scholarly journals The Structural Mechanism for Transcription Activation by MerR Family Member Multidrug Transporter Activation, N Terminus

2004 ◽  
Vol 279 (19) ◽  
pp. 20356-20362 ◽  
Author(s):  
Kate J. Newberry ◽  
Richard G. Brennan
Keyword(s):  
Crystal Structure ◽  
Dna Binding ◽  
Family Member ◽  
Coiled Coil ◽  
Transcription Activation ◽  
Activation Mechanism ◽  
Binding Modes ◽  
Structural Mechanism ◽  
Homologous Protein ◽  
Stress Signals

Transcription regulators of the MerR family respond to myriad stress signals to activate σ70/σA-targeted genes, which contain suboptimal 19-bp spacers between their -35 and -10 promoter elements. The crystal structure of a BmrR-TPP+-DNA complex provided initial insight into the transcription activation mechanism of the MerR family, which involves base pair distortion, DNA undertwisting and shortening of the spacer, and realignment of the -35 and -10 boxes. Here, we describe the crystal structure of MerR family member MtaN bound to themtapromoter. Although the global DNA binding modes of MtaN and BmrR differ somewhat, homologous protein-DNA interactions are maintained. Moreover, despite their different sequences, themtapromoter conformation is essentially identical to that of the BmrR-TPP+-boundbmrpromoter, indicating that this DNA distortion mechanism is common to the entire MerR family. Interestingly, DNA binding experiments reveal that the identity of the two central bases of themtaandbmrpromoters, which are conserved as either a thymidine or an adenine in nearly all MerR promoters, is not important for DNA affinity. Comparison of the free and DNA-bound MtaN structures reveals that a conformational hinge, centered at residues N-terminal to the ubiquitous coiled coil, is key formtapromoter binding. Analysis of the structures of BmrR, CueR, and ZntR indicates that this hinge may be common to all MerR family members.

scholarly journals Crystal Structure of MtaN, a Global Multidrug Transporter Gene Activator

2001 ◽  
Vol 276 (50) ◽  
pp. 47178-47184 ◽  
Author(s):  
Michael H. Godsey ◽  
Natalya N. Baranova ◽  
Alexander A. Neyfakh ◽  
Richard G. Brennan
Keyword(s):  
Crystal Structure ◽  
Family Member ◽  
Structural Changes ◽  
Coiled Coil ◽  
Activation Mechanism ◽  
Multidrug Transporter ◽  
Hydrophobic Core ◽  
Winged Helix ◽  
Truncation Mutant ◽  
Antiparallel Coiled Coil

MtaN (Multidrug Transporter Activation, N terminus) is a constitutive, transcriptionally active 109-residue truncation mutant, which contains only the N-terminal DNA-binding and dimerization domains of MerR family member Mta. The 2.75 Å resolution crystal structure of apo-MtaN reveals a winged helix-turn-helix protein with a protruding 8-turn helix (α5) that is involved in dimerization by the formation of an antiparallel coiled-coil. The hydrophobic core and helices α1 through α4 are structurally homologous to MerR family member BmrR bound to DNA, whereas one wing (Wing 1) is shifted. Differences between the orientation of α5 with respect to the core and the revolution of the antiparallel coiled-coil lead to significantly altered conformations of MtaN and BmrR dimers. These shifts result in a conformation of MtaN that appears to be incompatible with the transcription activation mechanism of BmrR and suggest that additional DNA-induced structural changes are necessary.

scholarly journals Sharp kinking of a coiled-coil in MutS allows DNA binding and release

2019 ◽  
Vol 47 (16) ◽  
pp. 8888-8898 ◽  
Author(s):  
Doreth Bhairosing-Kok ◽  
Flora S Groothuizen ◽  
Alexander Fish ◽  
Shreya Dharadhar ◽  
Herrie H K Winterwerp ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Escherichia Coli ◽  
Dna Binding ◽  
Mismatch Repair ◽  
Coiled Coil ◽  
Site Specific ◽  
Dna Mismatch ◽  
Hinge Point ◽  
Coiled Coil Region ◽  
Kink Site

Abstract DNA mismatch repair (MMR) corrects mismatches, small insertions and deletions in DNA during DNA replication. While scanning for mismatches, dimers of MutS embrace the DNA helix with their lever and clamp domains. Previous studies indicated generic flexibility of the lever and clamp domains of MutS prior to DNA binding, but whether this was important for MutS function was unknown. Here, we present a novel crystal structure of DNA-free Escherichia coli MutS. In this apo-structure, the clamp domains are repositioned due to kinking at specific sites in the coiled-coil region in the lever domains, suggesting a defined hinge point. We made mutations at the coiled-coil hinge point. The mutants made to disrupt the helical fold at the kink site diminish DNA binding, whereas those made to increase stability of coiled-coil result in stronger DNA binding. These data suggest that the site-specific kinking of the coiled-coil in the lever domain is important for loading of this ABC-ATPase on DNA.

scholarly journals Structural mechanism of DNA recognition by the p204 HIN domain

2021 ◽  
Vol 49 (5) ◽  
pp. 2959-2972
Author(s):  
Xiaojiao Fan ◽  
Jiansheng Jiang ◽  
Dan Zhao ◽  
Feng Chen ◽  
Huan Ma ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Structural Information ◽  
Dna Recognition ◽  
Binding Mode ◽  
Structural Mechanism ◽  
Homologous Protein ◽  
Dimerization Interface ◽  
Inducible Protein ◽  
Dsdna Binding ◽  
Shed Light

