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来自[具体来源未给出]的细菌酶琥珀酰二氨基庚二酸脱琥珀酰酶(DapE)的生化与结构分析

Biochemical and Structural Analysis of the Bacterial Enzyme Succinyl-Diaminopimelate Desuccinylase (DapE) from .

作者信息

Kelley Emma H, Minasov George, Konczak Katherine, Shuvalova Ludmilla, Brunzelle Joseph S, Shukla Shantanu, Beulke Megan, Thabthimthong Teerana, Olsen Kenneth W, Inniss Nicole L, Satchell Karla J F, Becker Daniel P

机构信息

Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States.

Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611, United States.

出版信息

ACS Omega. 2024 Jan 8;9(3):3905-3915. doi: 10.1021/acsomega.3c08231. eCollection 2024 Jan 23.


DOI:10.1021/acsomega.3c08231
PMID:38284080
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10809365/
Abstract

There is an urgent need for new antibiotics given the rise of antibiotic resistance, and succinyl-diaminopimelate desuccinylase (DapE, E.C. 3.5.1.18) has emerged as a promising bacterial enzyme target. DapE from (DapE) has been studied and inhibitors identified, but it is essential to explore DapE from different species to assess selective versus broad-spectrum therapeutics. We have determined the structure of DapE from the ESKAPE pathogen (DapE) and studied inhibition by known inhibitors of DapE. DapE is inhibited by captopril and sulfate comparable to DapE, but DapE was not significantly inhibited by a known indoline sulfonamide DapE inhibitor. Captopril and sulfate both stabilize DapE by increasing the thermal melting temperature () in thermal shift assays. By contrast, sulfate decreases the stability of the DapE enzyme, whereas captopril increases the stability. Further, we report two crystal structures of selenomethionine-substituted DapE in the closed conformation, one with DapE in complex with succinate derived from enzymatic hydrolysis of -methyl-l,l-SDAP substrate and acetate (PDB code 7T1Q, 2.25 Å resolution), and a crystal structure of DapE with bound succinate along with l-(S)-lactate, a product of degradation of citric acid from the crystallization buffer during X-ray irradiation (PDB code 8F8O, 2.10 Å resolution).

摘要

鉴于抗生素耐药性的增加,迫切需要新型抗生素,而琥珀酰二氨基庚二酸脱琥珀酰酶(DapE,E.C. 3.5.1.18)已成为一个有前景的细菌酶靶点。来自[具体物种]的DapE(DapE)已被研究并鉴定出抑制剂,但探索不同物种的DapE对于评估选择性与广谱治疗方法至关重要。我们已经确定了来自ESKAPE病原体[具体物种]的DapE(DapE)的结构,并研究了已知DapE抑制剂的抑制作用。卡托普利和硫酸盐对DapE的抑制作用与对DapE的抑制作用相当,但已知的吲哚啉磺酰胺DapE抑制剂对DapE没有显著抑制作用。在热位移分析中,卡托普利和硫酸盐都通过提高热解链温度()来稳定DapE。相比之下,硫酸盐会降低DapE酶的稳定性,而卡托普利会提高其稳定性。此外,我们报告了处于封闭构象的硒代甲硫氨酸取代的DapE的两个晶体结构,一个是DapE与源自 -甲基-l,l-SDAP底物酶促水解的琥珀酸盐和乙酸盐形成的复合物(PDB代码7T1Q,分辨率2.25 Å),另一个是结合了琥珀酸盐以及l-(S)-乳酸的DapE晶体结构,l-(S)-乳酸是X射线照射期间结晶缓冲液中柠檬酸降解的产物(PDB代码8F8O,分辨率2.10 Å)。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3eb2/10809365/33821721250a/ao3c08231_0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3eb2/10809365/5383b75fe8bb/ao3c08231_0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3eb2/10809365/5bbddfbfbac2/ao3c08231_0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3eb2/10809365/b4899e0a49bc/ao3c08231_0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3eb2/10809365/cffb7541c5f7/ao3c08231_0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3eb2/10809365/33821721250a/ao3c08231_0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3eb2/10809365/5383b75fe8bb/ao3c08231_0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3eb2/10809365/5bbddfbfbac2/ao3c08231_0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3eb2/10809365/b4899e0a49bc/ao3c08231_0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3eb2/10809365/cffb7541c5f7/ao3c08231_0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3eb2/10809365/33821721250a/ao3c08231_0003.jpg

相似文献

[1]
Biochemical and Structural Analysis of the Bacterial Enzyme Succinyl-Diaminopimelate Desuccinylase (DapE) from .

ACS Omega. 2024-1-8

[2]
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[6]
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[9]
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本文引用的文献

[1]
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Biochim Biophys Acta Gen Subj. 2023-5

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Biochemistry. 2021-3-30

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PLoS One. 2018-4-26

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Biochemistry. 2018-2-6

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