hydrolysis.…”

Section: Reviewmentioning

confidence: 99%

Structure, Oligomerization and Activity Modulation in N-Ribohydrolases

Degano

2022

IJMS

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Enzymes catalyzing the hydrolysis of the N-glycosidic bond in nucleosides and other ribosides (N-ribohydrolases, NHs) with diverse substrate specificities are found in all kingdoms of life. While the overall NH fold is highly conserved, limited substitutions and insertions can account for differences in substrate selection, catalytic efficiency, and distinct structural features. The NH structural module is also employed in monomeric proteins devoid of enzymatic activity with different physiological roles. The homo-oligomeric quaternary structure of active NHs parallels the different catalytic strategies used by each isozyme, while providing a buttressing effect to maintain the active site geometry and allow the conformational changes required for catalysis. The unique features of the NH catalytic strategy and structure make these proteins attractive targets for diverse therapeutic goals in different diseases.

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Ab initio phasing of a nucleoside hydrolase‐related hypothetical protein from Saccharophagus degradans that is associated with carbohydrate metabolism

Cited by 5 publications

References 23 publications

Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments

Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments

Crystal structure ofBifidobacterium bifidumglycoside hydrolase family 110 α-galactosidase specific for blood group B antigen

Structure, Oligomerization and Activity Modulation in N-Ribohydrolases

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