1
|
Kumar N, Goel N, Chand Yadav T, Pruthi V. Quantum chemical, ADMET and molecular docking studies of ferulic acid amide derivatives with a novel anticancer drug target. Med Chem Res 2017. [DOI: 10.1007/s00044-017-1893-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
2
|
Yang N, Sun C. The Inhibition and Resistance Mechanisms of Actinonin, Isolated from Marine Streptomyces sp. NHF165, against Vibrio anguillarum. Front Microbiol 2016; 7:1467. [PMID: 27679625 PMCID: PMC5020083 DOI: 10.3389/fmicb.2016.01467] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 09/01/2016] [Indexed: 11/29/2022] Open
Abstract
Vibrio sp. is the most serious pathogen in marine aquaculture, and the development of anti-Vibrio agents is urgently needed. However, it is extreme lack of high-throughput screening (HTS) model for searching anti-Vibrio compounds. Here, we established a protein-based HTS screening model to identify agents targeting peptide deformylase (PDF) of Vibrio anguillarum. To find potential anti-Vibrio compounds, crude extracts derived from marine actinomycetes were applied for screening with this model. Notably, crude extract of strain Streptomyces sp. NHF165 inhibited dramatically both on V. anguillarum PDF (VaPDF) activity and V. anguillarum cell growth. And actinonin was further identified as the functional component. Anti-VaPDF and anti-V. anguillarum activities of actinonin were dose-dependent, and the IC50 values were 6.94 and 2.85 μM, respectively. To understand the resistance of V. anguillarum against actinonin, spontaneous V. anguillarum mutants with resistance against actinonin were isolated. Surprisingly, for the resistant strains, the region between 774 and 852 base pairs was found to be absent in the gene folD which produces 10-formyl-tetrahydrofolate, a donor of N-formyl to Met-tRNAfmet. When compared to the wild type strain, ΔfolD mutant showed eight times of minimum inhibition concentration on actinonin, however, the folD complementary strain could not grow on the medium supplemented with actinonin, which suggested that folD gene mutation was mainly responsible for the actinonin resistance. To our knowledge, this is the first report showing that marine derived Streptomyces sp. could produce actinonin with anti-VaPDF activity and the resistance against actinonin by V. anguillarum is mediated by mutation in folD gene.
Collapse
Affiliation(s)
- Na Yang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of SciencesQingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
| | - Chaomin Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of SciencesQingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
| |
Collapse
|
3
|
Cui P, Wang Y, Chu W, Guo X, Yang F, Yu M, Zhao H, Dong Y, Xie Y, Gong W, Wu Z. How water molecules affect the catalytic activity of hydrolases--a XANES study of the local structures of peptide deformylase. Sci Rep 2014; 4:7453. [PMID: 25503313 PMCID: PMC4264029 DOI: 10.1038/srep07453] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 11/21/2014] [Indexed: 11/09/2022] Open
Abstract
Peptide deformylase (PDF) is a prokaryotic enzyme that catalyzes the deformylation of nascent peptides generated during protein synthesis and water molecules play a key role in these hydrolases. Using X-ray absorption near edge spectroscopy (XANES) and ab initio calculations we accurately probe the local atomic environment of the metal ion binding in the active site of PDF at different pH values and with different metal ions. This new approach is an effective way to monitor existing correlations among functions and structural changes. We show for the first time that the enzymatic activity depends on pH values and metal ions via the bond length of the nearest coordinating water (Wat1) to the metal ion. Combining experimental and theoretical data we may claim that PDF exhibits an enhanced enzymatic activity only when the distance of the Wat1 molecule with the metal ion falls in the limited range from 2.15 to 2.55 Å.
