Colicin biology

E Cascales, SK Buchanan, D Duché… - Microbiology and …, 2007 - Am Soc Microbiol
Colicins are proteins produced by and toxic for some strains of Escherichia coli. They are
produced by strains of E. coli carrying a colicinogenic plasmid that bears the genetic …

Roles of metal ions in nucleases

CM Dupureur - Current opinion in chemical biology, 2008 - Elsevier
The hydrolysis of phosphodiester bonds by metallonucleases is crucial to most aspects of
nucleic acid processing. In recent years, studies of the classical restriction endonucleases …

Context-aware geometric deep learning for protein sequence design

LF Krapp, FA Meireles, LA Abriata, J Devillard… - Nature …, 2024 - nature.com
Protein design and engineering are evolving at an unprecedented pace leveraging the
advances in deep learning. Current models nonetheless cannot natively consider non …

Method for the generation of compact TALE-nucleases and uses thereof

P Duchateau, J Valton, C Bertonati, JC Epinat… - US Patent …, 2016 - Google Patents
The present invention relates to a method for the generation of compact Transcription
Activator-Like Effector Nucleases (TALENs) that can efficiently target and process double …

An equivalent metal ion in one-and two-metal-ion catalysis

W Yang - Nature structural & molecular biology, 2008 - nature.com
Nucleotidyl-transfer enzymes, which synthesize, degrade and rearrange DNA and RNA,
often depend on metal ions for catalysis. All DNA and RNA polymerases, MutH-like or …

Nuclease colicins and their immunity proteins

G Papadakos, JA Wojdyla… - Quarterly reviews of …, 2012 - cambridge.org
It is more than 80 years since Gratia first described 'a remarkable antagonism between two
strains of Escherichia coli'. Shown subsequently to be due to the action of proteins (or …

Nicking mechanism underlying the DNA phosphorothioate-sensing antiphage defense by SspE

H Gao, X Gong, J Zhou, Y Zhang, J Duan, Y Wei… - Nature …, 2022 - nature.com
DNA phosphorothioate (PT) modification, with a nonbridging phosphate oxygen substituted
by sulfur, represents a widespread epigenetic marker in prokaryotes and provides protection …

Structural and functional characterization of deep-sea thermophilic bacteriophage GVE2 HNH endonuclease

L Zhang, D Xu, Y Huang, X Zhu, M Rui, T Wan… - Scientific reports, 2017 - nature.com
HNH endonucleases in bacteriophages play a variety of roles in the phage lifecycle as key
components of phage DNA packaging machines. The deep-sea thermophilic bacteriophage …

Structure of the ultra-high-affinity colicin E2 DNase–Im2 complex

JA Wojdyla, SJ Fleishman, D Baker… - Journal of molecular …, 2012 - Elsevier
How proteins achieve high-affinity binding to a specific protein partner while simultaneously
excluding all others is a major biological problem that has important implications for protein …

Crystal structure of the ββα-Me type II restriction endonuclease Hpy99I with target DNA

M Sokolowska, H Czapinska… - Nucleic acids research, 2009 - academic.oup.com
The ββα-Me restriction endonuclease (REase) Hpy99I recognizes the CGWCG target
sequence and cleaves it with unusual stagger (five nucleotide 5′-recessed ends). Here we …