Suppr超能文献

活性位点可塑性对于鲍曼不动杆菌OXA-58 D类β-内酰胺酶水解碳青霉烯至关重要。

Active-Site Plasticity Is Essential to Carbapenem Hydrolysis by OXA-58 Class D β-Lactamase of Acinetobacter baumannii.

作者信息

Pratap Shivendra, Katiki Madhusudhanarao, Gill Preet, Kumar Pravindra, Golemi-Kotra Dasantila

机构信息

Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India.

Department of Biology, York University, Toronto, Canada.

出版信息

Antimicrob Agents Chemother. 2015 Oct 12;60(1):75-86. doi: 10.1128/AAC.01393-15. Print 2016 Jan.

Abstract

Carbapenem-hydrolyzing class D β-lactamases (CHDLs) are a subgroup of class D β-lactamases, which are enzymes that hydrolyze β-lactams. They have attracted interest due to the emergence of multidrug-resistant Acinetobacter baumannii, which is not responsive to treatment with carbapenems, the usual antibiotics of choice for this bacterium. Unlike other class D β-lactamases, these enzymes efficiently hydrolyze carbapenem antibiotics. To explore the structural requirements for the catalysis of carbapenems by these enzymes, we determined the crystal structure of the OXA-58 CHDL of A. baumannii following acylation of its active-site serine by a 6α-hydroxymethyl penicillin derivative that is a structural mimetic for a carbapenem. In addition, several point mutation variants of the active site of OXA-58, as identified by the crystal structure analysis, were characterized kinetically. These combined studies confirm the mechanistic relevance of a hydrophobic bridge formed over the active site. This structural feature is suggested to stabilize the hydrolysis-productive acyl-enzyme species formed from the carbapenem substrates of this enzyme. Furthermore, our structural studies provide strong evidence that the hydroxyethyl group of carbapenems samples different orientations in the active sites of CHDLs, and the optimum orientation for catalysis depends on the topology of the active site allowing proper closure of the active site. We propose that CHDLs use the plasticity of the active site to drive the mechanism of carbapenem hydrolysis toward efficiency.

摘要

碳青霉烯水解D类β-内酰胺酶(CHDLs)是D类β-内酰胺酶的一个亚组,这类酶可水解β-内酰胺。由于多重耐药鲍曼不动杆菌的出现,它们引起了人们的关注,这种细菌对通常作为其首选抗生素的碳青霉烯治疗无反应。与其他D类β-内酰胺酶不同,这些酶能有效水解碳青霉烯抗生素。为了探究这些酶催化碳青霉烯的结构要求,我们通过一种6α-羟甲基青霉素衍生物对鲍曼不动杆菌的OXA-58 CHDL活性位点丝氨酸进行酰化后,确定了其晶体结构,该衍生物是碳青霉烯的结构模拟物。此外,通过晶体结构分析鉴定出的OXA-58活性位点的几个点突变变体进行了动力学表征。这些综合研究证实了活性位点上方形成的疏水桥的机制相关性。这一结构特征被认为可稳定由该酶的碳青霉烯底物形成的水解活性酰基酶物种。此外,我们的结构研究提供了有力证据,表明碳青霉烯的羟乙基在CHDLs活性位点呈现不同取向,催化的最佳取向取决于活性位点的拓扑结构,以允许活性位点适当闭合。我们提出,CHDLs利用活性位点的可塑性来推动碳青霉烯水解机制向高效方向发展。

相似文献

1
Active-Site Plasticity Is Essential to Carbapenem Hydrolysis by OXA-58 Class D β-Lactamase of Acinetobacter baumannii.
Antimicrob Agents Chemother. 2015 Oct 12;60(1):75-86. doi: 10.1128/AAC.01393-15. Print 2016 Jan.
3
Structural Insights into the Mechanism of Carbapenemase Activity of the OXA-48 β-Lactamase.
Antimicrob Agents Chemother. 2019 Sep 23;63(10). doi: 10.1128/AAC.01202-19. Print 2019 Oct.
4
Activity of the β-Lactamase Inhibitor LN-1-255 against Carbapenem-Hydrolyzing Class D β-Lactamases from Acinetobacter baumannii.
Antimicrob Agents Chemother. 2017 Oct 24;61(11). doi: 10.1128/AAC.01172-17. Print 2017 Nov.
5
Hydrolytic mechanism of OXA-58 enzyme, a carbapenem-hydrolyzing class D β-lactamase from Acinetobacter baumannii.
J Biol Chem. 2011 Oct 28;286(43):37292-303. doi: 10.1074/jbc.M111.280115. Epub 2011 Aug 31.
6
C6 Hydroxymethyl-Substituted Carbapenem MA-1-206 Inhibits the Major Carbapenemase OXA-23 by Impeding Deacylation.
mBio. 2022 Jun 28;13(3):e0036722. doi: 10.1128/mbio.00367-22. Epub 2022 Apr 14.
7
Expanded Substrate Activity of OXA-24/40 in Carbapenem-Resistant Acinetobacter baumannii Involves Enhanced Binding Loop Flexibility.
Biochemistry. 2016 Nov 29;55(47):6535-6544. doi: 10.1021/acs.biochem.6b00806. Epub 2016 Nov 11.
8
KPC-2 β-lactamase enables carbapenem antibiotic resistance through fast deacylation of the covalent intermediate.
J Biol Chem. 2021 Jan-Jun;296:100155. doi: 10.1074/jbc.RA120.015050. Epub 2020 Dec 10.
9
Crystal structure of carbapenemase OXA-58 from Acinetobacter baumannii.
Antimicrob Agents Chemother. 2014;58(4):2135-43. doi: 10.1128/AAC.01983-13. Epub 2014 Jan 27.
10
The role of conserved surface hydrophobic residues in the carbapenemase activity of the class D β-lactamases.
Acta Crystallogr D Struct Biol. 2017 Aug 1;73(Pt 8):692-701. doi: 10.1107/S2059798317008671. Epub 2017 Jul 28.

