☆ 4.8 Article

Structure Prediction and Genome Mining-Aided Discovery of the Bacterial C-Terminal Tryptophan Prenyltransferase PalQ

ADVANCED SCIENCE (2023)

相关参考文献

注意：仅列出部分参考文献，下载原文获取全部文献信息。

Article Chemistry, Multidisciplinary

Metal-dependent enzyme symmetry guides the biosynthetic flux of terpene precursors

Felix Ecker et al.

Summary: In this study, a metal-dependent, bifunctional isoprenyl diphosphate synthase from the leaf beetle Phaedon cochleariae was characterized. The cooperative effects within the homodimer strongly depend on the provided metal ions and regulate the biosynthetic flux of terpene precursors. A unique chain length determination domain adapts to form geranyl or farnesyl pyrophosphate by altering enzyme symmetry and ligand affinity between both subunits. Additionally, an allosteric geranyl-pyrophosphate-specific binding site similar to end-product inhibition in human farnesyl pyrophosphate synthase was identified. The findings reveal a deeply intertwined reaction mechanism in the P. cochleariae isoprenyl diphosphate synthase.

NATURE CHEMISTRY (2023)

添加到收藏夹

Article Biochemistry & Molecular Biology

antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation

Kai Blin et al.

Summary: Microorganisms produce small bioactive compounds that have antimicrobial, anticancer, antifungal, antiviral, or other bio-activities, making them important for medicine and agriculture. Genome mining is a widely-used method to explore and analyze the biodiversity of these compounds, and the 'antibiotics and secondary metabolite analysis shell-antiSMASH' is the most widely used tool for this purpose. The updated version 7 of antiSMASH, with improvements in cluster types, chemical structure prediction, enzymatic assembly-line visualization, and gene cluster regulation, is presented here.

NUCLEIC ACIDS RESEARCH (2023)

添加到收藏夹

Review Chemistry, Multidisciplinary

Chemical Synthesis and Semisynthesis of Lipidated Proteins

Cameron C. Hanna et al.

Summary: Lipidation is a common modification of peptides and proteins that can affect crucial biological activities. The use of synthetic techniques allows for the preparation of pure and homogeneously modified lipidated proteins, revealing the impact of these modifications on protein structure and function.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2022)

添加到收藏夹

Review Chemistry, Multidisciplinary

Catalysts for the Enzymatic Lipidation of Peptides

Yiwu Zheng et al.

Summary: Biologically active peptides, such as cyanobactins, are modified with lipids to enhance therapeutic potential. The F family of peptide prenyltransferases have diverse acceptor residue specificities, making them suitable for enzymatic prenylation of peptide substrates. These enzymes are attractive catalysts for synthetic biology approaches in generating high-value peptidic therapeutics.

ACCOUNTS OF CHEMICAL RESEARCH (2022)

添加到收藏夹

Article Biochemical Research Methods

ColabFold: making protein folding accessible to all

Milot Mirdita et al.

Summary: ColabFold combines fast homology search and optimized model utilization to offer accelerated prediction of protein structures and complexes, with a processing speed that is 40-60 times faster. It serves as a free and accessible platform for protein folding, capable of predicting close to 1,000 structures per day.

NATURE METHODS (2022)

添加到收藏夹

Article Biochemistry & Molecular Biology

Discovery, biochemical characterization, and bioengineering of cyanobactin prenyltransferases

Yuchen Zhang et al.

TRENDS IN BIOCHEMICAL SCIENCES (2022)

添加到收藏夹

Article Chemistry, Physical

LimF is a versatile prenyltransferase for histidine-C-geranylation on diverse non-natural substrates

Yuchen Zhang et al.

Summary: This study reports a new prenyltransferase, LimF, which geranylates the electron-deficient C2 atom of His imidazole and modifies diverse exotic peptides. Crystallographic analysis provides structural insights into the bifunctionality of LimF and its recognition of substrates. Moreover, the study shows the prenylation ability of LimF on various bioactive molecules containing an imidazole group.

NATURE CATALYSIS (2022)

添加到收藏夹

Article Biochemistry & Molecular Biology

Post-translational modification of RAS proteins

Sharon L. Campbell et al.

