scholarly journals DnaB helicase is recruited to the replication initiation complex via binding of DnaA domain I to the lateral surface of the DnaB N-terminal domain

2020 ◽  
Vol 295 (32) ◽  
pp. 11131-11143 ◽  
Author(s):  
Chihiro Hayashi ◽  
Erika Miyazaki ◽  
Shogo Ozaki ◽  
Yoshito Abe ◽  
Tsutomu Katayama
Keyword(s):  
Binding Site ◽  
Lateral Surface ◽  
Replication Initiation ◽  
Terminal Domain ◽  
Dnab Helicase ◽  
Functionally Impaired ◽  
Helicase Assay ◽  
Domain Iii ◽  
Domain I

The DNA replication protein DnaA in Escherichia coli constructs higher-order complexes on the origin, oriC, to unwind this region. DnaB helicase is loaded onto unwound oriC via interactions with the DnaC loader and the DnaA complex. The DnaB–DnaC complex is recruited to the DnaA complex via stable binding of DnaB to DnaA domain I. The DnaB–DnaC complex is then directed to unwound oriC via a weak interaction between DnaB and DnaA domain III. Previously, we showed that Phe46 in DnaA domain I binds to DnaB. Here, we searched for the DnaA domain I–binding site in DnaB. The DnaB L160A variant was impaired in binding to DnaA complex on oriC but retained its DnaC-binding and helicase activities. DnaC binding moderately stimulated DnaA binding of DnaB L160A, and loading of DnaB L160A onto oriC was consistently and moderately inhibited. In a helicase assay with partly single-stranded DNA bearing a DnaA-binding site, DnaA stimulated DnaB loading, which was strongly inhibited in DnaB L160A even in the presence of DnaC. DnaB L160A was functionally impaired in vivo. On the basis of these findings, we propose that DnaB Leu160 interacts with DnaA domain I Phe46. DnaB Leu160 is exposed on the lateral surface of the N-terminal domain, which can explain unobstructed interactions of DnaA domain I–bound DnaB with DnaC, DnaG primase, and DnaA domain III. We propose a probable structure for the DnaA–DnaB–DnaC complex, which could be relevant to the process of DnaB loading onto oriC.

A synthetic silencer mediates SIR-dependent functions in Saccharomyces cerevisiae

1991 ◽  
Vol 11 (11) ◽  
pp. 5648-5659
Author(s):  
F J McNally ◽  
J Rine
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Binding Site ◽  
Binding Sites ◽  
Consensus Sequence ◽  
Protein A ◽  
Replication Initiation ◽  
Yeast Saccharomyces Cerevisiae ◽  
Autonomously Replicating Sequence ◽  
Functional Components

Copies of the mating-type genes are present at three loci on chromosome III of the yeast Saccharomyces cerevisiae. The genes at the MAT locus are transcribed, whereas the identical genes at the silent loci, HML and HMR, are not transcribed. Several genes, including the four SIR genes, and two sites, HMR-E and HMR-I, are required for repression of transcription at the HMR locus. Three elements have been implicated in the function of the HMR-E silencer: a binding site for the RAP1 protein, a binding site for the ABF1 protein, and an 11-bp consensus sequence common to nearly all autonomously replicating sequence (ARS) elements (putative origins of DNA replication). RAP1 and ABF1 binding sites of different sequence than those found at HMR-E were joined with an 11-bp ARS consensus sequence to form a synthetic silencer. The synthetic silencer was able to repress transcription of the HMRa1 gene, confirming that binding sites for RAP1 and ABF1 and the 11-bp ARS consensus sequence were the functional components of the silencer in vivo. Mutations in the ABF1 binding site or in the ARS consensus sequence of the synthetic silencer caused nearly complete derepression of transcription at HMR. The ARS consensus sequence mutation also eliminated the ARS activity of the synthetic silencer. These data suggested that replication initiation at the HMR-E silencer was required for establishment of the repressed state at the HMR locus.

scholarly journals Bacillus thuringiensis Delta-Endotoxin Cry1C Domain III Can Function as a Specificity Determinant forSpodoptera exigua in Different, but Not All, Cry1-Cry1C Hybrids