Collapse
Affiliation(s)
- Peixin Cui
- 1] National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China [2] Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Yu Wang
- Shanghai Synchrotron Radiation Facilities, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
| | - Wangsheng Chu
- 1] National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China [2] Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Xiaoyun Guo
- 1] Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China [2] Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Feifei Yang
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China
| | - Meijuan Yu
- Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Haifeng Zhao
- Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Yuhui Dong
- Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Yaning Xie
- Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Weimin Gong
- 1] Institute of Biophysics, Chinese Academy of Sciences, Beijing, China [2] Hefei National Laboratory for Physical Sciences at the microscale, University of Science and Technology of China
| | - Ziyu Wu
- 1] National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China [2] Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
4
|
Fieulaine S, Desmadril M, Meinnel T, Giglione C. Understanding the highly efficient catalysis of prokaryotic peptide deformylases by shedding light on the determinants specifying the low activity of the human counterpart. ACTA ACUST UNITED AC 2014; 70:242-52. [DOI: 10.1107/s1399004713026461] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 09/24/2013] [Indexed: 11/11/2022]
Abstract
Peptide deformylases (PDFs), which are essential and ubiquitous enzymes involved in the removal of theN-formyl group from nascent chains, are classified into four subtypes based on the structural and sequence similarity of specific conserved domains. All PDFs share a similar three-dimensional structure, are functionally interchangeablein vivoand display similar propertiesin vitro, indicating that their molecular mechanism has been conserved during evolution. The human mitochondrial PDF is the only exception as despite its conserved fold it reveals a unique substrate-binding pocket together with an unusual kinetic behaviour. Unlike human PDF, the closely related mitochondrial PDF1As from plants have catalytic efficiencies and enzymatic parameters that are similar to those of other classes of PDFs. Here, the aim was to identify the structural basis underlying the properties of human PDF compared with all other PDFs by focusing on plant mitochondrial PDF1A. The construction of a chimaera composed of plant PDF1A with the nonrandom substitutions found in a conserved motif of its human homologue converted it into an enzyme with properties similar to the human enzyme, indicating the crucial role of these positions. The crystal structure of this human-like plant PDF revealed that substitution of two residues leads to a reduction in the volume of the ligand-binding site together with the introduction of negative charges, unravelling the origin of the weak affinity of human PDF for its substrate. In addition, the substitution of the two residues of human PDF modifies the transition state of the reaction through alteration of the network of interactions between the catalytic residues and the substrate, leading to an overall reduced reaction rate.
Collapse
|
5
|
Identification of crucial amino acids of bacterial Peptide deformylases affecting enzymatic activity in response to oxidative stress. J Bacteriol 2013; 196:90-9. [PMID: 24142250 DOI: 10.1128/jb.00916-13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Peptide deformylase (PDF) is an essential bacterial metalloprotease involved in deformylation of N-formyl group from nascent polypeptide chains during protein synthesis. Iron-containing variants of this enzyme from Salmonella enterica serovar Typhimurium (sPDF) and Mycobacterium tuberculosis (mPDF), although inhibited by oxidizing agents like H2O2, exhibited strikingly different 50% inhibitory concentrations (IC50s) that ranged from nanomolar (sPDF) to millimolar (mPDF) levels. Furthermore, the metal dissociation rate was higher in sPDF than mPDF. We hypothesized that a restriction in entry of environmental oxygen or oxidizing agents into the active site of mPDF might be the cause for such discrepancies between two enzymes. Since the active-site residues of the two proteins are similar, we evaluated the role of the oxidation-prone noncatalytic residue(s) in the process. Amino acid sequence analysis revealed that Cys-130 of sPDF corresponds to Met-145 of mPDF and that they are away from the active sites. Swapping methionine with cysteine in mPDF, the M145C protein displayed a drastic decrease in the IC50 for H2O2 and an increased metal dissociation rate compared to the wild type. Matrix-assisted laser desorption ionization (MALDI) analysis of a trypsin-digested fragment containing Cys-145 of the M145C protein also indicated its increased susceptibility to oxidation. To incorporate residues identical to those of mPDF, we created a double mutant of sPDF (C130M-V63C) that showed increased IC50 for H2O2 compared to the wild type. Interestingly, the oxidation state of cysteines in C130M-V63C was unaffected during H2O2 treatment. Taken together, our results unambiguously established the critical role of noncatalytic cysteine/methionine for enzymatic sensitivity to H2O2 and, thus, for conferring behavioral distinction of bacterial PDFs under oxidative stress conditions.