Summary: Mutations in RAS genes are the most common driving force behind cancer development. RAS proteins, acting as binary molecular switches, control cellular growth through a complex signaling pathway. In addition to nucleotide-binding properties, RAS proteins are also regulated by numerous post-translational modifications, which are currently a high priority for drug discovery research in the field of RAS biology.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2021)

添加到收藏夹

Article Chemistry, Multidisciplinary

Genome-Mining-Based Discovery of the Cyclic Peptide Tolypamide and TolF, a Ser/Thr Forward O-Prenyltransferase

Mugilarasi Purushothaman et al.

Summary: Genome mining was used to identify a novel cyanobactin metabolite tolypamide from the freshwater cyanobacterium Tolypothrix sp., which features an unprecedented post-translational prenylation modification on a threonine residue. The enzyme TolF shows strict selectivity for prenylation of serine or threonine, providing potential as a robust tool for synthetic biology.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2021)

添加到收藏夹

Article Chemistry, Multidisciplinary

Argicyclamides A-C Unveil Enzymatic Basis for Guanidine Bis-prenylation

Chin-Soon Phan et al.

Summary: The study identified a new class of cyanobactins called argicyclamides from Microcystis aeruginosa NIES-88, which exhibit unique mono- and bis-prenylations on guanidine moieties. By isolating and characterizing biosynthetic enzymes, including a new guanidine prenyltransferase AgcF, the genetic basis of argicyclamide biosynthesis was established, shedding light on the biosynthesis of prenylated guanidines and providing a new toolkit for peptide modification.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2021)

添加到收藏夹

Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

添加到收藏夹

Review Biochemistry & Molecular Biology

New developments in RiPP discovery, enzymology and engineering

Manuel Montalban-Lopez et al.

Summary: This article reviews the research progress of ribosomally-synthesized and post-translationally modified peptides (RiPPs) as of June 2020, including the discovery of new RiPP classes, deeper understanding of the mechanisms for the installation of post-translational modifications, and the mechanisms by which enzymes recognize leader peptides. Additionally, genome mining tools and strategies for RiPP engineering are also discussed in the review.

NATURAL PRODUCT REPORTS (2021)

添加到收藏夹

Article Biochemistry & Molecular Biology

Identification of critical residues for the catalytic activity of ComQ, a Bacillus prenylation enzyme for quorum sensing, by using a simple bioassay system

Kazutake Hirooka et al.

BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY (2020)

添加到收藏夹

Article Biochemistry & Molecular Biology

Comparative genome analysis and mining of secondary metabolites of Paenibacillus polymyxa

Buqing Wang et al.

GENES & GENETIC SYSTEMS (2020)

添加到收藏夹

Article Biochemistry & Molecular Biology

GGTase3 is a newly identified geranylgeranyltransferase targeting a ubiquitin ligase

Shafi Kuchay et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2019)

添加到收藏夹

Article Biochemistry & Molecular Biology

Biosynthesis of the Bis-Prenylated Alkaloids Muscoride A and B

Antti Mattila et al.

ACS CHEMICAL BIOLOGY (2019)

添加到收藏夹

Article Biochemistry & Molecular Biology

The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways

Remi Zallot et al.

BIOCHEMISTRY (2019)

添加到收藏夹

Review Chemistry, Multidisciplinary

Protein Lipidation: Occurrence, Mechanisms, Biological Functions, and Enabling Technologies

Hong Jiang et al.

CHEMICAL REVIEWS (2018)

添加到收藏夹

Review Biochemistry & Molecular Biology

Rce1: mechanism and inhibition

Shahienaz E. Hampton et al.

CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY (2018)

添加到收藏夹

Article Chemistry, Multidisciplinary

Post-Translational Tyrosine Geranylation in Cyanobactin Biosynthesis

Maho Morita et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2018)

添加到收藏夹

Article Multidisciplinary Sciences

Sphaerocyclamide, a prenylated cyanobactin from the cyanobacterium Sphaerospermopsis sp LEGE 00249

Joana Martins et al.

