Changing nucleotide specificity of the DEAD-box helicase Hera abrogates communication between the Q-motif and the P-loop.

Abstract:

:DEAD-box proteins disrupt or remodel RNA and protein/RNA complexes at the expense of ATP. The catalytic core is composed of two flexibly connected RecA-like domains. The N-terminal domain contains most of the motifs involved in nucleotide binding and serves as a minimalistic model for helicase/nucleotide interactions. A single conserved glutamine in the so-called Q-motif has been suggested as a conformational sensor for the nucleotide state. To reprogram the Thermus thermophilus RNA helicase Hera for use of oxo-ATP instead of ATP and to investigate the sensor function of the Q-motif, we analyzed helicase activity of Hera Q28E. Crystal structures of the Hera N-terminal domain Q28E mutant (TthDEAD_Q28E) in apo- and ligand-bound forms show that Q28E does change specificity from adenine to 8-oxoadenine. However, significant structural changes accompany the Q28E mutation, which prevent the P-loop from adopting its catalytically active conformation and explain the lack of helicase activity of Hera_Q28E with either ATP or 8-oxo-ATP as energy sources. 8-Oxo-adenosine, 8-oxo-AMP, and 8-oxo-ADP weakly bind to TthDEAD_Q28E but in non-canonical modes. These results indicate that the Q-motif not only senses the nucleotide state of the helicase but could also stabilize a catalytically competent conformation of the P-loop and other helicase signature motifs.

journal_name

Biol Chem

journal_title

Biological chemistry

authors

Strohmeier J,Hertel I,Diederichsen U,Rudolph MG,Klostermeier D

doi

10.1515/BC.2011.034

subject

Has Abstract

pub_date

2011-04-01 00:00:00

pages

357-69

issue

4

eissn

1431-6730

issn

1437-4315

journal_volume

392

pub_type

杂志文章
  • A structural network associated with the kallikrein-kinin and renin-angiotensin systems.

    abstract::The kallikrein-kinin and renin-angiotensin (KKS-RAS) systems represent two highly regulated proteolytic systems that are involved in several physiological and pathological processes. Although their protein-protein interactions can be studied using experimental approaches, it is difficult to differentiate between direc...

    journal_title:Biological chemistry

    pub_type: 杂志文章

    doi:10.1515/BC.2010.046

    authors: Stoka V,Turk V

    更新日期:2010-04-01 00:00:00

  • Ceramides induce programmed cell death in Arabidopsis cells in a calcium-dependent manner.

    abstract::While the role of C2-ceramide in the induction of programmed cell death (PCD) in animal systems has been well documented, little is known of its role in plant cells. Here we show that C2-ceramide induces PCD in Arabidopsis suspension cultures, which is preceded by the generation of a calcium transient and an increase ...

    journal_title:Biological chemistry

    pub_type: 杂志文章

    doi:10.1515/BC.2005.020

    authors: Townley HE,McDonald K,Jenkins GI,Knight MR,Leaver CJ

    更新日期:2005-02-01 00:00:00

  • Inhibition of cathepsin L-like proteases by cathepsin V propeptide.

    abstract::The N-terminal propeptide domains of several cathepsin L-like cysteine proteases have been shown to possess potent inhibitory activity. Here we report the first kinetic characterisation of the inhibition properties of the cathepsin V propeptide (CatV PP). Using a facile recombinant approach we demonstrate expression, ...

    journal_title:Biological chemistry

    pub_type: 杂志文章

    doi:10.1515/BC.2007.053

    authors: Burden RE,Snoddy P,Jefferies CA,Walker B,Scott CJ

    更新日期:2007-05-01 00:00:00

  • Characterization of a new toxin from the entomopathogenic fungus Metarhizium anisopliae: the ribotoxin anisoplin.

    abstract::Metarhizium anisopliae is an entomopathogenic fungus relevant in biotechnology with applications like malaria vector control. Studies of its virulence factors are therefore of great interest. Fungal ribotoxins are toxic ribonucleases with extraordinary efficiency against ribosomes and suggested as potential insecticid...

    journal_title:Biological chemistry

    pub_type: 杂志文章

    doi:10.1515/hsz-2016-0119

    authors: Olombrada M,Medina P,Budia F,Gavilanes JG,Martínez-Del-Pozo Á,García-Ortega L