2000 ◽  
Vol 66 (4) ◽  
pp. 1559-1563 ◽  
Author(s):  
Ruud A. de Maagd ◽  
Mieke Weemen-Hendriks ◽  
Willem Stiekema ◽  
Dirk Bosch
Keyword(s):  
Bacillus Thuringiensis ◽  
Manduca Sexta ◽  
Spodoptera Exigua ◽  
Hybrid Proteins ◽  
In Vivo Recombination ◽  
Delta Endotoxin ◽  
Domain Iii ◽  
Domain I

ABSTRACT In order to test our hypothesis that Bacillus thuringiensis delta-endotoxin Cry1Ca domain III functions as a determinant of specificity for Spodoptera exigua, regardless of the origins of domains I and II, we have constructed by cloning and in vivo recombination a collection of hybrid proteins containing domains I and II of various Cry1 toxins combined with domain III of Cry1Ca. Cry1Ab, Cry1Ac, Cry1Ba, Cry1Ea, and Cry1Fa all become more active against S. exigua when their domain III is replaced by (part of) that of Cry1Ca. This result shows that domain III of Cry1Ca is an important and versatile determinant of S. exigua specificity. The toxicity of the hybrids varied by a factor of 40, indicating that domain I and/or II modulate the activity as well. Cry1Da-Cry1Ca hybrids were an exception in that they were not significantly active against S. exigua or Manduca sexta, whereas both parental proteins were highly toxic. Incidentally, in a Cry1Ba-Cry1Ca hybrid, Cry1Ca domain III can also strongly increase toxicity for M. sexta.

scholarly journals Noncontiguous regions in the extracellular domain of EGF receptor define ligand-binding specificity.

1991 ◽  
Vol 2 (5) ◽  
pp. 337-345 ◽  
Author(s):  
I Lax ◽  
R Fischer ◽  
C Ng ◽  
J Segre ◽  
A Ullrich ◽  
...  
Keyword(s):  
Binding Energy ◽  
Ligand Binding ◽  
Binding Site ◽  
Binding Affinity ◽  
Egf Receptor ◽  
Binding Properties ◽  
Amino Terminal ◽  
High Affinity ◽  
Domain Iii ◽  
Domain I

Murine epidermal growth factor (EGF) binds with approximately 250-fold higher binding affinity to the human EGF receptor (EGFR) than to the chicken EGFR. This difference in binding affinity enabled the identification of a major ligand-binding domain for EGF by studying the binding properties of various chicken/human EGFR chimera expressed in transfected cells lacking endogenous EGFR. It was shown that domain III of EGFR is a major ligand-binding region. Here, we analyze the binding properties of novel chicken/human chimera to further delineate the contact sequences in domain III and to assess the role of other regions of EGFR for their contribution to the display of high-affinity EGF binding. The chimeric receptors include chicken EGFR containing domain I of the human EGFR, chicken receptor containing domain I and III of the human EGFR, and two chimeric chicken EGFR containing either the amino terminal or the carboxy terminal halves of domain III of human EGFR, respectively. In addition, the binding of various human-specific anti-EGFR monoclonal antibodies that interfere with EGF binding is also compared. It is concluded that noncontiguous regions of the EGFR contribute additively to the binding of EGF. Each of the two halves of domain III has a similar contribution to the binding energy, and the sum of both is close to that of the entire domain III. This suggests that the folding of domain III juxtaposes sequences that together constitute the ligand-binding site. Domain I also provides a contribution to the binding energy, and the added contributions of both domain I and III to the binding energy generate the high-affinity binding site typical of human EGFR.

scholarly journals Inhibition of the specific binding of human lactotransferrin to human peripheral-blood phytohaemagglutinin-stimulated lymphocytes by fluorescein labelling and location of the binding site

