Database for Polyphenol Utilized Proteins from gut microbiota
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Subfamily Sequences


Literature Information

Title Identification and functional expression of genes encoding flavonoid O‐ and C‐glycosidases in intestinal bacteria
Author Annett Braune, Wolfram Engst, Michael Blaut
DOI 10.1111/1462-2920.12864
Abstract Gut bacteria play a crucial role in the metabolism of dietary flavonoids and thereby influence the bioactivity of these compounds in the host. The intestinal Lachnospiraceae strain CG19‐1 and Eubacterium cellulosolvens are able to deglycosylate C‐ and O‐coupled flavonoid glucosides. Growth of strain CG19‐1 in the presence of the isoflavone C‐glucoside puerarin (daidzein 8‐C‐glucoside) led to the induction of two proteins (DfgC, DfgD). Heterologous expression of the encoding genes (dfgC, dfgD) in Escherichia coli revealed no C‐deglycosylating activity in the resulting cell extracts but cleavage of flavonoid O‐glucosides such as daidzin (daidzein 7‐O‐glucoside). The recombinant DfgC and DfgD proteins were purified and characterized with respect to their quaternary structure, substrate and cofactor specificity. The products of the corresponding genes (dfgC, dfgD) from E. cellulosolvens also catalysed the O‐deglycosylation of daidzin following their expression in E. coli. In combination with three recombinant proteins encoded by adjacent genes in E. cellulosolvens (dfgA, dfgB, dfgE), DfgC and DfgD from E*. cellulosolvens* catalysed the deglycosylation of the flavone C‐glucosides homoorientin (luteolin 6‐C‐glucoside) and isovitexin (apigenin 6‐C‐glucoside). Even intact cells of E*. coli* expressing the five E. cellulosolvens genes cleaved these flavone C‐glucosides and, also, flavonoid O‐glucosides to the corresponding aglycones.

Experimental results

  • Enzyme

Uniprot ID: A0A0E3TKF2

Protein: DfgC

Organism: Catenibacillus scindens

Length: 279 AA

Taxonomic identifier: 673271 [NCBI]

  • Pfam
Source Domain Start End E-value (Domain) Coverage
Pfam-A AP_endonuc_2 30 204 1.1e-18 0.914

Program: hmmscan

Version: 3.1b2 (February 2015)

Method: hmmscan --domtblout hmmscan.tbl --noali -E 1e-5 pfam query.fa

Date: Mon Jul 20 14:32:16 2020

Description:

AP_endonuc_2

Pfam

This TIM alpha/beta barrel structure is found in xylose isomerase (P19148) and in endonuclease IV (P12638 EC:3.1.21.2). This domain is also found in the N termini of bacterial myo-inositol catabolism proteins. These are involved in the myo-inositol catabolism pathway, and is required for growth on myo-inositol in Rhizobium leguminosarum bv. viciae[1].

InterPro

This entry represents a structural motif with a beta/alpha TIM barrel found in several proteins families:

▹ Endonuclease IV (3.1.21.2), an AP (apurinic/apyrimidinic) endonuclease that primes DNA repair synthesis by cleaving the DNA backbone 5’ of AP sites[2].

▹ L-rhamnose isomerase (5.3.1.14), a tetramer of four TIM barrels that catalyses the isomerisation between aldoses and ketoses, such as between L-rhamnose and L-rhamnulose[3].

▹ Xylose isomerase (5.3.1.5), which catalyses the first reaction in the catabolism of D-xylose by converting D-xylose to D-xylulose[4].

▹ Mannonate dehydratase UxuA, which along with mannonate oxidoreductase converts D-fructuronate to 2-keto-3-deoxy-D-gluconate[5].

These proteins share similar, but not identical, metal-binding sites. In addition, xylose isomerase and L-rhamnose isomerase each have additional alpha-helical domains involved in tetramer formation.

Information is taken from Pfam and InterPro web site.

  • Reaction

Recombined with A0A0E3TJD6

daidzindaidzein + glucose

[L1]daidzin
right_arrow
[R1]daidzein
plus
[R2]glucose

References

  1. Fry J, Wood M, Poole P S. Investigation of myo-inositol catabolism in Rhizobium leguminosarum bv. viciae and its effect on nodulation competitiveness[J]. Molecular plant-microbe interactions, 2001, 14(8): 1016-1025. ↩︎

  2. Hosfield D J, Guan Y, Haas B J, et al. Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis[J]. Cell, 1999, 98(3): 397-408. ↩︎

  3. Yoshida H, Yamada M, Ohyama Y, et al. The structures of L-rhamnose isomerase from Pseudomonas stutzeri in complexes with L-rhamnose and D-allose provide insights into broad substrate specificity[J]. Journal of molecular biology, 2007, 365(5): 1505-1516. ↩︎

  4. Meilleur F, Snell E H, Van der Woerd M J, et al. A quasi-Laue neutron crystallographic study of D-xylose isomerase[J]. European Biophysics Journal, 2006, 35(7): 601-609. ↩︎

  5. Robert-Baudouy J, Portalier R, Stoeber F. Regulation of hexuronate system genes in Escherichia coli K-12: multiple regulation of the uxu operon by exuR and uxuR gene products[J]. Journal of Bacteriology, 1981, 145(1): 211-220. ↩︎

