Faculty Opinions recommendation of Structural basis of DNA recognition by PCG2 reveals a novel DNA binding mode for winged helix-turn-helix domains.

MetR, a LysR-type transcriptional regulator (LTTR), has been extensively studied owing to its role in the control of methionine biosynthesis in proteobacteria. A MetR homodimer binds to a 24-base-pair operator region of themetgenes and specifically recognizes the interrupted palindromic sequence 5′-TGAA-N5-TTCA-3′. Mechanistic details underlying the interaction of MetR with its target DNA at the molecular level remain unknown. In this work, the crystal structure of the DNA-binding domain (DBD) of MetR was determined at 2.16 Å resolution. MetR-DBD adopts a winged-helix–turn–helix (wHTH) motif and shares significant fold similarity with the DBD of the LTTR protein BenM. Furthermore, a data-driven macromolecular-docking strategy was used to model the structure of MetR-DBD bound to DNA, which revealed that a bent conformation of DNA is required for the recognition helix α3 and the wing loop of the wHTH motif to interact with the major and minor grooves, respectively. Comparison of the MetR-DBD–DNA complex with the crystal structures of other LTTR-DBD–DNA complexes revealed residues that may confer operator-sequence binding specificity for MetR. Taken together, the results show that MetR-DBD uses a combination of direct base-specific interactions and indirect shape recognition of the promoter to regulate the transcription ofmetgenes.

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Geobacter uraniireducens NikR Displays a DNA Binding Mode Distinct from Other Members of the NikR Family

Journal of Bacteriology ◽

10.1128/jb.00152-10 ◽

2010 ◽

Vol 192 (17) ◽

pp. 4327-4336 ◽

Cited By ~ 10

Author(s):

Erin L. Benanti ◽

Peter T. Chivers

Keyword(s):

Dna Binding ◽

Inverted Repeat ◽

Dna Recognition ◽

Binding Mode ◽

Repeat Sequence ◽

Amino Acid Sequences ◽

Inverted Repeat Sequence ◽

Promoter Regions ◽

Β Sheets ◽

Β Sheet

ABSTRACT NikR is a nickel-responsive ribbon-helix-helix transcription factor present in many bacteria and archaea. The DNA binding properties of Escherichia coli and Helicobacter pylori NikR (factors EcNikR and HpNikR, respectively) have revealed variable features of DNA recognition. EcNikR represses a single operon by binding to a perfect inverted repeat sequence, whereas HpNikR binds to promoters from multiple genes that contain poorly conserved inverted repeats. These differences are due in large part to variations in the amino acid sequences of the DNA-contacting β-sheets, as well as residues preceding the β-sheets of these two proteins. We present here evidence of another variation in DNA recognition by the NikR protein from Geobacter uraniireducens (GuNikR). GuNikR has an Arg-Gly-Ser β-sheet that binds specifically to an inverted repeat sequence distinct from those recognized by Ec- or HpNikR. The N-terminal residues that precede the GuNikR β-sheet residues are required for high-affinity DNA binding. Mutation of individual arm residues dramatically reduced the affinity of GuNikR for specific DNA. Interestingly, GuNikR tetramers are capable of binding cooperatively to the promoter regions of two different genes, nik(MN)1 and nik(MN)2. Cooperativity was not observed for the closely related G. bemidjiensis NikR, which recognizes the same operator sequence. The cooperative mode of DNA binding displayed by GuNikR could affect the sensitivity of transporter gene expression to changes in intracellular nickel levels.

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Structural basis for DNA-mediated allosteric regulation facilitated by the AAA+module of Lon protease

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s139900471302631x ◽

2014 ◽

Vol 70 (2) ◽

pp. 218-230 ◽

Cited By ~ 6

Author(s):

Alan Yueh-Luen Lee ◽

Yu-Da Chen ◽

Yu-Yung Chang ◽

Yu-Ching Lin ◽

Chi-Fon Chang ◽

...

Keyword(s):

Crystal Structure ◽

Dna Binding ◽

Electrostatic Interactions ◽

Allosteric Regulation ◽

Binding Mode ◽

Negative Regulation ◽

Enzymatic Activities ◽

Structural Basis ◽

Lon Protease ◽

Arginine Residues

Lon belongs to a unique group of AAA+proteases that bind DNA. However, the DNA-mediated regulation of Lon remains elusive. Here, the crystal structure of the α subdomain of the Lon protease fromBrevibacillus thermoruber(Bt-Lon) is presented, together with biochemical data, and the DNA-binding mode is delineated, showing that Arg518, Arg557 and Arg566 play a crucial role in DNA binding. Electrostatic interactions contributed by arginine residues in the AAA+module are suggested to be important to DNA binding and allosteric regulation of enzymatic activities. Intriguingly, Arg557, which directly binds DNA in the α subdomain, has a dual role in the negative regulation of ATPase stimulation by DNA and in the domain–domain communication in allosteric regulation of Bt-Lon by substrate. In conclusion, structural and biochemical evidence is provided to show that electrostatic interaction in the AAA+module is important for DNA binding by Lon and allosteric regulation of its enzymatic activities by DNA and substrate.