1991 ◽  
Vol 276 (3) ◽  
pp. 733-738 ◽  
Author(s):  
D Legrand ◽  
J Mazurier ◽  
P Maes ◽  
E Rochard ◽  
J Montreuil ◽  
...  
Keyword(s):  
Binding Site ◽  
Receptor Binding ◽  
Peripheral Blood ◽  
Human Peripheral Blood ◽  
Specific Binding ◽  
Peripheral Blood Lymphocytes ◽  
Receptor Binding Site ◽  
Terminal Domain ◽  
Total Fluorescence ◽  
Domain I

Labelling of human lactotransferrin with fluorescein 5′-isothiocyanate (FITC) in an equimolar ratio inhibits the binding of the protein to phytohaemagglutinin-activated human peripheral-blood lymphocytes. Therefore it can be assumed that FITC reacts at, or near, the receptor-binding site. Three FITC-labelled peptides have been purified from a tryptic digest of the FITC-labelled lactotransferrin. The determination of their amino acid sequence and their localization on the primary structure of the protein permitted the identification of two FITC-accessible areas in the N-terminal lobe and one in the C-terminal lobe. In fact, only 10% of the total FITC was conjugated to one lysine residue (Lys579) of the C-terminal lobe, whereas most (80%) of the FITC was conjugated to three close lysine residues [Lys263 (65% of total fluorescence), Lys280 and Lys282 (15% of total fluorescence)] located in beta-turn structures, of the N-terminal domain I of human lactotransferrin. The results obtained show that the receptor-binding site should be located in the vicinity of the FITC-accessible Lys263, Lys280 and Lys282, and corroborate our preliminary results reporting the involvement of the N-terminal domain I in the binding of human lactotransferrin to mitogen-stimulated lymphocytes [Rochard, Legrand, Mazurier, Montreuil & Spik (1989) FEBS Lett. 255, 201-204]. In any case, FITC labelling is not suitable for studying the binding of lactotransferrin to activated lymphocytes and its use may lead to erroneous interpretations of cell binding experiments.

scholarly journals A synthetic silencer mediates SIR-dependent functions in Saccharomyces cerevisiae.

1991 ◽  
Vol 11 (11) ◽  
pp. 5648-5659 ◽  
Author(s):  
F J McNally ◽  
J Rine
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Binding Site ◽  
Binding Sites ◽  
Consensus Sequence ◽  
Protein A ◽  
Replication Initiation ◽  
Yeast Saccharomyces Cerevisiae ◽  
Autonomously Replicating Sequence ◽  
Functional Components

Copies of the mating-type genes are present at three loci on chromosome III of the yeast Saccharomyces cerevisiae. The genes at the MAT locus are transcribed, whereas the identical genes at the silent loci, HML and HMR, are not transcribed. Several genes, including the four SIR genes, and two sites, HMR-E and HMR-I, are required for repression of transcription at the HMR locus. Three elements have been implicated in the function of the HMR-E silencer: a binding site for the RAP1 protein, a binding site for the ABF1 protein, and an 11-bp consensus sequence common to nearly all autonomously replicating sequence (ARS) elements (putative origins of DNA replication). RAP1 and ABF1 binding sites of different sequence than those found at HMR-E were joined with an 11-bp ARS consensus sequence to form a synthetic silencer. The synthetic silencer was able to repress transcription of the HMRa1 gene, confirming that binding sites for RAP1 and ABF1 and the 11-bp ARS consensus sequence were the functional components of the silencer in vivo. Mutations in the ABF1 binding site or in the ARS consensus sequence of the synthetic silencer caused nearly complete derepression of transcription at HMR. The ARS consensus sequence mutation also eliminated the ARS activity of the synthetic silencer. These data suggested that replication initiation at the HMR-E silencer was required for establishment of the repressed state at the HMR locus.

scholarly journals Ezrin self-association involves binding of an N-terminal domain to a normally masked C-terminal domain that includes the F-actin binding site.