Collapse
|
6
|
Fieulaine S, Boularot A, Artaud I, Desmadril M, Dardel F, Meinnel T, Giglione C. Trapping conformational states along ligand-binding dynamics of peptide deformylase: the impact of induced fit on enzyme catalysis. PLoS Biol 2011; 9:e1001066. [PMID: 21629676 PMCID: PMC3101196 DOI: 10.1371/journal.pbio.1001066] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Accepted: 04/14/2011] [Indexed: 11/18/2022] Open
Abstract
For several decades, molecular recognition has been considered one of the most fundamental processes in biochemistry. For enzymes, substrate binding is often coupled to conformational changes that alter the local environment of the active site to align the reactive groups for efficient catalysis and to reach the transition state. Adaptive substrate recognition is a well-known concept; however, it has been poorly characterized at a structural level because of its dynamic nature. Here, we provide a detailed mechanism for an induced-fit process at atomic resolution. We take advantage of a slow, tight binding inhibitor-enzyme system, actinonin-peptide deformylase. Crystal structures of the initial open state and final closed state were solved, as well as those of several intermediate mimics captured during the process. Ligand-induced reshaping of a hydrophobic pocket drives closure of the active site, which is finally “zipped up” by additional binding interactions. Together with biochemical analyses, these data allow a coherent reconstruction of the sequence of events leading from the encounter complex to the key-lock binding state of the enzyme. A “movie” that reconstructs this entire process can be further extrapolated to catalysis. The notion of induced fit when a protein binds its ligand—like a glove adapting to the shape of a hand—is a central concept of structural biochemistry introduced over 50 years ago. A detailed molecular demonstration of this phenomenon has eluded biochemists, however, largely due to the difficulty of capturing the steps of this very transient process: the “conformational change.” In this study, we were able to see this process by using X-ray diffraction to determine more than 10 distinct structures adopted by a single enzyme when it binds a ligand. To do this, we took advantage of the “slow, tight-binding” of a potent inhibitor to its specific target enzyme to trap intermediates in the binding process, which allowed us to monitor the action of an enzyme in real-time at atomic resolution. We showed the kinetics of the conformational change from an initial open state, including the encounter complex, to the final closed state of the enzyme. From these data and other biochemical and biophysical analyses, we make a coherent causal reconstruction of the sequence of events leading to inhibition of the enzyme's activity. We also generated a movie that reconstructs the sequence of events during the encounter. Our data provide new insights into how enzymes achieve a catalytically competent conformation in which the reactive groups are brought into close proximity, resulting in catalysis.
Collapse
Affiliation(s)
| | | | - Isabelle Artaud
- Université Paris Descartes, UMR8601, Paris, France
- CNRS, UMR8601, Paris, France
| | - Michel Desmadril
- Université Paris-Sud, IBBMC, UMR8619, Orsay, France
- CNRS, IBBMC, UMR8619, Orsay, France
| | - Frédéric Dardel
- Université Paris Descartes, UMR8015, Paris, France
- CNRS, UMR8015, Paris, France
| | - Thierry Meinnel
- CNRS, ISV, UPR2355, Gif-sur-Yvette, France
- * E-mail: (TM); (CG)
| | | |
Collapse
|
7
|
Lin P, Hu T, Hu J, Yu W, Han C, Zhang J, Qin G, Yu K, Götz F, Shen X, Jiang H, Qu D. Characterization of peptide deformylase homologues from Staphylococcus epidermidis. MICROBIOLOGY-SGM 2010; 156:3194-3202. [PMID: 20656778 DOI: 10.1099/mic.0.038174-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The emergence of multi-drug-resistant strains of Staphylococcus epidermidis emphasizes the need to develop new antibiotics. The unique and essential role of the peptide deformylase (PDF) in catalysing the removal of the N-terminal formyl group from newly synthesized polypeptides in eubacteria makes it an attractive antibacterial drug target. In the present study, both deformylase homologues from S. epidermidis (SePDF-1 and SePDF-2) were cloned and expressed, and their enzymic activities were characterized. Co(2+)-substituted SePDF-1 exhibited much higher enzymic activity (k(cat)/K(m) 6.3 × 10(4) M(-1) s(-1)) than those of Ni(2+)- and Zn(2+)-substituted SePDF-1, and SePDF-1 showed much weaker binding ability towards Ni(2+) than towards Co(2+) and Zn(2+), which is different from PDF in Staphylococcus aureus (SaPDF), although they share 80 % amino-acid sequence identity. The determined crystal structure of SePDF-1 was similar to that of (SaPDF), except for differences in the metal-binding sites. The other deformylase homologue, SePDF-2, was shown to have no peptide deformylase activity; the function of SePDF-2 needs to be further investigated.