Abstract The interferon gamma-inducible protein 16 (IFI16) and its murine homologous protein p204 function in non-sequence specific dsDNA sensing; however, the exact dsDNA recognition mechanisms of IFI16/p204, which harbour two HIN domains, remain unclear. In the present study, we determined crystal structures of p204 HINa and HINb domains, which are highly similar to those of other PYHIN family proteins. Moreover, we obtained the crystal structure of p204 HINab domain in complex with dsDNA and provided insights into the dsDNA binding mode. p204 HINab binds dsDNA mainly through α2 helix of HINa and HINb, and the linker between them, revealing a similar HIN:DNA binding mode. Both HINa and HINb are vital for HINab recognition of dsDNA, as confirmed by fluorescence polarization assays. Furthermore, a HINa dimerization interface was observed in structures of p204 HINa and HINab:dsDNA complex, which is involved in binding dsDNA. The linker between HINa and HINb reveals dynamic flexibility in solution and changes its direction at ∼90° angle in comparison with crystal structure of HINab:dsDNA complex. These structural information provide insights into the mechanism of DNA recognition by different HIN domains, and shed light on the unique roles of two HIN domains in activating the IFI16/p204 signaling pathway.

scholarly journals Crystal Structure of Cytomegalovirus IE1 Protein Reveals Targeting of TRIM Family Member PML via Coiled-Coil Interactions

2014 ◽  
Vol 10 (11) ◽  
pp. e1004512 ◽  
Author(s):  
Myriam Scherer ◽  
Stefan Klingl ◽  
Madhumati Sevvana ◽  
Victoria Otto ◽  
Eva-Maria Schilling ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Family Member ◽  
Coiled Coil

scholarly journals Activation of the DNA-binding ability of human heat shock transcription factor 1 may involve the transition from an intramolecular to an intermolecular triple-stranded coiled-coil structure.

1994 ◽  
Vol 14 (11) ◽  
pp. 7557-7568 ◽  
Author(s):  
J Zuo ◽  
R Baler ◽  
G Dahl ◽  
R Voellmy
Keyword(s):  
Transcription Factor ◽  
Heat Stress ◽  
Heat Shock ◽  
Dna Binding ◽  
Hydrophobic Interactions ◽  
Coiled Coil ◽  
Heat Shock Transcription Factor ◽  
Single Amino Acid ◽  
Binding Ability ◽  
Heat Shock Element

Heat stress regulation of human heat shock genes is mediated by human heat shock transcription factor hHSF1, which contains three 4-3 hydrophobic repeats (LZ1 to LZ3). In unstressed human cells (37 degrees C), hHSF1 appears to be in an inactive, monomeric state that may be maintained through intramolecular interactions stabilized by transient interaction with hsp70. Heat stress (39 to 42 degrees C) disrupts these interactions, and hHSF1 homotrimerizes and acquires heat shock element DNA-binding ability. hHSF1 expressed in Xenopus oocytes also assumes a monomeric, non-DNA-binding state and is converted to a trimeric, DNA-binding form upon exposure of the oocytes to heat shock (35 to 37 degrees C in this organism). Because endogenous HSF DNA-binding activity is low and anti-hHSF1 antibody does not recognize Xenopus HSF, we employed this system for mapping regions in hHSF1 that are required for the maintenance of the monomeric state. The results of mutagenesis analyses strongly suggest that the inactive hHSF1 monomer is stabilized by hydrophobic interactions involving all three leucine zippers which may form a triple-stranded coiled coil. Trimerization may enable the DNA-binding function of hHSF1 by facilitating cooperative binding of monomeric DNA-binding domains to the heat shock element motif. This view is supported by observations that several different LexA DNA-binding domain-hHSF1 chimeras bind to a LexA-binding site in a heat-regulated fashion, that single amino acid replacements disrupting the integrity of hydrophobic repeats render these chimeras constitutively trimeric and DNA binding, and that LexA itself binds stably to DNA only as a dimer but not as a monomer in our assays.

scholarly journals PARP Power: A Structural Perspective on PARP1, PARP2, and PARP3 in DNA Damage Repair and Nucleosome Remodelling

2021 ◽  
Vol 22 (10) ◽  
pp. 5112
Author(s):  
Lotte van Beek ◽  
Éilís McClay ◽  
Saleha Patel ◽  
Marianne Schimpl ◽  
Laura Spagnolo ◽  
...  
Keyword(s):  
Dna Damage ◽  
Dna Binding ◽  
Parp Inhibitors ◽  
Covalent Modification ◽  
Activation Mechanism ◽  
Cancer Therapies ◽  
Damage Repair ◽  
Complementary Role ◽  
Functional Understanding

Poly (ADP-ribose) polymerases (PARP) 1-3 are well-known multi-domain enzymes, catalysing the covalent modification of proteins, DNA, and themselves. They attach mono- or poly-ADP-ribose to targets using NAD+ as a substrate. Poly-ADP-ribosylation (PARylation) is central to the important functions of PARP enzymes in the DNA damage response and nucleosome remodelling. Activation of PARP happens through DNA binding via zinc fingers and/or the WGR domain. Modulation of their activity using PARP inhibitors occupying the NAD+ binding site has proven successful in cancer therapies. For decades, studies set out to elucidate their full-length molecular structure and activation mechanism. In the last five years, significant advances have progressed the structural and functional understanding of PARP1-3, such as understanding allosteric activation via inter-domain contacts, how PARP senses damaged DNA in the crowded nucleus, and the complementary role of histone PARylation factor 1 in modulating the active site of PARP. Here, we review these advances together with the versatility of PARP domains involved in DNA binding, the targets and shape of PARylation and the role of PARPs in nucleosome remodelling.

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