1995 ◽  
Vol 6 (8) ◽  
pp. 1061-1075 ◽  
Author(s):  
R Gary ◽  
A Bretscher
Keyword(s):  
Amino Acids ◽  
Binding Site ◽  
Sodium Dodecyl ◽  
Actin Binding ◽  
Terminal Domain ◽  
Cell Extracts ◽  
C Terminus ◽  
Self Association ◽  
Actin Binding Site

Ezrin is a membrane-cytoskeletal linking protein that is concentrated in actin-rich surface structures. It is closely related to the microvillar proteins radixin and moesin and to the tumor suppressor merlin/schwannomin. Cell extracts contain ezrin dimers and ezrin-moesin heterodimers in addition to monomers. Truncated ezrin fusion proteins were assayed by blot overlay to determine which regions mediate self-association. Here we report that ezrin self-association occurs by head-to-tail joining of distinct N-terminal and C-terminal domains. It is likely that these domains, termed N- and C-ERMADs (ezrin-radixin-moesin association domain), are responsible for homotypic and heterotypic associations among ERM family members. The N-ERMAD of ezrin resided within amino acids 1-296; deletion of 10 additional residues resulted in loss of activity. The C-ERMAD was mapped to the last 107 amino acids of ezrin, residues 479-585. The two residues at the C-terminus were required for activity, and the region from 530-585 was insufficient. The C-ERMAD was masked in the native monomer. Exposure of this domain required unfolding ezrin with sodium dodecyl sulfate or expressing the domain as part of a truncated protein. Intermolecular association could not occur unless the C-ERMAD had been made accessible to its N-terminal partner. It can be inferred that dimerization in vivo requires an activation step that exposes this masked domain. The conformationally inaccessible C-terminal region included the F-actin binding site, suggesting that this activity is likewise regulated by masking.

scholarly journals In Vivo Function of Hsp90 Is Dependent on ATP Binding and ATP Hydrolysis

1998 ◽  
Vol 143 (4) ◽  
pp. 901-910 ◽  
Author(s):  
Wolfgang M.J. Obermann ◽  
Holger Sondermann ◽  
Alicia A. Russo ◽  
Nikola P. Pavletich ◽  
F. Ulrich Hartl
Keyword(s):  
Crystal Structure ◽  
Atpase Activity ◽  
Binding Site ◽  
Atp Hydrolysis ◽  
Specific Inhibitor ◽  
Nucleotide Binding ◽  
Basic Mechanism ◽  
Atp Binding ◽  
Terminal Domain

Heat shock protein 90 (Hsp90), an abundant molecular chaperone in the eukaryotic cytosol, is involved in the folding of a set of cell regulatory proteins and in the re-folding of stress-denatured polypeptides. The basic mechanism of action of Hsp90 is not yet understood. In particular, it has been debated whether Hsp90 function is ATP dependent. A recent crystal structure of the NH2-terminal domain of yeast Hsp90 established the presence of a conserved nucleotide binding site that is identical with the binding site of geldanamycin, a specific inhibitor of Hsp90. The functional significance of nucleotide binding by Hsp90 has remained unclear. Here we present evidence for a slow but clearly detectable ATPase activity in purified Hsp90. Based on a new crystal structure of the NH2-terminal domain of human Hsp90 with bound ADP-Mg and on the structural homology of this domain with the ATPase domain of Escherichia coli DNA gyrase, the residues of Hsp90 critical in ATP binding (D93) and ATP hydrolysis (E47) were identified. The corresponding mutations were made in the yeast Hsp90 homologue, Hsp82, and tested for their ability to functionally replace wild-type Hsp82. Our results show that both ATP binding and hydrolysis are required for Hsp82 function in vivo. The mutant Hsp90 proteins tested are defective in the binding and ATP hydrolysis–dependent cycling of the co-chaperone p23, which is thought to regulate the binding and release of substrate polypeptide from Hsp90. Remarkably, the complete Hsp90 protein is required for ATPase activity and for the interaction with p23, suggesting an intricate allosteric communication between the domains of the Hsp90 dimer. Our results establish Hsp90 as an ATP-dependent chaperone.

scholarly journals Interactions of Elongation Factor 1α with F-Actin and β-Actin mRNA: Implications for Anchoring mRNA in Cell Protrusions

