Abstract：
:DNA polymerases catalyze efficient and high-fidelity DNA synthesis. While this reaction favors nucleotide incorporation, polymerases also catalyze a reverse reaction, pyrophosphorolysis, that removes the DNA primer terminus and generates deoxynucleoside triphosphates. Because pyrophosphorolysis can influence polymerase fidelity and sensitivity to chain-terminating nucleosides, we analyzed pyrophosphorolysis with human DNA polymerase β and found the reaction to be inefficient. The lack of a thio-elemental effect indicated that this reaction was limited by a nonchemical step. Use of a pyrophosphate analog, in which the bridging oxygen is replaced with an imido group (PNP), increased the rate of the reverse reaction and displayed a large thio-elemental effect, indicating that chemistry was now rate determining. Time-lapse crystallography with PNP captured structures consistent with a chemical equilibrium favoring the reverse reaction. These results highlight the importance of the bridging atom between the β- and γ-phosphates of the incoming nucleotide in reaction chemistry, enzyme conformational changes, and overall reaction equilibrium.
journal_name
Nat Chem Bioljournal_title
Nature chemical biologyauthors
Shock DD,Freudenthal BD,Beard WA,Wilson SHdoi
10.1038/nchembio.2450subject
Has Abstractpub_date
2017-10-01 00:00:00pages
1074-1080issue
10eissn
1552-4450issn
1552-4469pii
nchembio.2450journal_volume
13pub_type
杂志文章abstract：:Lysostaphin is a bacteriolytic enzyme targeting peptidoglycan, the essential component of the bacterial cell envelope. It displays a very potent and specific activity toward staphylococci, including methicillin-resistant Staphylococcus aureus. Lysostaphin causes rapid cell lysis and disrupts biofilms, and is therefore...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/s41589-019-0393-4
更新日期：2020-01-01 00:00:00
abstract：:Specific chemicals can prime the plant immune system for augmented defense. β-aminobutyric acid (BABA) is a priming agent that provides broad-spectrum disease protection. However, BABA also suppresses plant growth when applied in high doses, which has hampered its application as a crop defense activator. Here we descr...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/nchembio.1520
更新日期：2014-06-01 00:00:00
abstract：:Bile salt hydrolase (BSH) enzymes are widely expressed by human gut bacteria and catalyze the gateway reaction leading to secondary bile acid formation. Bile acids regulate key metabolic and immune processes by binding to host receptors. There is an unmet need for a potent tool to inhibit BSHs across all gut bacteria ...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/s41589-020-0467-3
更新日期：2020-03-01 00:00:00
abstract：:Gentamicin B (GB), a valuable starting material for the preparation of the semisynthetic aminoglycoside antibiotic isepamicin, is produced in trace amounts by the wild-type Micromonospora echinospora. Though the biosynthetic pathway to GB has remained obscure for decades, we have now identified three hidden pathways t...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/s41589-018-0203-4
更新日期：2019-03-01 00:00:00
abstract：:Protein serine-threonine kinase casein kinase II (CK2) is involved in a myriad of cellular processes including cell growth and proliferation through its phosphorylation of hundreds of substrates, yet how CK2 function is regulated is poorly understood. Here we report that the CK2 catalytic subunit CK2α is modified by O...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/nchembio.771
更新日期：2012-01-22 00:00:00
abstract：:The catalytic versatility of cytochrome P450 monooxygenases is remarkable. Here, we present mechanistic and structural characterizations of TleB from Streptomyces blastmyceticus and its homolog HinD from Streptoalloteichus hindustanus, which catalyze unusual intramolecular C-N bond formation to generate indolactam V f...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/s41589-019-0380-9
更新日期：2019-12-01 00:00:00
abstract：:Phosphorylation and glycosylation of the tau protein, which is implicated in neurodegenerative diseases, are intimately linked. In vivo pharmacological inhibition of tau deglycosylation may be a new way to suppress abnormal tau phosphorylation, known to be involved in the formation of neurofibrillary tangles in the br...