Collapse
Affiliation(s)
- Penghui Lin
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institute of Medical Microbiology and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Tiancen Hu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jian Hu
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institute of Medical Microbiology and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Wenqi Yu
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institute of Medical Microbiology and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Cong Han
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institute of Medical Microbiology and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education of China, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
| | - Guangrong Qin
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, China
| | - Kunqian Yu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, China
| | - Friedrich Götz
- Microbial Genetics, University of Tübingen, Auf der Morgenstelle 28, D-72076 Tübingen, Germany
| | - Xu Shen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, China
| | - Di Qu
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institute of Medical Microbiology and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| |
Collapse
|
8
|
Dong M, Liu H. Origins of the Different Metal Preferences of Escherichia coli Peptide Deformylase and Bacillus thermoproteolyticus Thermolysin: A Comparative Quantum Mechanical/Molecular Mechanical Study. J Phys Chem B 2008; 112:10280-90. [DOI: 10.1021/jp711209j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Minghui Dong
- Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China (USTC), Hefei, Anhui, 230027, China
| | - Haiyan Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China (USTC), Hefei, Anhui, 230027, China
| |
Collapse
|
9
|
Saxena R, Kanudia P, Datt M, Dar HH, Karthikeyan S, Singh B, Chakraborti PK. Three consecutive arginines are important for the mycobacterial peptide deformylase enzyme activity. J Biol Chem 2008; 283:23754-64. [PMID: 18574247 DOI: 10.1074/jbc.m709672200] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Genes encoding the peptide deformylase enzyme (def) are present in all eubacteria and are involved in the deformylation of the N-formyl group of newly synthesized polypeptides during protein synthesis. We compared the amino acid sequences of this enzyme in different mycobacterial species and found that they are highly conserved (76% homology with 62% identity); however, when this comparison was extended to other eubacterial homologs, it emerged that the mycobacterial proteins have an insertion region containing three consecutive arginine residues (residues 77-79 in Mycobacterium tuberculosis peptide deformylase (mPDF)). Here, we demonstrate that these three arginines are important for the activity of mPDF. Circular dichroism studies of wild-type mPDF and of mPDF containing individual conservative substitutions (R77K, R78K, or R79K) or combined substitutions incorporated into a triple mutant (R77K/R78K/R79K) indicate that such mutations cause mPDF to undergo structural alterations. Molecular modeling of mPDF suggests that the three arginines are distal to the active site. Molecular dynamics simulations of wild-type and mutant mPDF structures indicate that the arginines may be involved in the stabilization of substrate binding pocket residues for their proper interaction with peptide(s). Treatment with 5'-phosphothiorate-modified antisense oligodeoxyribonucleotides directed against different regions of def from M. tuberculosis inhibits growth of Mycobacterium smegmatis in culture. Taken together, these results hold out the possibility of future design of novel mycobacteria-specific PDF inhibitors.
