7BR2

BT4096 a gut microbial diltiazem-metabolizing enzyme

Summary for 7BR2

• Entry DOI: 10.2210/pdb7br2/pdb
• Descriptor: Lipolytic enzyme, G-D-S-L family (2 entities in total)
• Functional Keywords: gut microbe, diltiazem, drug metabolism, sgnh, gdsl, serine esterase, hydrolase
• Biological source: Bacteroides thetaiotaomicron
• Total number of polymer chains: 4
• Total formula weight: 206859.41

Authors

Ko, T.-P.,Chen, C.-C.,Guo, R.-T. (deposition date: 2020-03-26, release date: 2020-05-06, Last modification date: 2024-03-27)

Primary citation

Zhou, S.,Ko, T.P.,Huang, J.W.,Liu, W.,Zheng, Y.,Wu, S.,Wang, Q.,Xie, Z.,Liu, Z.,Chen, C.C.,Guo, R.T.
Structure of a gut microbial diltiazem-metabolizing enzyme suggests possible substrate binding mode.
Biochem.Biophys.Res.Commun., 527:799-804, 2020

PubMed Abstract: When administrated orally, the vasodilating drug diltiazem can be metabolized into diacetyl diltiazem in the presence of Bacteroides thetaiotaomicron, a human gut microbe. The removal of acetyl group from the parent drug is carried out by the GDSL/SGNH-family hydrolase BT4096. Here the crystal structure of the enzyme was solved by mercury soaking and single-wavelength anomalous diffraction. The protein folds into two parts. The N-terminal part comprises the catalytic domain which is similar to other GDSL/SGNH hydrolases. The flanking C-terminal part is made up of a β-barrel subdomain and an α-helical subdomain. Structural comparison shows that the catalytic domain is most akin to acetyl-xylooligosaccharide esterase and allows a plausible binding mode of diltiazem to be proposed. The β-barrel subdomain is similar in topology to the immunoglobulin-like domains, including some carbohydrate-binding modules, of various bacterial glycoside hydrolases. Consequently, BT4096 might originally function as an oligosaccharide deacetylase with additional subdomains that could enhance substrate binding, and it acts on diltiazem just by accident.

PubMed: 32423809
DOI: 10.1016/j.bbrc.2020.04.116

Experimental method

X-RAY DIFFRACTION (2.33 Å)