Literature Information

Title Identification and functional expression of genes encoding flavonoid O‐ and C‐glycosidases in intestinal bacteria
Author Annett Braune, Wolfram Engst, Michael Blaut
DOI 10.1111/1462-2920.12864
Abstract Gut bacteria play a crucial role in the metabolism of dietary flavonoids and thereby influence the bioactivity of these compounds in the host. The intestinal Lachnospiraceae strain CG19‐1 and Eubacterium cellulosolvens are able to deglycosylate C‐ and O‐coupled flavonoid glucosides. Growth of strain CG19‐1 in the presence of the isoflavone C‐glucoside puerarin (daidzein 8‐C‐glucoside) led to the induction of two proteins (DfgC, DfgD). Heterologous expression of the encoding genes (dfgC, dfgD) in Escherichia coli revealed no C‐deglycosylating activity in the resulting cell extracts but cleavage of flavonoid O‐glucosides such as daidzin (daidzein 7‐O‐glucoside). The recombinant DfgC and DfgD proteins were purified and characterized with respect to their quaternary structure, substrate and cofactor specificity. The products of the corresponding genes (dfgC, dfgD) from E. cellulosolvens also catalysed the O‐deglycosylation of daidzin following their expression in E. coli. In combination with three recombinant proteins encoded by adjacent genes in E. cellulosolvens (dfgA, dfgB, dfgE), DfgC and DfgD from E*. cellulosolvens* catalysed the deglycosylation of the flavone C‐glucosides homoorientin (luteolin 6‐C‐glucoside) and isovitexin (apigenin 6‐C‐glucoside). Even intact cells of E*. coli* expressing the five E. cellulosolvens genes cleaved these flavone C‐glucosides and, also, flavonoid O‐glucosides to the corresponding aglycones.

Experimental results

  • Enzyme

Uniprot ID: I5AX48

Protein: Sugar phosphate isomerase/epimerase

Organism: [Eubacterium] cellulosolvens 6

Length: 278 AA

Taxonomic identifier: 633697 [NCBI]

  • Pfam
Source Domain Start End E-value (Domain) Coverage
Pfam-A AP_endonuc_2 29 206 1.4e-19 0.983

Program: hmmscan

Version: 3.1b2 (February 2015)

Method: hmmscan --domtblout hmmscan.tbl --noali -E 1e-5 pfam query.fa

Date: Mon Jul 20 14:32:16 2020

Description:

AP_endonuc_2

Pfam

This TIM alpha/beta barrel structure is found in xylose isomerase (P19148) and in endonuclease IV (P12638 EC:3.1.21.2). This domain is also found in the N termini of bacterial myo-inositol catabolism proteins. These are involved in the myo-inositol catabolism pathway, and is required for growth on myo-inositol in Rhizobium leguminosarum bv. viciae[1].

InterPro

This entry represents a structural motif with a beta/alpha TIM barrel found in several proteins families:

▹ Endonuclease IV (3.1.21.2), an AP (apurinic/apyrimidinic) endonuclease that primes DNA repair synthesis by cleaving the DNA backbone 5’ of AP sites[2].

▹ L-rhamnose isomerase (5.3.1.14), a tetramer of four TIM barrels that catalyses the isomerisation between aldoses and ketoses, such as between L-rhamnose and L-rhamnulose[3].

▹ Xylose isomerase (5.3.1.5), which catalyses the first reaction in the catabolism of D-xylose by converting D-xylose to D-xylulose[4].

▹ Mannonate dehydratase UxuA, which along with mannonate oxidoreductase converts D-fructuronate to 2-keto-3-deoxy-D-gluconate[5].

These proteins share similar, but not identical, metal-binding sites. In addition, xylose isomerase and L-rhamnose isomerase each have additional alpha-helical domains involved in tetramer formation.

Information is taken from Pfam and InterPro web site.

  • Reaction

Catalyse reaction with expression of I5AX46/I5AX47/I5AX48/I5AX49/I5AX50 simultaneously

daidzindaidzein + glucose

[L1]daidzin
right_arrow
[R1]daidzein
plus
[R2]glucose

References

  1. Fry J, Wood M, Poole P S. Investigation of myo-inositol catabolism in Rhizobium leguminosarum bv. viciae and its effect on nodulation competitiveness[J]. Molecular plant-microbe interactions, 2001, 14(8): 1016-1025. ↩︎

  2. Hosfield D J, Guan Y, Haas B J, et al. Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis[J]. Cell, 1999, 98(3): 397-408. ↩︎

  3. Yoshida H, Yamada M, Ohyama Y, et al. The structures of L-rhamnose isomerase from Pseudomonas stutzeri in complexes with L-rhamnose and D-allose provide insights into broad substrate specificity[J]. Journal of molecular biology, 2007, 365(5): 1505-1516. ↩︎

  4. Meilleur F, Snell E H, Van der Woerd M J, et al. A quasi-Laue neutron crystallographic study of D-xylose isomerase[J]. European Biophysics Journal, 2006, 35(7): 601-609. ↩︎

  5. Robert-Baudouy J, Portalier R, Stoeber F. Regulation of hexuronate system genes in Escherichia coli K-12: multiple regulation of the uxu operon by exuR and uxuR gene products[J]. Journal of Bacteriology, 1981, 145(1): 211-220. ↩︎


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