Collapse
Affiliation(s)
- Rahul Saxena
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | | | | | | | | | | | | |
Collapse
|
10
|
Abstract
Peptide deformylase (PDF) is a metalloenzyme that removes the N-terminal formyl groups from newly synthesized proteins. It is essential for bacterial survival, and is therefore-considered as a potential target for antimicrobial chemotherapy. However, some bacteria including medically relevant pathogens possess two or more def-like genes. Here we have examined two PDFs from Bacillus cereus. The two share only 32% sequence identity and the crystal structures show overall similarity with PDF2 having a longer C-terminus. However, there are differences at the two active sites, and these differences appear to contribute to the activity difference seen between the two. BcPDF2 is found as a dimer in the crystal form with two additional actinonin bound at that interface.
Collapse
Affiliation(s)
- Joon Kyu Park
- Life Sciences Division, Korea Institute of Science and Technology, 39-1 Hawolkok-dong, Sungbuk-gu, Seoul 136-791, Korea
| | | | | | | |
Collapse
|
11
|
Nguyen KT, Wu JC, Boylan JA, Gherardini FC, Pei D. Zinc is the metal cofactor of Borrelia burgdorferi peptide deformylase. Arch Biochem Biophys 2007; 468:217-25. [PMID: 17977509 DOI: 10.1016/j.abb.2007.09.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2007] [Revised: 09/21/2007] [Accepted: 09/22/2007] [Indexed: 11/26/2022]
Abstract
Peptide deformylase (PDF, E.C. 3.5.1.88) catalyzes the removal of N-terminal formyl groups from nascent ribosome-synthesized polypeptides. PDF contains a catalytically essential divalent metal ion, which is tetrahedrally coordinated by three protein ligands (His, His, and Cys) and a water molecule. Previous studies revealed that the metal cofactor is a Fe2+ ion in Escherichia coli and many other bacterial PDFs. In this work, we found that PDFs from two iron-deficient bacteria, Borrelia burgdorferi and Lactobacillus plantarum, are stable and highly active under aerobic conditions. The native B. burgdorferi PDF (BbPDF) was purified 1200-fold and metal analysis revealed that it contains approximately 1.1 Zn2+ ion/polypeptide but no iron. Our studies suggest that PDF utilizes different metal ions in different organisms. These data have important implications in designing PDF inhibitors and should help address some of the unresolved issues regarding PDF structure and catalytic function.
Collapse
Affiliation(s)
- Kiet T Nguyen
- Department of Chemistry and Ohio State Biochemistry Program, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
| | | | | | | | | |
Collapse
|
12
|
Wu XH, Quan JM, Wu YD. Theoretical Study of the Catalytic Mechanism and Metal-Ion Dependence of Peptide Deformylase. J Phys Chem B 2007; 111:6236-44. [PMID: 17497768 DOI: 10.1021/jp068611m] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reaction pathway of deformylation catalyzed by E. coli peptide deformylase (PDF) has been investigated by the density functional theory method of PBE1PBE on a small model and by a two-layer ONIOM method on a realistic protein model. The deformylation proceeds in sequential steps involving nucleophilic addition of metal-coordinated water/hydroxide to the carbonyl carbon of the formyl group, proton transfer, and cleavage of the C-N bond. The first step is rate-determining for the deformylation, which occurs through a pentacoordinated metal center. The estimated activation energies with the ONIOM method are about 23.0, 15.0, and 14.9 kcal/mol for Zn-, Ni-, and Fe-PDFs, respectively. These calculated barriers are in close agreement with experimental observations. Our results demonstrate that the preference for metal coordination geometry exerts a significant influence on the catalytic activity of PDFs by affecting the activation of the carbonyl group of the substrate, the deprotonation of the metal-coordinated water, and the stabilization of the transition state. This preference for coordination geometry is mainly determined by the ligand environment and the intrinsic electronic structures of the metal center in the active site of the PDFs.
Collapse
Affiliation(s)
- Xian-Hui Wu
- Laboratory of Chemical Genomics, Shenzhen Graduate School of Peking University, Shenzhen, China
| | | | | |
Collapse
|
13
|
Namuswe F, Goldberg DP. A combinatorial approach to minimal peptide models of a metalloprotein active site. Chem Commun (Camb) 2006:2326-8. [PMID: 16733568 DOI: 10.1039/b601407k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Screening of a "one-bead-one-compound" peptide library containing biomimetic His/Cys ligands has led to the discovery of sequences that hydrolyze ester substrates in combination with Zn2+.