journal_title：Nature chemical biology
pub_type： 评论,杂志文章,评审
doi：10.1038/nchembio0808-448
更新日期：2008-08-01 00:00:00
abstract：:Identifying targets of antibacterial compounds remains a challenging step in the development of antibiotics. We have developed a two-pronged functional genomics approach to predict mechanism of action that uses mutant fitness data from antibiotic-treated transposon libraries containing both upregulation and inactivati...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/s41589-018-0041-4
更新日期：2018-06-01 00:00:00
abstract：:A 2.4-Å-resolution X-ray crystal structure of the carrier-protein-independent halogenase WelO5 in complex with its welwitindolinone precursor substrate, 12-epi-fischerindole U, reveals that the C13 chlorination target is proximal to the anticipated site of the oxo group in a presumptive cis-halo-oxo-iron(IV) (haloferr...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/nchembio.2112
更新日期：2016-08-01 00:00:00
abstract：:Helical membrane proteins are typically assumed to attain stable transmembrane topologies immediately upon co-translational membrane insertion. Here we show that unassembled monomers of the small multidrug resistance (SMR) family exist in a dynamic equilibrium where the N-terminal transmembrane helix flips in and out ...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/s41589-019-0356-9
更新日期：2019-10-01 00:00:00
abstract：:Here we present a natural product discovery approach, whereby structures are bioinformatically predicted from primary sequence and produced by chemical synthesis (synthetic-bioinformatic natural products, syn-BNPs), circumventing the need for bacterial culture and gene expression. When we applied the approach to nonri...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/nchembio.2207
更新日期：2016-12-01 00:00:00
abstract：:The phytohormone auxin indole-3-acetic acid (IAA) regulates nearly all aspects of plant growth and development. Despite substantial progress in our understanding of auxin biology, delineating specific auxin response remains a major challenge. Auxin regulates transcriptional response via its receptors, TIR1 and AFB F-b...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/nchembio.2555
更新日期：2018-03-01 00:00:00
abstract：:Cell polarity is the asymmetric compartmentalization of cellular components. An opposing gradient of partitioning-defective protein kinases, atypical protein kinase C (aPKC) and PAR-1, at the cell cortex guides diverse asymmetries in the structure of metazoan cells, but the mechanism underlying their spatial patternin...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/s41589-018-0117-1
更新日期：2018-10-01 00:00:00
abstract：:The MerR-family transcription factors (TFs) are a large group of bacterial proteins responding to cellular metal ions and multiple antibiotics by binding within central RNA polymerase-binding regions of a promoter. While most TFs alter transcription through protein-protein interactions, MerR TFs are capable of reshapi...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/s41589-020-00653-x
更新日期：2021-01-01 00:00:00
abstract：:Foldamers are sequence-specific oligomers akin to peptides, proteins and oligonucleotides that fold into well-defined three-dimensional structures. They offer the chemical biologist a broad pallet of building blocks for the construction of molecules that test and extend our understanding of protein folding and functio...
journal_title：Nature chemical biology
pub_type： 杂志文章,评审
doi：10.1038/nchembio876
更新日期：2007-05-01 00:00:00
abstract：:Linking bioactive compounds to their cellular targets is a central challenge in chemical biology. Here we report the mode of action of theonellamides, bicyclic peptides derived from marine sponges. We generated a chemical-genomic profile of theonellamide F using a collection of fission yeast strains in which each open...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/nchembio.387
更新日期：2010-07-01 00:00:00
abstract：:Identifying the interaction partners of noncoding RNAs is essential for elucidating their functions. We have developed an approach, termed microRNA crosslinking and immunoprecipitation (miR-CLIP), using pre-miRNAs modified with psoralen and biotin to capture their targets in cells. Photo-crosslinking and Argonaute 2 i...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/nchembio.1713
更新日期：2015-02-01 00:00:00
abstract：:We identify an Arabidopsis pyridoxal-phosphate-dependent aminotransferase, VAS1, whose loss-of-function simultaneously increases amounts of the phytohormone auxin and the ethylene precursor 1-aminocyclopropane-1-carboxylate. VAS1 uses the ethylene biosynthetic intermediate methionine as an amino donor and the auxin bi...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/nchembio.1178
更新日期：2013-04-01 00:00:00