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Structural basis for DNA recognition by STAT6

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1611228113 ◽

2016 ◽

Vol 113 (46) ◽

pp. 13015-13020 ◽

Cited By ~ 18

Author(s):

Jing Li ◽

Jose Pindado Rodriguez ◽

Fengfeng Niu ◽

Mengchen Pu ◽

Jinan Wang ◽

...

Keyword(s):

Dna Binding ◽

Dna Recognition ◽

Dynamics Simulation ◽

Structural Basis ◽

Innate Immune Responses ◽

Site Analysis ◽

X Ray Scattering ◽

Dna Binding Site

STAT6 participates in classical IL-4/IL-13 signaling and stimulator of interferon genes-mediated antiviral innate immune responses. Aberrations in STAT6-mediated signaling are linked to development of asthma and diseases of the immune system. In addition, STAT6 remains constitutively active in multiple types of cancer. Therefore, targeting STAT6 is an attractive proposition for treating related diseases. Although a lot is known about the role of STAT6 in transcriptional regulation, molecular details on how STAT6 recognizes and binds specific segments of DNA to exert its function are not clearly understood. Here, we report the crystal structures of a homodimer of phosphorylated STAT6 core fragment (STAT6CF) alone and bound with the N3 and N4 DNA binding site. Analysis of the structures reveals that STAT6 undergoes a dramatic conformational change on DNA binding, which was further validated by performing molecular dynamics simulation studies and small angle X-ray scattering analysis. Our data show that a larger angle at the intersection where the two protomers of STAT meet and the presence of a unique residue, H415, in the DNA-binding domain play important roles in discrimination of the N4 site DNA from the N3 site by STAT6. H415N mutation of STAT6CF decreased affinity of the protein for the N4 site DNA, but increased its affinity for N3 site DNA, both in vitro and in vivo. Results of our structure–function studies on STAT6 shed light on mechanism of DNA recognition by STATs in general and explain the reasons underlying STAT6’s preference for N4 site DNA over N3.

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The N-Terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition

10.26434/chemrxiv.12195372 ◽

2020 ◽

Author(s):

Marina Corbella ◽

Qinghua Liao ◽

Catia Moreira ◽

Peter M. Kasson ◽

Shina Caroline Lynn Kamerlin

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Dna Sequences ◽

Dynamical Behavior ◽

Dna Recognition ◽

Tight Binding ◽

Binding Mode ◽

Binding Modes ◽

Efficient Design ◽

Terminal Loop

<div> <div> <p>DNA-binding proteins play an important role in gene regulation and cellular function. The transcription factors MarA and Rob are two homologous members of the AraC/XylS family that regulate multidrug resistance. They share a common DNA-binding domain, and Rob possesses an additional C-terminal domain that permits binding of low-molecular weight effectors. Both proteins possess two helix-turn-helix (HTH) motifs capable of binding DNA; however, while MarA interacts with its promoter through both HTH-motifs, prior studies indicate that Rob binding to DNA via a single HTH-motif is sufficient for tight binding. In the present work, we perform microsecond time scale all-atom simulations of the binding of both transcription factors to different DNA sequences to understand the determinants of DNA recognition and binding. Our simulations characterize sequence-specific changes in dynamical behavior upon DNA binding, showcasing the role of Arg40 of the N-terminal HTH-motif in allowing for specific tight binding. Finally, our simulations demonstrate that an acidic C-terminal loop of Rob can control the DNA binding mode, facilitating interconversion between the distinct DNA binding modes observed in MarA and Rob. In doing so, we provide detailed molecular insight into DNA binding and recognition by these proteins, which in turn is an important step towards the efficient design of anti-virulence agents that target these proteins.</p> </div> </div>

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Structural basis of G-quadruplex DNA recognition by the yeast telomeric protein Rap1

Nucleic Acids Research ◽

10.1093/nar/gkaa171 ◽

2020 ◽

Vol 48 (8) ◽

pp. 4562-4571 ◽

Cited By ~ 4

Author(s):

Anna Traczyk ◽

Chong Wai Liew ◽

David James Gill ◽

Daniela Rhodes

Keyword(s):

