scholarly journals DNA-dependent binding of nargenicin to DnaE1 inhibits replication in Mycobacterium tuberculosis

2021 ◽  
Author(s):  
Melissa D. Chengalroyen ◽  
Mandy K. Mason ◽  
Alessandro Borsellini ◽  
Raffaella Tassoni ◽  
Garth L. Abrahams ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Mycobacterium Tuberculosis ◽  
Dna Polymerase ◽  
Dna Damage Response ◽  
Bacterial Species ◽  
Antimycobacterial Activity ◽  
Cryo Electron Microscopy ◽  
Damage Response ◽  
Dna Binding Affinity ◽  
Dna Substrate

Natural products provide a rich source of potential antimicrobials for use in treating infectious diseases for which drug resistance has emerged. Foremost among these is tuberculosis. Assessment of the antimycobacterial activity of nargenicin, a natural product that targets the replicative DNA polymerase of Staphylococcus aureus, revealed that it is a bactericidal genotoxin that induces a DNA damage response in Mycobacterium tuberculosis (Mtb) and inhibits growth by blocking the replicative DNA polymerase, DnaE1. Cryo-electron microscopy revealed that binding of nargenicin to Mtb DnaE1 requires the DNA substrate such that nargenicin is wedged between the terminal base pair and the polymerase and occupies the position of both the incoming nucleotide and templating base. Comparative analysis across three bacterial species suggests that the activity of nargenicin is partly attributable to the DNA binding affinity of the replicative polymerase. This work has laid the foundation for target-led drug discovery efforts focused on Mtb DnaE1.

scholarly journals Depletion of the DarG antitoxin in Mycobacterium tuberculosis triggers the DNA‐damage response and leads to cell death

2020 ◽  
Vol 114 (4) ◽  
pp. 641-652 ◽  
Author(s):  
Anisha Zaveri ◽  
Ruojun Wang ◽  
Laure Botella ◽  
Ritu Sharma ◽  
Linnan Zhu ◽  
...  
Keyword(s):  
Dna Damage ◽  
Cell Death ◽  
Mycobacterium Tuberculosis ◽  
Dna Damage Response ◽  
Damage Response

scholarly journals p53 suppression overwhelms DNA polymerase η deficiency in determining the cellular UV DNA damage response

DNA Repair ◽  
2007 ◽  
Vol 6 (12) ◽  
pp. 1794-1804 ◽  
Author(s):  
Rebecca R. Laposa ◽  
Luzviminda Feeney ◽  
Eileen Crowley ◽  
Sebastien de Feraudy ◽  
James E. Cleaver
Keyword(s):  
Dna Damage ◽  
Dna Polymerase ◽  
Dna Damage Response ◽  
Damage Response

scholarly journals Structural basis of prokaryotic ubiquitin-like protein engagement and translocation by the mycobacterial Mpa-proteasome complex

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Mikhail Kavalchuk ◽  
Ahmad Jomaa ◽  
Andreas U. Müller ◽  
Eilika Weber-Ban
Keyword(s):  
Electron Microscopy ◽  
Mycobacterium Tuberculosis ◽  
Early Stage ◽  
Structural Basis ◽  
Human Pathogen ◽  
Core Particle ◽  
Cryo Electron Microscopy ◽  
Complementary Interactions

AbstractProteasomes are present in eukaryotes, archaea and Actinobacteria, including the human pathogen Mycobacterium tuberculosis, where proteasomal degradation supports persistence inside the host. In mycobacteria and other members of Actinobacteria, prokaryotic ubiquitin-like protein (Pup) serves as a degradation tag post-translationally conjugated to target proteins for their recruitment to the mycobacterial proteasome ATPase (Mpa). Here, we use single-particle cryo-electron microscopy to determine the structure of Mpa in complex with the 20S core particle at an early stage of pupylated substrate recruitment, shedding light on the mechanism of substrate translocation. Two conformational states of Mpa show how substrate is translocated stepwise towards the degradation chamber of the proteasome core particle. We also demonstrate, in vitro and in vivo, the importance of a structural feature in Mpa that allows formation of alternating charge-complementary interactions with the proteasome resulting in radial, rail-guided movements during the ATPase conformational cycle.

