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Shaw GX, Fan L, Cherry S, Shi G, Tropea JE, Ji X. Structure of Helicobacter pylori dihydroneopterin aldolase suggests a fragment-based strategy for isozyme-specific inhibitor design. Curr Res Struct Biol 2023; 5:100095. [PMID: 36820301 PMCID: PMC9937910 DOI: 10.1016/j.crstbi.2023.100095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/27/2022] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Dihydroneopterin aldolase (DHNA) is essential for folate biosynthesis in microorganisms. Without a counterpart in mammals, DHNA is an attractive target for antimicrobial agents. Helicobacter pylori infection occurs in human stomach of over 50% of the world population, but first-line therapies for the infection are facing rapidly increasing resistance. Novel antibiotics are urgently needed, toward which structural information on potential targets is critical. We have determined the crystal structure of H. pylori DHNA (HpDHNA) in complex with a pterin molecule (HpDHNA:Pterin) at 1.49-Å resolution. The HpDHNA:Pterin complex forms a tetramer in crystal. The tetramer is also observed in solution by dynamic light scattering and confirmed by small-angle X-ray scattering. To date, all but one reported DHNA structures are octameric complexes. As the only exception, ligand-free Mycobacterium tuberculosis DHNA (apo-MtDHNA) forms a tetramer in crystal, but its active sites are only partially formed. In contrast, the tetrameric HpDHNA:Pterin complex has well-formed active sites. Each active site accommodates one pterin molecule, but the exit of active site is blocked by two amino acid residues exhibiting a contact distance of 5.2 Å. In contrast, the corresponding contact distance in Staphylococcus aureus DHNA (SaDHNA) is twice the size, ranging from 9.8 to 10.5 Å, for ligand-free enzyme, the substrate complex, the product complex, and an inhibitor complex. This large contact distance indicates that the active site of SaDHNA is wide open. We propose that this isozyme-specific contact distance (ISCD) is a characteristic feature of DHNA active site. Comparative analysis of HpDHNA and SaDHNA structures suggests a fragment-based strategy for the development of isozyme-specific inhibitors.
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Key Words
- ANL, Argonne National Laboratory
- APS, Advanced Photon Source
- Antibiotic
- DHFS, dihydrofolate synthase
- DHNA, dihydroneopterin aldolase
- DHNP, 7,8-dihydroneopterin
- DHPS, dihydropteroate synthase
- DLS, dynamic light scattering
- Dihydroneopterin aldolase
- Dmax, maximum dimension
- EcDHNA, Escherichia coli DHNA
- FBDD, fragment-based drug discovery
- Folate biosynthesis
- Fragment-based drug discovery
- GA, glycoaldehyde
- HP, 6-hydroxymethyl-7,8-dihydropterin
- HPPK, 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
- Helicobacter pylori
- HpDHNA, Helicobacter pylori DHNA
- ISCD, isozyme-specific contact distance
- MW, molecular weight
- MtDHNA, Mycobacterium tuberculosis DHNA
- NP, neopterin
- P(r), pair-distance distribution function
- PCR, polymerase chain reaction
- Rg, radius of gyration
- SAXS, small-angle X-ray scattering
- SER-CAT, Southeast Regional Collaborative Access Team
- SaDHNA, Staphylococcus aureus DHNA
- SpDHNA, Streptococcus pneumoniae DHNA
- TCEP, tris(2-carboxyethyl)phosphine
- TEV, tobacco etch virus
- wwPDB, Worldwide Protein Data Bank
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Affiliation(s)
- Gary X. Shaw
- Center for Structural Biology, National Cancer Institute, National Institutes of Health, 1050 Boyles Street, Frederick, MD, 21702, USA
| | - Lixin Fan
- Basic Research Program, Frederick National Laboratory for Cancer Research, Small-angle X-ray Scattering Core Facility, National Cancer Institute, National Institutes of Health, 1050 Boyles Street, Frederick, MD, 21702, USA
| | - Scott Cherry
- Center for Structural Biology, National Cancer Institute, National Institutes of Health, 1050 Boyles Street, Frederick, MD, 21702, USA
| | - Genbin Shi
- Center for Structural Biology, National Cancer Institute, National Institutes of Health, 1050 Boyles Street, Frederick, MD, 21702, USA
| | - Joseph E. Tropea
- Center for Structural Biology, National Cancer Institute, National Institutes of Health, 1050 Boyles Street, Frederick, MD, 21702, USA
| | - Xinhua Ji
- Center for Structural Biology, National Cancer Institute, National Institutes of Health, 1050 Boyles Street, Frederick, MD, 21702, USA
- Corresponding author. 1050 Boyles Street, Frederick, MD, 21702, USA.