引用本文的文献

1
Structural comparison of substrate-binding pockets of serine β-lactamases in classes A, C, and D.
J Enzyme Inhib Med Chem. 2025 Dec;40(1):2435365. doi: 10.1080/14756366.2024.2435365. Epub 2024 Dec 23.
2
Two non-active site residues W165 and L166 prominently influence the beta-lactam hydrolytic ability of OXA-23 beta-lactamase.
J Antibiot (Tokyo). 2023 Aug;76(8):489-498. doi: 10.1038/s41429-023-00624-z. Epub 2023 Apr 24.
4
A review on the mechanistic details of OXA enzymes of ESKAPE pathogens.
Pathog Glob Health. 2023 May;117(3):219-234. doi: 10.1080/20477724.2022.2088496. Epub 2022 Jun 26.
5
β-Lactamases and β-Lactamase Inhibitors in the 21st Century.
J Mol Biol. 2019 Aug 23;431(18):3472-3500. doi: 10.1016/j.jmb.2019.04.002. Epub 2019 Apr 5.
6
Role of the Hydrophobic Bridge in the Carbapenemase Activity of Class D β-Lactamases.
Antimicrob Agents Chemother. 2019 Jan 29;63(2). doi: 10.1128/AAC.02191-18. Print 2019 Feb.
7
Systematic Identification and Classification of β-Lactamases Based on Sequence Similarity Criteria: β-Lactamase Annotation.
Evol Bioinform Online. 2018 Sep 10;14:1176934318797351. doi: 10.1177/1176934318797351. eCollection 2018.
8
Comparative assessment of strategies to identify similar ligand-binding pockets in proteins.
BMC Bioinformatics. 2018 Mar 9;19(1):91. doi: 10.1186/s12859-018-2109-2.
9
A New Mechanism for β-Lactamases: Class D Enzymes Degrade 1β-Methyl Carbapenems through Lactone Formation.
Angew Chem Int Ed Engl. 2018 Jan 26;57(5):1282-1285. doi: 10.1002/anie.201711308. Epub 2018 Jan 5.
10
Activity of the β-Lactamase Inhibitor LN-1-255 against Carbapenem-Hydrolyzing Class D β-Lactamases from Acinetobacter baumannii.
Antimicrob Agents Chemother. 2017 Oct 24;61(11). doi: 10.1128/AAC.01172-17. Print 2017 Nov.

本文引用的文献

1
Acquired Class D β-Lactamases.
Antibiotics (Basel). 2014 Aug 21;3(3):398-434. doi: 10.3390/antibiotics3030398.
3
OXA β-lactamases.
Clin Microbiol Rev. 2014 Apr;27(2):241-63. doi: 10.1128/CMR.00117-13.
4
Worldwide dissemination of acquired carbapenem-hydrolysing class D β-lactamases in Acinetobacter spp. other than Acinetobacter baumannii.
Int J Antimicrob Agents. 2014 Apr;43(4):375-7. doi: 10.1016/j.ijantimicag.2014.01.012. Epub 2014 Feb 12.
5
Crystal structure of carbapenemase OXA-58 from Acinetobacter baumannii.
Antimicrob Agents Chemother. 2014;58(4):2135-43. doi: 10.1128/AAC.01983-13. Epub 2014 Jan 27.
6
Structural basis for carbapenemase activity of the OXA-23 β-lactamase from Acinetobacter baumannii.
Chem Biol. 2013 Sep 19;20(9):1107-15. doi: 10.1016/j.chembiol.2013.07.015. Epub 2013 Sep 5.
8
Chloroquine binding reveals flavin redox switch function of quinone reductase 2.
J Biol Chem. 2013 Apr 19;288(16):11242-51. doi: 10.1074/jbc.M113.457002. Epub 2013 Mar 7.
9
Evolution to carbapenem-hydrolyzing activity in noncarbapenemase class D β-lactamase OXA-10 by rational protein design.
Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18424-9. doi: 10.1073/pnas.1110530108. Epub 2011 Oct 31.
10
Hydrolytic mechanism of OXA-58 enzyme, a carbapenem-hydrolyzing class D β-lactamase from Acinetobacter baumannii.
J Biol Chem. 2011 Oct 28;286(43):37292-303. doi: 10.1074/jbc.M111.280115. Epub 2011 Aug 31.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验