SCIENTIFIC REPORTS (2018)

添加到收藏夹

Article Biochemistry & Molecular Biology

N-Prenylation of Tryptophan by an Aromatic Prenyltransferase from the Cyanobactin Biosynthetic Pathway

Luca Dalponte et al.

BIOCHEMISTRY (2018)

添加到收藏夹

Article Chemistry, Multidisciplinary

Enzymatic N- and C-Protection in Cyanobactin RiPP Natural Products

Debosmita Sardar et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2017)

添加到收藏夹

Review Biotechnology & Applied Microbiology

Current knowledge and perspectives of Paenibacillus: a review

Elliot Nicholas Grady et al.

MICROBIAL CELL FACTORIES (2016)

添加到收藏夹

Article Biochemistry & Molecular Biology

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules

Haim Ashkenazy et al.

NUCLEIC ACIDS RESEARCH (2016)

添加到收藏夹

Article Multidisciplinary Sciences

Metabolic model for diversity-generating biosynthesis

Ma. Diarey Tianero et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

添加到收藏夹

Article Multidisciplinary Sciences

Molecular basis for the broad substrate selectivity of a peptide prenyltransferase

Yue Hao et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

添加到收藏夹

Review Biochemistry & Molecular Biology

Mechanistic studies on the indole prenyltransferases

Martin E. Tanner

NATURAL PRODUCT REPORTS (2015)

添加到收藏夹

Article Chemistry, Multidisciplinary

GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations

Jaewoon Jung et al.

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2015)

添加到收藏夹

Article Biochemistry & Molecular Biology

A region corresponding to second aspartate-rich motif in tryptophan isoprenylating enzyme, ComQ, serves as a substrate-binding site

Masahiro Okada et al.

BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY (2014)

添加到收藏夹

Article Biochemistry & Molecular Biology

ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites

Janez Konc et al.

NUCLEIC ACIDS RESEARCH (2014)

添加到收藏夹

Article Biochemistry & Molecular Biology

Genome Mining Expands the Chemical Diversity of the Cyanobactin Family to Include Highly Modified Linear Peptides

Niina Leikoski et al.

CHEMISTRY & BIOLOGY (2013)

添加到收藏夹

Article Multidisciplinary Sciences

Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily

Frank H. Wallrapp et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

添加到收藏夹

Article Biochemistry & Molecular Biology

Lack of the Consensus Sequence Necessary for Tryptophan Prenylation in the ComX Pheromone Precursor

Fumitada Tsuji et al.

BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY (2012)

添加到收藏夹

Article Chemistry, Multidisciplinary

Enzymatic Basis of Ribosomal Peptide Prenylation in Cyanobacteria

John A. McIntosh et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2011)

添加到收藏夹

Article Biology

Expansion of ribosomally produced natural products: a nitrile hydratase-and Nif11-related precursor family

Daniel H. Haft et al.

BMC BIOLOGY (2010)

添加到收藏夹

Article Biochemistry & Molecular Biology

Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts

Yang Shen et al.

JOURNAL OF BIOMOLECULAR NMR (2010)

添加到收藏夹

Article Chemistry, Multidisciplinary

Mechanism of Dimethylallyltryptophan Synthase: Evidence for a Dimethylallyl Cation Intermediate in an Aromatic Prenyltransferase Reaction

Louis Y. P. Luk et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2009)

添加到收藏夹

Article Biochemistry & Molecular Biology

Chemical structure of posttranslational modification with a Farnesyl group on tryptophan

Masahiro Okada et al.

BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY (2008)

添加到收藏夹

Review Biochemistry & Molecular Biology

Structural biology of protein farnesyltransferase and geranylgeranyltransferase type I

KT Lane et al.

JOURNAL OF LIPID RESEARCH (2006)

添加到收藏夹

Article Biochemistry & Molecular Biology

Structure of the Bacillus subtilis quorum-sensing peptide pheromone ComX

M Okada et al.

NATURE CHEMICAL BIOLOGY (2005)

添加到收藏夹

Article Biochemistry & Molecular Biology

Cytoscape: A software environment for integrated models of biomolecular interaction networks

P Shannon et al.

GENOME RESEARCH (2003)

添加到收藏夹

© Peeref 2019-2024. All rights reserved.