abstract：:Hundreds of human proteins are modified by reversible palmitoylation of cysteine residues (S-palmitoylation), but the regulation of depalmitoylation is poorly understood. Here, we develop 'depalmitoylation probes' (DPPs), small-molecule fluorophores, to monitor the endogenous activity levels of 'erasers' of S-palmitoy...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/nchembio.2262
更新日期：2017-02-01 00:00:00
abstract：:The discovery of functional RNAs that are critical for normal and disease physiology continues to expand at a breakneck pace. Many RNA functions are controlled by the formation of specific structures, and an understanding of each structural component is necessary to elucidate its function. Measuring solvent accessibil...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/nchembio.2548
更新日期：2018-03-01 00:00:00
abstract：:Benzylisoquinoline alkaloids (BIAs) are a diverse family of plant-specialized metabolites that include the pharmaceuticals codeine and morphine and their derivatives. Microbial synthesis of BIAs holds promise as an alternative to traditional crop-based manufacturing. Here we demonstrate the production of the key BIA i...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/nchembio.1816
更新日期：2015-07-01 00:00:00
abstract：:Regio- and stereospecific incorporation of a halogen atom to an unactivated sp(3) carbon in a freestanding molecule is a challenging transformation that is currently missing in the inventory of enzyme-mediated reactions. Here we report what is to our knowledge the first example of a nonheme iron enzyme (WelO5) in the ...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/nchembio.1625
更新日期：2014-11-01 00:00:00
abstract：:Subtilosin A is a 35-residue, ribosomally synthesized bacteriocin encoded by the sbo-alb operon of Bacillus subtilis. It is composed of a head-to-tail circular peptide backbone that is additionally restrained by three unusual thioether bonds between three cysteines and the α-carbon of one threonine and two phenylalani...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/nchembio.798
更新日期：2012-02-26 00:00:00
abstract：:A required course in communication at the graduate school level may help cure the disorder of poor scientific writing. ...
journal_title：Nature chemical biology
pub_type： 社论
doi：10.1038/nchembio0906-443
更新日期：2006-09-01 00:00:00
abstract：:Lipid rafts in plasma membranes have emerged as possible platforms for the entry of HIV and other viruses into cells. However, little is known about how lipid phase heterogeneity contributes to viral entry because of the fine-grained and still poorly understood complexity of biological membranes. We used model systems...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/nchembio.1800
更新日期：2015-06-01 00:00:00
abstract：:Small molecules that specifically activate an intracellular protein of interest are highly desirable. A generally applicable strategy, however, remains elusive. Herein we describe a small molecule-triggered bioorthogonal protein decaging technique that relies on the inverse electron-demand Diels-Alder reaction for eli...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/nchembio.1656
更新日期：2014-12-01 00:00:00
abstract：:The N-end rule pathway senses the N-terminal destabilizing residues of degradation substrates for the ubiquitin-proteasome system, whose integrity shields against various human syndromes including cancer and cardiovascular diseases. GID4, a subunit of the ubiquitin ligase GID complex, has been recently identified as t...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/s41589-018-0036-1
更新日期：2018-05-01 00:00:00
abstract：:Although the protein synthesis inhibitor cycloheximide (CHX) has been known for decades, its precise mechanism of action remains incompletely understood. The glutarimide portion of CHX is seen in a family of structurally related natural products including migrastatin, isomigrastatin and lactimidomycin (LTM). We found ...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/nchembio.304
更新日期：2010-03-01 00:00:00
abstract：:Receptor-mediated endocytosis is an integral part of signal transduction as it mediates signal attenuation and provides spatial and temporal dimensions to signaling events. One of the best-studied leucine-rich repeat receptor-like kinases in plants, BRASSINOSTEROID INSENSITIVE 1 (BRI1), perceives its ligand, the brass...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/nchembio.958
更新日期：2012-05-06 00:00:00
abstract：:Small ubiquitin-like modifier (SUMO) family proteins regulate target-protein functions by post-translational modification. However, a potent and selective inhibitor targeting the SUMO pathway has been lacking. Here we describe ML-792, a mechanism-based SUMO-activating enzyme (SAE) inhibitor with nanomolar potency in c...
journal_title：Nature chemical biology
pub_type： 杂志文章
doi：10.1038/nchembio.2463
更新日期：2017-11-01 00:00:00