2002 ◽  
Vol 13 (2) ◽  
pp. 579-592 ◽  
Author(s):  
Gang Liu ◽  
Wayne M. Grant ◽  
Daniel Persky ◽  
Vaughan M. Latham ◽  
Robert H. Singer ◽  
...  
Keyword(s):  
Binding Site ◽  
Chicken Embryo ◽  
Elongation Factor ◽  
Actin Binding ◽  
Elongation Factor 1Α ◽  
Actin Mrna ◽  
Domain Iii ◽  
Chicken Embryo Fibroblasts

The targeting of mRNA and local protein synthesis is important for the generation and maintenance of cell polarity. As part of the translational machinery as well as an actin/microtubule-binding protein, elongation factor 1α (EF1α) is a candidate linker between the protein translation apparatus and the cytoskeleton. We demonstrate in this work that EF1α colocalizes with β-actin mRNA and F-actin in protrusions of chicken embryo fibroblasts and binds directly to F-actin and β-actin mRNA simultaneously in vitro in actin cosedimentation and enzyme-linked immunosorbent assays. To investigate the role of EF1α in mRNA targeting, we mapped the two actin-binding sites on EF1α at high resolution and defined one site at the N-terminal 49 residues of domain I and the other at the C-terminal 54 residues of domain III. In vitro actin-binding assays and localization in vivo of recombinant full-length EF1α and its various truncates demonstrated that the C terminus of domain III was the dominant actin-binding site both in vitro and in vivo. We propose that the EF1α–F-actin complex is the scaffold that is important for β-actin mRNA anchoring. Disruption of this complex would lead to delocalization of the mRNA. This hypothesis was tested by using two dominant negative polypeptides: the actin-binding domain III of EF1α and the EF1α-binding site of yeast Bni1p, a protein that inhibits EF1α binding to F-actin and also is required for yeast mRNA localization. We demonstrate that either domain III of EF1α or the EF1α-binding site of Bni1p inhibits EF1α binding to β-actin mRNA in vitro and causes delocalization of β-actin mRNA in chicken embryo fibroblasts. Taken together, these results implicate EF1α in the anchoring of β-actin mRNA to the protrusion in crawling cells.

scholarly journals The C-terminal domain of feline and bovine SAMHD1 proteins has a crucial role in lentiviral restriction

2020 ◽  
Vol 295 (13) ◽  
pp. 4252-4264 ◽  
Author(s):  
Chu Wang ◽  
Kaikai Zhang ◽  
Lina Meng ◽  
Xin Zhang ◽  
Yanan Song ◽  
...  
Keyword(s):  
Proteasomal Degradation ◽  
Acid Sites ◽  
Accessory Protein ◽  
Restriction Profile ◽  
Biological Functions ◽  
Terminal Domain ◽  
Functional Regions ◽  
Viral Restriction ◽  
Primate Lentiviruses

SAM and HD domain-containing protein 1 (SAMHD1) is a host factor that restricts reverse transcription of lentiviruses such as HIV in myeloid cells and resting T cells through its dNTP triphosphohydrolase (dNTPase) activity. Lentiviruses counteract this restriction by expressing the accessory protein Vpx or Vpr, which targets SAMHD1 for proteasomal degradation. SAMHD1 is conserved among mammals, and the feline and bovine SAMHD1 proteins (fSAM and bSAM) restrict lentiviruses by reducing cellular dNTP concentrations. However, the functional regions of fSAM and bSAM that are required for their biological functions are not well-characterized. Here, to establish alternative models to investigate SAMHD1 in vivo, we studied the restriction profile of fSAM and bSAM against different primate lentiviruses. We found that both fSAM and bSAM strongly restrict primate lentiviruses and that Vpx induces the proteasomal degradation of both fSAM and bSAM. Further investigation identified one and five amino acid sites in the C-terminal domain (CTD) of fSAM and bSAM, respectively, that are required for Vpx-mediated degradation. We also found that the CTD of bSAM is directly involved in mediating bSAM's antiviral activity by regulating dNTPase activity, whereas the CTD of fSAM is not. Our results suggest that the CTDs of fSAM and bSAM have important roles in their antiviral functions. These findings advance our understanding of the mechanism of fSAM- and bSAM-mediated viral restriction and might inform strategies for improving HIV animal models.

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