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Chen G, Khan IM, He W, Li Y, Jin P, Campanella OH, Zhang H, Huo Y, Chen Y, Yang H, Miao M. Rebuilding the lid region from conformational and dynamic features to engineering applications of lipase in foods: Current status and future prospects. Compr Rev Food Sci Food Saf 2022; 21:2688-2714. [PMID: 35470946 DOI: 10.1111/1541-4337.12965] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 03/17/2022] [Accepted: 03/25/2022] [Indexed: 02/06/2023]
Abstract
The applications of lipases in esterification, amidation, and transesterification have broadened their potential in the production of fine compounds with high cumulative values. Mostly, the catalytic triad of lipases is covered by either one or two mobile peptides called the "lid" that control the substrate channel to the catalytic center. The lid holds unique conformational allostery via interfacial activation to regulate the dynamics and catalytic functions of lipases, thereby highlighting its importance in redesigning these enzymes for industrial applications. The structural characteristic of lipase, the dynamics of lids, and the roles of lid in lipase catalysis were summarized, providing opportunities for rebuilding lid region by biotechniques (e.g., metagenomic technology and protein engineering) and enzyme immobilization. The review focused on the advantages and disadvantages of strategies rebuilding the lid region. The main shortcomings of biotechnologies on lid rebuilding were discussed such as negative effects on lipase (e.g., a decrease of activity). Additionally, the main shortcomings (e.g., enzyme desorption at high temperatre) in immobilization on hydrophobic supports via interfacial action were presented. Solutions to the mentioned problems were proposed by combinations of computational design with biotechnologies, and improvements of lipase immobilization (e.g., immobilization protocols and support design). Finally, the review provides future perspectives about designing hyperfunctional lipases as biocatalysts in the food industry based on lid conformation and dynamics.
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Affiliation(s)
- Gang Chen
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Imran Mahmood Khan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wensen He
- School of Food Science and Technology, Jiangsu University, Zhenjiang, China
| | - Yongxin Li
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Peng Jin
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Osvaldo H Campanella
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Department of Food Science and Technology, Ohio State University, Columbus, Ohio, USA
| | - Haihua Zhang
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Yanrong Huo
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Yang Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Huqing Yang
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Ming Miao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
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Folate biosynthesis pathway: mechanisms and insights into drug design for infectious diseases. Future Med Chem 2018; 10:935-959. [PMID: 29629843 DOI: 10.4155/fmc-2017-0168] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Folate pathway is a key target for the development of new drugs against infectious diseases since the discovery of sulfa drugs and trimethoprim. The knowledge about this pathway has increased in the last years and the catalytic mechanism and structures of all enzymes of the pathway are fairly understood. In addition, differences among enzymes from prokaryotes and eukaryotes could be used for the design of specific inhibitors. In this review, we show a panorama of progress that has been achieved within the folate pathway obtained in the last years. We explored the structure and mechanism of enzymes, several genetic features, strategies, and approaches used in the design of new inhibitors that have been used as targets in pathogen chemotherapy.
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Chaudhary B, Singh N, Pandey DK. Bioengineering of crop plants for improved tetrahydrofolate production. Bioengineered 2018; 9:152-158. [PMID: 28873007 PMCID: PMC5972932 DOI: 10.1080/21655979.2017.1373537] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 08/03/2017] [Accepted: 08/03/2017] [Indexed: 10/28/2022] Open
Abstract
De novo synthesis of folates in plants is tightly regulated through feedback-regulation of certain pathway catalysts. Recently, we investigated the prospects of incessant production of folates in an evolutionary conjunction, through the overexpression of feedback targeted and evolutionarily conserved heterologous E.coli dihydroneopterin aldolase (EcDHNA) in tobacco. 1 The enhanced production of folates in the transgenic lines was associated with differential allosteric regulatory cavities accessible at EcDHNA surface having critical amino-acid differences as Ile 64 (His_63), Val 70 (Phe_69), His 75 (Arg_78) and Arg 79 (Glu_72). These structural characteristics are indicative of evolutionary signatures of the catalytic feedback-regulation of folate manufacturing. We exploited the biotechnological potential of such allosterically diverged trans-DHNA for improved folate production in plants. Nonetheless, genetic manipulation of single enzymes modulating complex pathways such as folate biosynthesis is often inadequate to achieve desired phenotypes; therefore, multi-gene integration with explicit genic-combination for folate enrichment in plants has also been projected for future folate agri-biofortification schemes.