    更新日期:2017-01-01 00:00:00

  • The XPD helicase: XPanDing archaeal XPD structures to get a grip on human DNA repair.

    abstract::Xeroderma pigmentosum complementation group D protein (XPD) is an iron-sulfur cluster containing 5'-3' helicase and, in humans, part of the transcription factor TFIIH. TFIIH is involved in nucleotide excision repair as well as in transcription initiation. Recently, three different groups have reported the structures o...

    journal_title:Biological chemistry

    pub_type: 杂志文章,评审

    doi:10.1515/BC.2010.076

    authors: Wolski SC,Kuper J,Kisker C

    更新日期:2010-07-01 00:00:00

  • Characterization of the specific DNA nicking activity of restriction endonuclease N.BstNBI.

    abstract::N.BstNBI is a unique restriction endonuclease isolated from Bacillus stearothermophilus. We have characterized the recognition sequence and the cleavage site of N.BstNBI. Mapping of cleavage sites of N.BstNBI showed that it recognizes an asymmetric sequence, 5' GAGTC 3', and cleaves only on the top strand 4 base pairs...

    journal_title:Biological chemistry

    pub_type: 杂志文章

    doi:10.1515/BC.2000.137

    authors: Morgan RD,Calvet C,Demeter M,Agra R,Kong H

    更新日期:2000-11-01 00:00:00

  • Redefining proteostasis transcription factors in organismal stress responses, development, metabolism, and health.

    abstract::Eukaryotic organisms have evolved complex and robust cellular stress response pathways to ensure maintenance of proteostasis and survival during fluctuating environmental conditions. Highly conserved stress response pathways can be triggered and coordinated at the cell-autonomous and cell-nonautonomous level by proteo...

    journal_title:Biological chemistry

    pub_type: 杂志文章,评审

    doi:10.1515/hsz-2019-0385

    authors: Jones LM,Chen Y,van Oosten-Hawle P

    更新日期:2020-08-27 00:00:00

  • Kallikrein-related peptidase (KLK) family mRNA variants and protein isoforms in hormone-related cancers: do they have a function?

    abstract::The kallikrein-related peptidase (KLK) gene family of 15 serine proteases encodes many proteins, including prostate specific antigen (PSA or KLK3), that are well described and/or are potential biomarkers for hormone-related cancers. Variant mRNA transcripts produced by alternative splicing, polyadenylation or AUG site...

    journal_title:Biological chemistry

    pub_type: 杂志文章,评审

    doi:10.1515/BC.2006.088

    authors: Tan OL,Whitbread AK,Clements JA,Dong Y

    更新日期:2006-06-01 00:00:00

  • Emerging mechanisms of drug-induced phospholipidosis.

    abstract::Drug-induced phospholipidosis is a lysosomal storage disorder characterized by excessive accumulation of phospholipids. Its cellular mechanism is still not well understood, but it is known that cationic amphiphilic drugs can induce it. These drugs have a hydrophilic amine head group that can be protonated in the endol...

    journal_title:Biological chemistry

    pub_type: 杂志文章,评审

    doi:10.1515/hsz-2019-0270

    authors: Breiden B,Sandhoff K

    更新日期:2019-12-18 00:00:00

  • 19F NMR as a versatile tool to study membrane protein structure and dynamics.

    abstract::To elucidate the structures and dynamics of membrane proteins, highly advanced biophysical methods have been developed that often require significant resources, both for sample preparation and experimental analyses. For very complex systems, such as membrane transporters, ion channels or G-protein coupled receptors (G...

    journal_title:Biological chemistry

    pub_type: 杂志文章,评审

    doi:10.1515/hsz-2018-0473

    authors: Rose-Sperling D,Tran MA,Lauth LM,Goretzki B,Hellmich UA

    更新日期:2019-09-25 00:00:00

  • The polysaccharide scaffold of PrP 27-30 is a common compound of natural prions and consists of alpha-linked polyglucose.

    abstract::An inert polysaccharide scaffold identified as a 5-15% component of prion rods (PrP 27-30) is unambiguously distinguishable from the N-glycosyl groups and the GPI anchor of PrP, and consists predominantly of 1,4-linked glucose with some branching via 1,4,6-linked glucose. We show that this polysaccharide scaffold is a...