Collapse
Affiliation(s)
- Frances Namuswe
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | | |
Collapse
|
14
|
Saxena R, Chakraborti PK. Identification of regions involved in enzymatic stability of peptide deformylase of Mycobacterium tuberculosis. J Bacteriol 2005; 187:8216-20. [PMID: 16291698 PMCID: PMC1291256 DOI: 10.1128/jb.187.23.8216-8220.2005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sequence analysis of peptide deformylase of Mycobacterium tuberculosis revealed the presence of insertions (residues 74 to 85) and an unusually long carboxy-terminal end (residues 182 to 197). Our results with deletion mutants indicated the contribution of these regions in maintaining enzymatic stability. Furthermore, we showed that the region spanning the insertions was responsible for maintaining resistance to oxidizing agents, like H(2)O(2).
Collapse
Affiliation(s)
- Rahul Saxena
- Institute of Microbial Technology, Chandigarh, India
| | | |
Collapse
|
15
|
Zhou Z, Song X, Gong W. Novel conformational states of peptide deformylase from pathogenic bacterium Leptospira interrogans: implications for population shift. J Biol Chem 2005; 280:42391-6. [PMID: 16239225 DOI: 10.1074/jbc.m506370200] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Peptide deformylase is an attractive target for developing novel antibiotics. Previous studies at pH 3.0 showed peptide deformylase from Leptospira interrogans (LiPDF) exists as a dimer in which one monomer is in a closed form and the other is in an open form, with different conformations of the CD-loop controlling the entrance to the active pocket. Here we present structures of LiPDF at its active pH range. LiPDF forms a similar dimer at pH values 6.5-8.0 as it does at pH 3.0. Interestingly, both of the monomers are almost in the same closed form as that observed at pH 3.0. However, when the enzyme is complexed with the natural inhibitor actinotin, the conformation of the CD-loop is half-open. Two pairs of Arg109-mediated cation-pi interactions, as well as hydrogen bonds, have been identified to stabilize the different CD-loop conformations. These results indicate that LiPDF may be found in different structural states, a feature that has never before been observed in the peptide deformylase family. Based on our results, a novel substrate binding model, featured by an equilibrium between the closed and the open forms, is proposed. Our results present crystallographic evidence supporting population shift theory, which is distinguished from the conventional lock-and-key or induced-fit models. These results not only facilitate the development of peptide deformylase-targeted drugs but also provide structural insights into the mechanism of an unusual type of protein binding event.
Collapse
Affiliation(s)
- Zhaocai Zhou
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | | | | |
Collapse
|
16
|
Fieulaine S, Juillan-Binard C, Serero A, Dardel F, Giglione C, Meinnel T, Ferrer JL. The crystal structure of mitochondrial (Type 1A) peptide deformylase provides clear guidelines for the design of inhibitors specific for the bacterial forms. J Biol Chem 2005; 280:42315-24. [PMID: 16192279 DOI: 10.1074/jbc.m507155200] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Peptide deformylase (PDF) inhibitors have a strong potential to be used as a new class of antibiotics. However, recent studies have shown that the mitochondria of most eukaryotes, including humans, contain an essential PDF, PDF1A. The crystal structure of the Arabidopsis thaliana PDF1A (AtPDF1A), considered representative of PDF1As in general, has been determined. This structure displays several similarities to that of known bacterial PDFs. AtPDF1A behaves as a dimer, with the C-terminal residues responsible for linking the two subunits. This arrangement is similar to that of Leptospira interrogans PDF, the only other dimeric PDF identified to date. AtPDF1A is the first PDF for which zinc has been identified as the catalytic ion. However, the zinc binding pocket does not differ from the binding pockets of PDFs with iron rather than zinc. The crystal structure of AtPDF1A in complex with a substrate analog revealed that the substrate binding pocket of PDF1A displays strong modifications. The S1' binding pocket is significantly narrower, due to the creation of a floor from residues present in all PDF1As but not in bacterial PDFs. A true S3' pocket is created by the residues of a helical CD-loop, which is very long in PDF1As. Finally, these modified substrate binding pockets modify the position of the substrate in the active site. These differences provide guidelines for the design of bacterial PDF inhibitors that will not target mitochondrial PDFs.
