Crystallographic snapshots along a protein-induced DNA-bending pathway

Horton, Nancy C.; Perona, John J.

doi:10.1073/pnas.090370797

Cited by 44 publications

(69 citation statements)

References 38 publications

(39 reference statements)

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“…This observation is also consistent with previous studies showing that κB sequences are bent to various degrees upon NF-κB binding (6,29). DNA bending is a common prerequisite to the formation of a fully active transcriptional complex (30).…”

Section: Protein-dna Supercomplex In the Presence Of Pirin Is Compactsupporting

confidence: 81%

Pirin is an iron-dependent redox regulator of NF-κB

Liu

Rehmani²,

Esaki³

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

107

146

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Pirin is a nuclear nonheme Fe protein of unknown function present in all human tissues. Here we describe that pirin may act as a redox sensor for the nuclear factor κB (NF-κB) transcription factor, a critical mediator of intracellular signaling that has been linked to cellular responses to proinflammatory signals and controls the expression of a vast array of genes involved in immune and stress responses. Pirin's regulatory effect was tested with several metals and at different oxidations states, and our spectroscopic results show that only the ferric form of pirin substantially facilitates binding of NF-κB proteins to target κB genes, a finding that suggests that pirin performs a redox-sensing role in NF-κB regulation. The molecular mechanism of such a metal identity-and redox state-dependent regulation is revealed by our structural studies of pirin. The ferrous and ferric pirin proteins differ only by one electron, yet they have distinct conformations. The Fe center is shown to play an allosteric role on an R-shaped surface area that has two distinct conformations based on the identity and the formal redox state of the metal. We show that the R-shaped area composes the interface for pirin-NF-κB binding that is responsible for modulation of NF-κB's DNAbinding properties. The nonheme Fe protein pirin is proposed to serve as a reversible functional switch that enables NF-κB to respond to changes in the redox levels of the cell nucleus.metalloprotein | coregulator | reactive oxygen species (ROS) | oxidative stress | signal transduction activation

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Section: Protein-dna Supercomplex In the Presence Of Pirin Is Compactsupporting

confidence: 81%

Pirin is an iron-dependent redox regulator of NF-κB

Liu

Rehmani²,

Esaki³

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

107

146

View full text Add to dashboard Cite

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“…Restriction endonucleases require divalent metal cations for catalysis, Mg 2+ usually being the most efficient [167]. Ca 2+ , however, inhibits the reaction, despite the fact it has been demonstrated to bind in a catalytically relevant position with the same octahedral geometry as Mg 2+ (BamHI: [154]; EcoRV: [168,169]), indicating that electronic rather than geometric factors are required for ion selectivity [170]. Most phosphodiester hydrolyzing enzymes are optimized for Mg 2+ .…”

Section: Three-metal Ion Mechanismmentioning

confidence: 98%

Type II restriction endonucleases: structure and mechanism

Pingoud

Fuxreiter

Pingoud

et al. 2005

CMLS, Cell. Mol. Life Sci.

441

494

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Type II restriction endonucleases are components of restriction modification systems that protect bacteria and archaea against invading foreign DNA. Most are homodimeric or tetrameric enzymes that cleave DNA at defined sites of 4-8 bp in length and require Mg2+ ions for catalysis. They differ in the details of the recognition process and the mode of cleavage, indicators that these enzymes are more diverse than originally thought. Still, most of them have a similar structural core and seem to share a common mechanism of DNA cleavage, suggesting that they evolved from a common ancestor. Only a few restriction endonucleases discovered thus far do not belong to the PD...D/ExK family of enzymes, but rather have active sites typical of other endonuclease families. The present review deals with new developments in the field of Type II restriction endonucleases. One of the more interesting aspects is the increasing awareness of the diversity of Type II restriction enzymes. Nevertheless, structural studies summarized herein deal with the more common subtypes. A major emphasis of this review will be on target site location and the mechanism of catalysis, two problems currently being addressed in the literature.

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“…It is the primary mode of DNA bending and is especially important in protein-DNA interaction. 31,[72][73][74] Two atoms are considered here to form a hydrogen bond if the acceptor-hydrogen distance is b 2.4 Å and the acceptor-hydrogen donor angle is N135°. Hydrogen-bond occupancy is calculated as the ratio of the time when the hydrogen bond is formed to the total time of the trajectory.…”

Section: Analysis Of Trajectoriesmentioning

confidence: 99%

Mechanism of DNA Recognition by the Restriction Enzyme EcoRV

Zahran

Daidone

Smith

et al. 2010

Journal of Molecular Biology

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EcoRV, a restriction enzyme in Escherichia coli, destroys invading foreign DNA by cleaving it at the center step of a GATATC sequence. In the EcoRV-cognate DNA crystallographic complex, a sharp kink of 50 degrees has been found at the center base-pair step (TA). Here, we examine the interplay between the intrinsic propensity of the cognate sequence to kink and the induction by the enzyme by performing all-atom molecular dynamics simulations of EcoRV unbound and interacting with three DNA sequences: the cognate sequence, GATATC (TA); the non-cognate sequence, GAATTC (AT); and with the cognate sequence methylated on the first adenine GA(CH(3))TATC (TA-CH(3)). In the unbound EcoRV, the cleft between the two C-terminal subdomains is found to be open. Binding to AT narrows the cleft and forms a partially bound state. However, the intrinsic bending propensity of AT is insufficient to allow tight binding. In contrast, the cognate TA sequence is easier to bend, allowing specific, high-occupancy hydrogen bonds to form in the complex. The absence of cleavage for this methylated sequence is found to arise from the loss of specific hydrogen bonds between the first adenine of the recognition sequence and Asn185. On the basis of the results, we suggest a three-step recognition mechanism. In the first step, EcoRV, in an open conformation, binds to the DNA at a random sequence and slides along it. In the second step, when the two outer base pairs, GAxxTC, are recognized, the R loops of the protein become more ordered, forming strong hydrogen-bonding interactions, resulting in a partially bound EcoRV-DNA complex. In the third step, the flexibility of the center base pair is probed, and in the case of the full cognate sequence the DNA bends, the complex strengthens and the protein and DNA interact more closely, allowing cleavage.

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Crystallographic snapshots along a protein-induced DNA-bending pathway

Cited by 44 publications

References 38 publications

Pirin is an iron-dependent redox regulator of NF-κB

Pirin is an iron-dependent redox regulator of NF-κB

Type II restriction endonucleases: structure and mechanism

Mechanism of DNA Recognition by the Restriction Enzyme EcoRV

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