    journal_title:Biological chemistry

    pub_type: 杂志文章

    doi:10.1515/BC.2005.131

    authors: Dumpitak C,Beekes M,Weinmann N,Metzger S,Winklhofer KF,Tatzelt J,Riesner D

    更新日期:2005-11-01 00:00:00

  • Inhibitory effect of the sugarcane cystatin CaneCPI-4 on cathepsins B and L and human breast cancer cell invasion.

    abstract::The lysosomal cysteine proteases cathepsin B and L play important roles in tumor cell invasion. An imbalance between these cathepsins and their endogenous inhibitors, the cystatins, has been associated with development of the metastatic phenotype. Accordingly, many studies have indicated potential use of cystatins in ...

    journal_title:Biological chemistry

    pub_type: 杂志文章

    doi:10.1515/BC.2008.035

    authors: Gianotti A,Sommer CA,Carmona AK,Henrique-Silva F

    更新日期:2008-04-01 00:00:00

  • ACE inhibition enhances bradykinin relaxations through nitric oxide and B1 receptor activation in bovine coronary arteries.

    abstract::Bradykinin causes vascular relaxations through release of endothelial relaxing factors including prostacyclin, nitric oxide (NO) and epoxyeicosatrienoic acids (EETs). Bradykinin is metabolized by angiotensin converting enzyme (ACE) and ACE inhibition enhances bradykinin relaxations. Our goal was to characterize the ro...

    journal_title:Biological chemistry

    pub_type: 杂志文章

    doi:10.1515/hsz-2012-0348

    authors: Gauthier KM,Cepura CJ,Campbell WB

    更新日期:2013-09-01 00:00:00

  • Synthetic peptides and fluorogenic substrates related to the reactive site sequence of Kunitz-type inhibitors isolated from Bauhinia: interaction with human plasma kallikrein.

    abstract::We have previously described Kunitz-type serine proteinase inhibitors purified from Bauhinia seeds. Human plasma kallikrein shows different susceptibility to those inhibitors. In this communication, we describe the interaction of human plasma kallikrein with fluorogenic and non-fluorogenic peptides based on the Bauhin...

    journal_title:Biological chemistry

    pub_type: 杂志文章

    doi:10.1515/BC.2001.016

    authors: Oliva ML,Santomauro-Vaz EM,Andrade SA,Juliano MA,Pott VJ,Sampaio MU,Sampaio CA

    更新日期:2001-01-01 00:00:00

  • Mg2+ homeostasis and transport in cyanobacteria - at the crossroads of bacterial and chloroplast Mg2+ import.

    abstract::Magnesium cation (Mg2+) is the most abundant divalent cation in living cells, where it is required for various intracellular functions. In chloroplasts and cyanobacteria, established photosynthetic model systems, Mg2+ is the central ion in chlorophylls, and Mg2+ flux across the thylakoid membrane is required for count...

    journal_title:Biological chemistry

    pub_type: 杂志文章,评审

    doi:10.1515/hsz-2018-0476

    authors: Pohland AC,Schneider D

    更新日期:2019-09-25 00:00:00

  • The macromolecular crowding effect--from in vitro into the cell.

    abstract::The influence of the cellular milieu, a complex and crowded solvent, is often neglected when biomolecular structure and function are studied in vitro. To mimic the cellular environment, crowding effects are commonly induced in vitro using artificial crowding agents like Ficoll or dextran. However, it is unclear if suc...

    journal_title:Biological chemistry

    pub_type: 杂志文章,评审

    doi:10.1515/hsz-2015-0161

    authors: Gnutt D,Ebbinghaus S

    更新日期:2016-01-01 00:00:00

  • Functional analysis of the Escherichia coli molybdopterin cofactor biosynthesis protein MoeA by site-directed mutagenesis.

    abstract::Five moeA mutants were generated by replacing some conserved amino acids of MoeA by site-directed mutagenesis. The mutants were assayed for the ability to restore in vivo nitrate reductase activity of the moeA mutant Escherichia coli JRG97 and in vitro Neurospora crassa nit-1 nitrate reductase activity. The replacemen...

    journal_title:Biological chemistry

    pub_type: 杂志文章

    doi:10.1515/BC.2002.034

    authors: Sandu C,Brandsch R

    更新日期:2002-02-01 00:00:00

  • Cross talk between kinin and angiotensin II receptors in mouse abdominal aorta.