Collapse
Affiliation(s)
- Sonia Fieulaine
- Institut de Biologie Structurale J-P. Ebel CEA-CNRS-UJF, UMR5075, Laboratoire de Cristallographie et Cristallogenèse des Protéines (LCCP/GSY), 41 Rue Jules Horowitz, F-38027 Grenoble Cedex 1, France
| | | | | | | | | | | | | |
Collapse
|
17
|
Saxena R, Chakraborti PK. The carboxy-terminal end of the peptide deformylase from Mycobacterium tuberculosis is indispensable for its enzymatic activity. Biochem Biophys Res Commun 2005; 332:418-25. [PMID: 15896710 DOI: 10.1016/j.bbrc.2005.04.142] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2005] [Accepted: 04/19/2005] [Indexed: 10/25/2022]
Abstract
The peptide deformylase in bacteria is involved in removal of N-formyl group from newly synthesized proteins. The gene encoding this enzyme from Mycobacterium tuberculosis was cloned and expressed in Escherichia coli. The enzyme activity of the recombinant protein (mPDF) was insensitive to modulation by common monovalent/divalent cations. Kinetic analysis, using N-formylmethionine-alanine as the substrate, yielded K(cat)/K(m) of approximately 1220 M(-1)s(-1). Actinonin, a naturally occurring antibiotic, and 1,10-ortho-phenanthroline strongly inhibited the enzyme activity. The mPDF was very stable at 30 degrees C with a half-life of approximately 4h and exhibited resistance to oxidizing agents, like H(2)O(2). Thus, the mPDF achieved distinction in its behavior among any reported iron-containing peptide deformylases. Furthermore, amino acid sequence analysis of mPDF revealed the presence of an unusually long carboxy-terminal end (residues 182-197), which is atypical for any gram-positive bacteria. Our results, through deletion analysis, for the first time established the role of this region in mPDF enzyme activity.
Collapse
Affiliation(s)
- Rahul Saxena
- Institute of Microbial Technology, Sector 39A, Chandigarh 160 036, India
| | | |
Collapse
|
18
|
Lee MD, She Y, Soskis MJ, Borella CP, Gardner JR, Hayes PA, Dy BM, Heaney ML, Philips MR, Bornmann WG, Sirotnak FM, Scheinberg DA. Human mitochondrial peptide deformylase, a new anticancer target of actinonin-based antibiotics. J Clin Invest 2004; 114:1107-16. [PMID: 15489958 PMCID: PMC522256 DOI: 10.1172/jci22269] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2004] [Accepted: 08/31/2004] [Indexed: 12/22/2022] Open
Abstract
Peptide deformylase activity was thought to be limited to ribosomal protein synthesis in prokaryotes, where new peptides are initiated with an N-formylated methionine. We describe here a new human peptide deformylase (Homo sapiens PDF, or HsPDF) that is localized to the mitochondria. HsPDF is capable of removing formyl groups from N-terminal methionines of newly synthesized mitochondrial proteins, an activity previously not thought to be necessary in mammalian cells. We show that actinonin, a peptidomimetic antibiotic that inhibits HsPDF, also inhibits the proliferation of 16 human cancer cell lines. We designed and synthesized 33 chemical analogs of actinonin; all of the molecules with potent activity against HsPDF also inhibited tumor cell growth, and vice versa, confirming target specificity. Small interfering RNA inhibition of HsPDF protein expression was also antiproliferative. Actinonin treatment of cells led to a tumor-specific mitochondrial membrane depolarization and ATP depletion in a time- and dose-dependent manner; removal of actinonin led to a recovery of the membrane potential consistent with indirect effects on the electron transport chain. In animal models, oral or parenteral actinonin was well tolerated and inhibited human prostate cancer and lung cancer growth. We conclude that HsPDF is a new human mitochondrial enzyme that may provide a novel selective target for anticancer therapy by use of actinonin-based antibiotics.
