The α-Helical Cap Domain of a Novel Esterase from Gut Alistipes shahii Shaping the Substrate-Binding Pocket

Xue Wei; Yu Lu Wang; Bo Ting Wen; Shu Jun Liu; Luyao Wang; Lichao Sun; Tian Yi Gu; Zhen Li; Yuming Bao; Shi Long Fan; Huan Zhou; Fengzhong Wang; Fengjiao Xin

doi:10.1021/acs.jafc.1c00940

The α-Helical Cap Domain of a Novel Esterase from Gut Alistipes shahii Shaping the Substrate-Binding Pocket

Xue Wei, Yu Lu Wang, Bo Ting Wen, Shu Jun Liu, Luyao Wang, Lichao Sun, Tian Yi Gu, Zhen Li, Yuming Bao, Shi Long Fan, Huan Zhou, Fengzhong Wang^*, Fengjiao Xin^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

11 Citations (Scopus)

Abstract

The human gut microbiota regulates nutritional metabolism, especially by encoding specific ferulic acid esterases (FAEs) to release functional ferulic acid (FA) from dietary fiber. In our previous study, we observed seven upregulated FAE genes during in vitro fecal slurry fermentation using wheat bran. Here, a 29 kDa FAE (AsFAE) from Alistipes shahii of Bacteroides was characterized and identified as the type-A FAE. The X-ray structure of AsFAE has been determined, revealing a unique α-helical domain comprising five α-helices, which was first characterized in FAEs from the gut microbiota. Further molecular docking analysis and biochemical studies revealed that Tyr100, Thr122, Tyr219, and Ile220 are essential for substrate binding and catalytic efficiency. Additionally, Glu129 and Lys130 in the cap domain shaped the substrate-binding pocket and affected the substrate preference. This is the first report on A. shahii FAE, providing a theoretical basis for the dietary metabolism in the human gut.

Original language	English
Pages (from-to)	6064-6072
Number of pages	9
Journal	Journal of Agricultural and Food Chemistry
Volume	69
Issue number	21
DOIs	https://doi.org/10.1021/acs.jafc.1c00940
Publication status	Published - 2 Jun 2021
Externally published	Yes

Keywords

Alistipes shahii
cap domain
crystal structure
ferulic acid esterase
gut microbiota

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10.1021/acs.jafc.1c00940

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title = "The α-Helical Cap Domain of a Novel Esterase from Gut Alistipes shahii Shaping the Substrate-Binding Pocket",

abstract = "The human gut microbiota regulates nutritional metabolism, especially by encoding specific ferulic acid esterases (FAEs) to release functional ferulic acid (FA) from dietary fiber. In our previous study, we observed seven upregulated FAE genes during in vitro fecal slurry fermentation using wheat bran. Here, a 29 kDa FAE (AsFAE) from Alistipes shahii of Bacteroides was characterized and identified as the type-A FAE. The X-ray structure of AsFAE has been determined, revealing a unique α-helical domain comprising five α-helices, which was first characterized in FAEs from the gut microbiota. Further molecular docking analysis and biochemical studies revealed that Tyr100, Thr122, Tyr219, and Ile220 are essential for substrate binding and catalytic efficiency. Additionally, Glu129 and Lys130 in the cap domain shaped the substrate-binding pocket and affected the substrate preference. This is the first report on A. shahii FAE, providing a theoretical basis for the dietary metabolism in the human gut.",

keywords = "Alistipes shahii, cap domain, crystal structure, ferulic acid esterase, gut microbiota",

author = "Xue Wei and Wang, {Yu Lu} and Wen, {Bo Ting} and Liu, {Shu Jun} and Luyao Wang and Lichao Sun and Gu, {Tian Yi} and Zhen Li and Yuming Bao and Fan, {Shi Long} and Huan Zhou and Fengzhong Wang and Fengjiao Xin",

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month = jun,

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doi = "10.1021/acs.jafc.1c00940",

language = "English",

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T1 - The α-Helical Cap Domain of a Novel Esterase from Gut Alistipes shahii Shaping the Substrate-Binding Pocket

AU - Wei, Xue

AU - Wang, Yu Lu

AU - Wen, Bo Ting

AU - Liu, Shu Jun

AU - Wang, Luyao

AU - Sun, Lichao

AU - Gu, Tian Yi

AU - Li, Zhen

AU - Bao, Yuming

AU - Fan, Shi Long

AU - Zhou, Huan

AU - Wang, Fengzhong

AU - Xin, Fengjiao

PY - 2021/6/2

Y1 - 2021/6/2

N2 - The human gut microbiota regulates nutritional metabolism, especially by encoding specific ferulic acid esterases (FAEs) to release functional ferulic acid (FA) from dietary fiber. In our previous study, we observed seven upregulated FAE genes during in vitro fecal slurry fermentation using wheat bran. Here, a 29 kDa FAE (AsFAE) from Alistipes shahii of Bacteroides was characterized and identified as the type-A FAE. The X-ray structure of AsFAE has been determined, revealing a unique α-helical domain comprising five α-helices, which was first characterized in FAEs from the gut microbiota. Further molecular docking analysis and biochemical studies revealed that Tyr100, Thr122, Tyr219, and Ile220 are essential for substrate binding and catalytic efficiency. Additionally, Glu129 and Lys130 in the cap domain shaped the substrate-binding pocket and affected the substrate preference. This is the first report on A. shahii FAE, providing a theoretical basis for the dietary metabolism in the human gut.

AB - The human gut microbiota regulates nutritional metabolism, especially by encoding specific ferulic acid esterases (FAEs) to release functional ferulic acid (FA) from dietary fiber. In our previous study, we observed seven upregulated FAE genes during in vitro fecal slurry fermentation using wheat bran. Here, a 29 kDa FAE (AsFAE) from Alistipes shahii of Bacteroides was characterized and identified as the type-A FAE. The X-ray structure of AsFAE has been determined, revealing a unique α-helical domain comprising five α-helices, which was first characterized in FAEs from the gut microbiota. Further molecular docking analysis and biochemical studies revealed that Tyr100, Thr122, Tyr219, and Ile220 are essential for substrate binding and catalytic efficiency. Additionally, Glu129 and Lys130 in the cap domain shaped the substrate-binding pocket and affected the substrate preference. This is the first report on A. shahii FAE, providing a theoretical basis for the dietary metabolism in the human gut.

KW - Alistipes shahii

KW - cap domain

KW - crystal structure

KW - ferulic acid esterase

KW - gut microbiota

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U2 - 10.1021/acs.jafc.1c00940

DO - 10.1021/acs.jafc.1c00940

M3 - Article

C2 - 33979121

AN - SCOPUS:85106386218

SN - 0021-8561

VL - 69

SP - 6064

EP - 6072

JO - Journal of Agricultural and Food Chemistry

JF - Journal of Agricultural and Food Chemistry

IS - 21

ER -

The α-Helical Cap Domain of a Novel Esterase from Gut Alistipes shahii Shaping the Substrate-Binding Pocket

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