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Affiliation(s)
- Bhupendra Chaudhary
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. India
| | - Nagendra Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. India
| | - Dhananjay K. Pandey
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. India
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Pandey DK, Kumar A, Rathore JS, Singh N, Chaudhary B. Recombinant overexpression of dihydroneopterin aldolase catalyst potentially regulates folate-biofortification. J Basic Microbiol 2017; 57:517-524. [PMID: 28418068 DOI: 10.1002/jobm.201600721] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 02/17/2017] [Accepted: 03/28/2017] [Indexed: 01/18/2023]
Abstract
We aim to investigate the prospects of increased production of folate through the overexpression of heterologous dihydroneopterin aldolase catalyst. The gene encoding aldolase catalyst was cloned into an expression vector and the induced recombinant protein was purified through metal-affinity chromatography which appeared at 14 kDa position on polyacrylamide-gel. Remarkably, a periodic increase in the extracellular and intracellular folic acid concentration was observed at 4 h growth of induced recombinant DHNA samples than control in a pH-dependent manner. Maximum folate concentration was observed with at least twofold increase in induced recombinant samples at pH8.0 compared to the significant decline at 6 h growth. Consistently, heterologous overexpression of bacterial aldolase through Agrobacterium-mediated genetic transformation of tobacco led to more than 2.5-fold increase in the folate concentration in the transgenic leaves than control tissues. These data are veritable inspecting metabolic flux in both bacterial and plant systems, thus providing directions for future research on folate agri-fortification.
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Affiliation(s)
- Dhananjay K Pandey
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P., India
| | - Atul Kumar
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P., India
| | - Jitendra S Rathore
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P., India
| | - Nagendra Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P., India
| | - Bhupendra Chaudhary
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P., India
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Papaleo E, Saladino G, Lambrughi M, Lindorff-Larsen K, Gervasio FL, Nussinov R. The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery. Chem Rev 2016; 116:6391-423. [DOI: 10.1021/acs.chemrev.5b00623] [Citation(s) in RCA: 239] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Elena Papaleo
- Computational
Biology Laboratory, Unit of Statistics, Bioinformatics and Registry, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
- Structural
Biology and NMR Laboratory, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Giorgio Saladino
- Department
of Chemistry, University College London, London WC1E 6BT, United Kingdom
| | - Matteo Lambrughi
- Department
of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza
della Scienza 2, 20126 Milan, Italy
| | - Kresten Lindorff-Larsen
- Structural
Biology and NMR Laboratory, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Ruth Nussinov
- Cancer
and Inflammation Program, Leidos Biomedical Research, Inc., Frederick
National Laboratory for Cancer Research, National Cancer Institute Frederick, Frederick, Maryland 21702, United States
- Sackler Institute
of Molecular Medicine, Department of Human Genetics and Molecular
Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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Zakharov MA, Fetisov GV, Veligzhanin AA, Bykov MA, Paseshnichenko KA, Dunaev SF, Aslanov LA. Solutions of complex copper salts in low-transition-temperature mixture (LTTM). Dalton Trans 2015; 44:18576-84. [PMID: 26448612 DOI: 10.1039/c5dt02941d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structure and properties of diethanolamine complexes of copper(ii) triflates dissolved in an excess of diethanolamine (DH2) were studied. The copper containing substance was found to be a solution of copper(ii) complex salt [Cu(2+)DH2(DH(-))]OTf(-) in LTTM composition [(DH2)4H(+)](OTf(-)), where LTTM = low-transition-temperature mixture, OTf(-) = triflate anion. According to the EXAFS data, the coordination number of copper(ii) atoms in solution does not exceed four. Addition of even negligible amounts of acid significantly changes DH2 volatility and decomposition conditions.
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Affiliation(s)
- Maxim A Zakharov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russian Federation.
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