Collapse
Affiliation(s)
- Mona D Lee
- Department of Molecular Pharmacology and Chemistry, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Lee MD, She Y, Soskis MJ, Borella CP, Gardner JR, Hayes PA, Dy BM, Heaney ML, Philips MR, Bornmann WG, Sirotnak FM, Scheinberg DA. Human mitochondrial peptide deformylase, a new anticancer target of actinonin-based antibiotics. J Clin Invest 2004. [DOI: 10.1172/jci200422269] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
20
|
Han C, Wang Q, Dong L, Sun H, Peng S, Chen J, Yang Y, Yue J, Shen X, Jiang H. Molecular cloning and characterization of a new peptide deformylase from human pathogenic bacterium Helicobacter pylori. Biochem Biophys Res Commun 2004; 319:1292-8. [PMID: 15194508 DOI: 10.1016/j.bbrc.2004.05.120] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2004] [Indexed: 11/26/2022]
Abstract
Helicobacter pylori is a gram-negative pathogenic bacterium, which is associated with peptic ulcer disease and gastric cancer. It is urgent to discover novel drug targets for appropriate antimicrobial agents against this human pathogen. In bacteria, peptide deformylase (PDF) catalyzes the removal of a formyl group from the N-termini of nascent polypeptides. Due to its essentiality and absence in mammalian cells, PDF has been considered as an attractive target for the discovery of novel antibiotics. In this work, a new PDF gene (def) from H. pylori strain SS1 was cloned, expressed, and purified in Escherichia coli system. Sequence alignment shows that H. pylori PDF (HpPDF) shares about 40% identity to E. coli PDF (EcPDF). The enzymatic properties of HpPDF demonstrate its relatively high activity toward formyl-Met-Ala-Ser, with K(cat) of 3.4s(-1), K(m) of 1.7 mM, and K(cat) / K(m) of 2000M(-1)s(-1). HpPDF enzyme appears to be fully active at pH between 8.0 and 9.0, and temperature 50 degrees C. The enzyme activity of Co(2+)-containing HpPDF is apparently higher than that of Zn(2+)-containing HpPDF. This present work thereby supplies a potential platform that facilitates the discovery of novel HpPDF inhibitors and further of possible antimicrobial agents against H. pylori.
Collapse
Affiliation(s)
- Cong Han
- Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 201203, China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Zhou Z, Song X, Li Y, Gong W. Unique structural characteristics of peptide deformylase from pathogenic bacterium Leptospira interrogans. J Mol Biol 2004; 339:207-15. [PMID: 15123432 DOI: 10.1016/j.jmb.2004.03.045] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2003] [Revised: 03/16/2004] [Accepted: 03/16/2004] [Indexed: 11/29/2022]
Abstract
Peptide deformylase (PDF), which is essential for normal growth of bacteria but not for higher organisms, is explored as an attractive target for developing novel antibiotics. Here, we present the crystal structure of Leptospira interrogans PDF (LiPDF) at 2.2A resolution. To our knowledge, this is the first crystal structure of PDF associating in a stable dimer. The key loop (named the CD-loop: amino acid residues 66-76) near the active-site pocket adopts "closed" or "open" conformations in the two monomers forming the dimer. In the closed subunit, the CD-loop and residue Arg109 block the entry of the substrate-binding pocket, while the active-site pocket of the open subunit is occupied by the C-terminal tail from the neighbouring molecule. Moreover, a formate group, as one product of deformylisation, is observed bound with the active-site zinc ion. LiPDF displays significant structural differences in the C-terminal region compared to both type-I and type-II PDFs, suggesting a new family of PDFs.
Collapse
Affiliation(s)
- Zhaocai Zhou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | | | | | | |
Collapse
|