Dna Binding ◽

Dna Recognition ◽

Binding Domain ◽

Telomere Maintenance ◽

Structural Basis ◽

Dna Binding Domain ◽

Double Stranded Dna ◽

G Quadruplex ◽

Quadruplex Formation ◽

Telomeric Protein

Abstract G-quadruplexes are four-stranded nucleic acid structures involved in multiple cellular pathways including DNA replication and telomere maintenance. Such structures are formed by G-rich DNA sequences typified by telomeric DNA repeats. Whilst there is evidence for proteins that bind and regulate G-quadruplex formation, the molecular basis for this remains poorly understood. The budding yeast telomeric protein Rap1, originally identified as a transcriptional regulator functioning by recognizing double-stranded DNA binding sites, was one of the first proteins to be discovered to also bind and promote G-quadruplex formation in vitro. Here, we present the 2.4 Å resolution crystal structure of the Rap1 DNA-binding domain in complex with a G-quadruplex. Our structure not only provides a detailed insight into the structural basis for G-quadruplex recognition by a protein, but also gives a mechanistic understanding of how the same DNA-binding domain adapts to specifically recognize different DNA structures. The key observation is the DNA-recognition helix functions in a bimodal manner: In double-stranded DNA recognition one helix face makes electrostatic interactions with the major groove of DNA, whereas in G-quadruplex recognition a different helix face is used to make primarily hydrophobic interactions with the planar face of a G-tetrad.

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Structural Basis for DNA Recognition of a Single-stranded DNA-binding Protein from Enterobacter Phage Enc34

Scientific Reports ◽

10.1038/s41598-017-15774-y ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 4

Author(s):

Elina Cernooka ◽

Janis Rumnieks ◽

Kaspars Tars ◽

Andris Kazaks

Keyword(s):

Dna Binding ◽

Binding Protein ◽

Dna Recognition ◽

Dna Binding Protein ◽

Structural Basis ◽

Single Stranded Dna

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The DNA-binding domain of BenM reveals the structural basis for the recognition of a T-N11-A sequence motif by LysR-type transcriptional regulators

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s0907444913017320 ◽

2013 ◽

Vol 69 (10) ◽

pp. 1995-2007 ◽

Cited By ~ 27

Author(s):

Amer M. Alanazi ◽

Ellen L. Neidle ◽

Cory Momany

Keyword(s):

Amino Acids ◽

Dna Binding ◽

Dna Recognition ◽

Transcriptional Regulators ◽

Binding Domain ◽

Structural Basis ◽

Binding Motif ◽

Sequence Motif ◽

Dna Binding Domain ◽

Half Site

LysR-type transcriptional regulators (LTTRs) play critical roles in metabolism and constitute the largest family of bacterial regulators. To understand protein–DNA interactions, atomic structures of the DNA-binding domain and linker-helix regions of a prototypical LTTR, BenM, were determined by X-ray crystallography. BenM structures with and without bound DNA reveal a set of highly conserved amino acids that interact directly with DNA bases. At the N-terminal end of the recognition helix (α3) of a winged-helix–turn–helix DNA-binding motif, several residues create hydrophobic pockets (Pro30, Pro31 and Ser33). These pockets interact with the methyl groups of two thymines in the DNA-recognition motif and its complementary strand, T-N11-A. This motif usually includes some dyad symmetry, as exemplified by a sequence that binds two subunits of a BenM tetramer (ATAC-N7-GTAT). Gln29 forms hydrogen bonds to adenine in the first position of the recognition half-site (ATAC). Another hydrophobic pocket defined by Ala28, Pro30 and Pro31 interacts with the methyl group of thymine, complementary to the base at the third position of the half-site. Arg34 interacts with the complementary base of the 3′ position. Arg53, in the wing, provides AT-tract recognition in the minor groove. For DNA recognition, LTTRs use highly conserved interactions between amino acids and nucleotide bases as well as numerous less-conserved secondary interactions.

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The N-Terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition

10.26434/chemrxiv.12195372.v3 ◽

2021 ◽

Author(s):

Marina Corbella ◽

Qinghua Liao ◽

Catia Moreira ◽

Peter M. Kasson ◽

Shina Caroline Lynn Kamerlin

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Dna Sequences ◽

Dynamical Behavior ◽

Dna Recognition ◽

Tight Binding ◽

Binding Mode ◽

Binding Modes ◽

Efficient Design ◽

Terminal Loop

<div> <div> <p>DNA-binding proteins play an important role in gene regulation and cellular function. The transcription factors MarA and Rob are two homologous members of the AraC/XylS family that regulate multidrug resistance. They share a common DNA-binding domain, and Rob possesses an additional C-terminal domain that permits binding of low-molecular weight effectors. Both proteins possess two helix-turn-helix (HTH) motifs capable of binding DNA; however, while MarA interacts with its promoter through both HTH-motifs, prior studies indicate that Rob binding to DNA via a single HTH-motif is sufficient for tight binding. In the present work, we perform microsecond time scale all-atom simulations of the binding of both transcription factors to different DNA sequences to understand the determinants of DNA recognition and binding. Our simulations characterize sequence-specific changes in dynamical behavior upon DNA binding, showcasing the role of Arg40 of the N-terminal HTH-motif in allowing for specific tight binding. Finally, our simulations demonstrate that an acidic C-terminal loop of Rob can control the DNA binding mode, facilitating interconversion between the distinct DNA binding modes observed in MarA and Rob. In doing so, we provide detailed molecular insight into DNA binding and recognition by these proteins, which in turn is an important step towards the efficient design of anti-virulence agents that target these proteins.</p> </div> </div>

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