Structure of Saccharomyces cerevisiae DNA polymerase epsilon by cryo–electron microscopy

2005 ◽  
Vol 13 (1) ◽  
pp. 35-43 ◽  
Author(s):  
Francisco J Asturias ◽  
Iris K Cheung ◽  
Nasim Sabouri ◽  
Olga Chilkova ◽  
Daniel Wepplo ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Saccharomyces Cerevisiae ◽  
Dna Polymerase ◽  
Dna Polymerase Epsilon ◽  
Cryo Electron Microscopy ◽  
Polymerase Epsilon

scholarly journals 2D-QSAR, Docking Studies, and In Silico ADMET Prediction of Polyphenolic Acetates as Substrates for Protein Acetyltransferase Function of Glutamine Synthetase of Mycobacterium tuberculosis

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
Prija Ponnan ◽  
Shikhar Gupta ◽  
Madhu Chopra ◽  
Rashmi Tandon ◽  
Anil S. Baghel ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Glutamine Synthetase ◽  
Bacterial Species ◽  
Antimycobacterial Activity ◽  
Docking Studies ◽  
Linear Regression Method ◽  
Glutathione S Transferase ◽  
Qsar Studies ◽  
2D Qsar ◽  
In Silico Admet

A novel transacetylase (TAase) function of glutamine synthetase (GS) in bacterial species such as Mycobacterium smegmatis and Mycobacterium tuberculosis H37Rv was established by us, termed as mycobacterial TAase (MTAase). Several polyphenolic acetates (PAs) were found to be substrates for MTAase by inhibiting certain receptor proteins such as glutathione S-transferase by way of acetylation. The present work describes the descriptor-based 2D-QSAR studies developed for a series of PA synthesized by us and evaluated for MTAase and antimycobacterial activity using stepwise multiple linear regression method with the kinetic constants and the minimum inhibitory constant (MIC) as the dependent variables, to address the fact that TAase activity was leading to the antimycobacterial activity. Further, blind docking methods using AutoDock were carried out to study the interaction of potent PA with the crystal structure of M. tuberculosis GS. PAs were predicted to bind M. tuberculosis GS on the protein surface away from the known active site of GS. Subsequent focussed/refined docking of potent PA with GS showed that the ε-amino group of Lys4 of GS formed a cation-π interaction with the benzene ring of PA. Also, ADMET-related descriptors were calculated to predict the pharmacokinetic properties for the selection of the effective and bioavailable compounds.

scholarly journals Characterization of the effects of cisplatin and carboplatin on cell cycle progression and DNA damage response activation in DNA polymerase eta-deficient human cells

Cell Cycle ◽  
2009 ◽  
Vol 8 (18) ◽  
pp. 3043-3054 ◽  
Author(s):  
Séverine Cruet-Hennequart ◽  
Sangamitra Villalan ◽  
Agnieszka Kaczmarczyk ◽  
Elaine O’Meara ◽  
Anna M. Sokol ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Dna Polymerase ◽  
Dna Damage Response ◽  
Cell Cycle Progression ◽  
Cycle Progression ◽  
Polymerase Eta ◽  
Dna Polymerase Eta ◽  
Damage Response ◽  
Response Activation

scholarly journals Two conformations of DNA polymerase D-PCNA-DNA, an archaeal replisome complex, revealed by cryo-electron microscopy

BMC Biology ◽  
2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Kouta Mayanagi ◽  
Keisuke Oki ◽  
Naoyuki Miyazaki ◽  
Sonoko Ishino ◽  
Takeshi Yamagami ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Dna Polymerase ◽  
Structural Model ◽  
Contact Point ◽  
Dna Polymerases ◽  
3D Structure ◽  
Nuclear Antigen ◽  
Structural Level ◽  
Cryo Electron Microscopy ◽  
Dna Complex

Abstract Background DNA polymerase D (PolD) is the representative member of the D family of DNA polymerases. It is an archaea-specific DNA polymerase required for replication and unrelated to other known DNA polymerases. PolD consists of a heterodimer of two subunits, DP1 and DP2, which contain catalytic sites for 3′-5′ editing exonuclease and DNA polymerase activities, respectively, with both proteins being mutually required for the full activities of each enzyme. However, the processivity of the replicase holoenzyme has additionally been shown to be enhanced by the clamp molecule proliferating cell nuclear antigen (PCNA), making it crucial to elucidate the interaction between PolD and PCNA on a structural level for a full understanding of its functional relevance. We present here the 3D structure of a PolD-PCNA-DNA complex from Thermococcus kodakarensis using single-particle cryo-electron microscopy (EM). Results Two distinct forms of the PolD-PCNA-DNA complex were identified by 3D classification analysis. Fitting the reported crystal structures of truncated forms of DP1 and DP2 from Pyrococcus abyssi onto our EM map showed the 3D atomic structural model of PolD-PCNA-DNA. In addition to the canonical interaction between PCNA and PolD via PIP (PCNA-interacting protein)-box motif, we found a new contact point consisting of a glutamate residue at position 171 in a β-hairpin of PCNA, which mediates interactions with DP1 and DP2. The DNA synthesis activity of a mutant PolD with disruption of the E171-mediated PCNA interaction was not stimulated by PCNA in vitro. Conclusions Based on our analyses, we propose that glutamate residues at position 171 in each subunit of the PCNA homotrimer ring can function as hooks to lock PolD conformation on PCNA for conversion of its activity. This hook function of the clamp molecule may be conserved in the three domains of life.

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