    abstract::Bradykinin (BK) is a vasorelaxant, algesic and inflammatory agent. Angiotensin II (AngII) is known to control vascular tone and promote growth, inflammation and artherogenesis. There is evidence for cross talking between BK and AngII receptors. Therefore, the effect of lack of kinin receptors was assessed in mice with...

    journal_title:Biological chemistry

    pub_type: 杂志文章

    doi:10.1515/BC.2009.081

    authors: Rodrigues ES,Martin RP,Felipe SA,Bader M,Oliveira SM,Shimuta SI

    更新日期:2009-09-01 00:00:00

  • Pyrimidine-2,4,6-Triones: a new effective and selective class of matrix metalloproteinase inhibitors.

    abstract::Matrix metalloproteinases (MMPs) are a family of zinc endopeptidases that have been implicated in various disease processes. Different classes of MMP inhibitors, including hydroxamic acids, phosphinic acids and thiols, have been previously described. Most of these mimic peptides and most likely bind in a similar way t...

    journal_title:Biological chemistry

    pub_type: 杂志文章

    doi:10.1515/BC.2001.159

    authors: Grams F,Brandstetter H,D'Alò S,Geppert D,Krell HW,Leinert H,Livi V,Menta E,Oliva A,Zimmermann G,Gram F,Brandstetter H,D'Alò S,Geppert D,Krell HW,Leinert H,Livi VMenta E,Oliva A,Zimmermann G

    更新日期:2001-08-01 00:00:00

  • Synthetic biology of B cell activation: understanding signal amplification at the B cell antigen receptor using a rebuilding approach.

    abstract::Upon activation of the B cell antigen receptor (BCR), the spleen tyrosine kinase (Syk) and the Src family kinase Lyn phosphorylate tyrosines of the immunoreceptor tyrosine-based activation motif (ITAM) of Igα and Igβ which further serve as binding sites for the SH2 domains of these kinases. Using a synthetic biology a...

    journal_title:Biological chemistry

    pub_type: 杂志文章

    doi:10.1515/hsz-2018-0308

    authors: Kulathu Y,Zuern C,Yang J,Reth M

    更新日期:2019-03-26 00:00:00

  • Specific inhibition of interleukin-13 activity by a recombinant human single-chain immunoglobulin domain directed against the IL-13 receptor alpha1 chain.

    abstract::Interleukin-13 (IL-13) is a T-cell-derived pleiotropic cytokine of particular medical importance because of its critical role in the development of allergic asthma. The effects of IL-13 on its target cells are mediated through a dimeric transmembrane receptor (IL-13R), which shares the IL-4Ralpha subunit with the IL-4...

    journal_title:Biological chemistry

    pub_type: 杂志文章

    doi:10.1515/BC.2007.036

    authors: Knackmuss S,Krause S,Engel K,Reusch U,Virchow JC,Mueller T,Kraich M,Little M,Luttmann W,Friedrich K

    更新日期:2007-03-01 00:00:00

  • Tapasin and other chaperones: models of the MHC class I loading complex.

    abstract::MHC (major histocompatibility complex) class I molecules bind intracellular virus-derived peptides in the endoplasmic reticulum (ER) and present them at the cell surface to cytotoxic T lymphocytes. Peptide-free class I molecules at the cell surface, however, could lead to aberrant T cell killing. Therefore, cells ensu...

    journal_title:Biological chemistry

    pub_type: 杂志文章,评审

    doi:10.1515/BC.2004.100

    authors: Wright CA,Kozik P,Zacharias M,Springer S

    更新日期:2004-09-01 00:00:00

  • Functional mapping of the EcoRV DNA methyltransferase by random mutagenesis and screening for catalytically inactive mutants.

    abstract::M.EcoRV is an alpha-adenine DNA methyltransferase. According to structure predictions, the enzyme consists of a catalytic domain, which has a structure similar to all other DNA-methyltransferases, and a smaller DNA-recognition domain. We have investigated this enzyme by random mutagenesis, using error-prone PCR, follo...

    journal_title:Biological chemistry

    pub_type: 杂志文章

    doi:10.1515/bchm.1998.379.4-5.475

    authors: Friedrich T,Roth M,Helm-Kruse S,Jeltsch A

    更新日期:1998-04-01 00:00:00

  • Functional ribosome biogenesis is a prerequisite for p53 destabilization: impact of chemotherapy on nucleolar functions and RNA metabolism.

    abstract::The production and processing of ribosomal RNA is a complex and well-coordinated nucleolar process for ribosome biogenesis. Progress in understanding nucleolar structure and function has lead to the unexpected discovery of the nucleolus as a highly sensitive sensor of cellular stress and an important regulator of the ...

    journal_title:Biological chemistry

    pub_type: 杂志文章,评审

    doi:10.1515/hsz-2013-0153

    authors: Burger K,Eick D

    更新日期:2013-09-01 00:00:00

  • Differential effects of novel tumour-derived p53 mutations on the transformation of NIH-3T3 cells.

    abstract::The p53 tumour suppressor gene is frequently mutated in human tumours and different tumour-derived mutations have varying effects on cells. The effect of a novel tumour-derived p53 mutation and two recently described mutations from South African breast cancer patients on the growth rate, colony formation, cell cycle a...

    journal_title:Biological chemistry

    pub_type: 杂志文章

    doi:10.1515/BC.2008.010

    authors: Donninger H,Binder A,Bohm L,Parker MI

    更新日期:2008-01-01 00:00:00

  • Zinc-induced activation of GPR39 regulates glucose homeostasis through glucose-dependent insulinotropic polypeptide secretion from enteroendocrine K-cells.

    abstract::The role of Zn2+-sensing receptor GPR39 on glucose homeostasis and incretin regulation was assessed in enteroendocrine L- and K-cells. Anti-hyperglycaemic, insulinotropic and incretin secreting properties of Zn2+ were explored in normal, diabetic and incretin receptor knockout mice. Compared to intraperitoneal injecti...

    journal_title:Biological chemistry

    pub_type: 杂志文章

    doi:10.1515/hsz-2018-0393

    authors: Moran BM,Miskelly MG,Abdel-Wahab YHA,Flatt PR,McKillop AM

    更新日期:2019-06-20 00:00:00

  • Switchable inteins for conditional protein splicing.

    abstract::Synthetic biologists aim at engineering controllable biological parts such as DNA, RNA and proteins in order to steer biological activities using external inputs. Proteins can be controlled in several ways, for instance by regulating the expression of their encoding genes with small molecules or light. However, post-t...

    journal_title:Biological chemistry

    pub_type: 杂志文章,评审

    doi:10.1515/hsz-2018-0309

    authors: Di Ventura B,Mootz HD

    更新日期:2019-03-26 00:00:00

  • Exploratory cell dynamics: a sense of touch for cells?

    abstract::Cells need to process multifaceted external cues to steer their dynamic behavior. To efficiently perform this task, cells implement several exploratory mechanisms to actively sample their environment. In particular, cells can use exploratory actin-based cell protrusions and contractions to engage and squeeze the envir...

    journal_title:Biological chemistry

    pub_type: 杂志文章,评审

    doi:10.1515/hsz-2017-0341

    authors: Nalbant P,Dehmelt L

    更新日期:2018-07-26 00:00:00

  • The human steroid hydroxylases CYP1B1 and CYP11B2.

    abstract::Major advances have been made during the last decade in our understanding of adrenal steroid hormone biosynthesis. Two key players in these pathways are the human mitochondrial cytochrome P450 enzymes CYP11B1 and CYP11B2, which catalyze the final steps in the biosynthesis of cortisol and aldosterone. Using data from m...

    journal_title:Biological chemistry

    pub_type: 杂志文章,评审

    doi:10.1515/BC.2002.174

    authors: Bureik M,Lisurek M,Bernhardt R

    更新日期:2002-10-01 00:00:00

  • Molecular mechanisms of signal transduction via adiponectin and adiponectin receptors.

    abstract::The adipocytokine adiponectin and its receptor (AdipoR) comprise a new receptor-ligand system that is involved in a variety of clinically important morbidities such as obesity, type 2 diabetes and cardiovascular diseases. Adiponectin exerts a multitude of beneficial and tissue specific effects depending on its unique,...

    journal_title:Biological chemistry

    pub_type: 杂志文章,评审

    doi:10.1515/BC.2010.104

    authors: Heiker JT,Kosel D,Beck-Sickinger AG

    更新日期:2010-09-01 00:00:00