The DNA-binding domain of OmpR: crystal structures of a winged helix transcription factor

Martı́nez-Hackert, Erik; Stock, Ann

doi:10.1016/s0969-2126(97)00170-6

Cited by 227 publications

(199 citation statements)

References 71 publications

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“…These oligonucleotides are listed in Table I as group A. The linker is defined in this case based on structural determination by x-ray crystallography (20,21). The linker is defined by the lack of electron density, and its edges are the first residue after the ␣ 5 helix in the receiver (amino terminus) domain and the last residue before the ␤ strand of the carboxyl-terminal DNA-binding domain.…”

Section: Methodsmentioning

confidence: 99%

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The Linker Region Plays an Important Role in the Interdomain Communication of the Response Regulator OmpR

Mattison¹,

Oropeza²,

Kenney

2002

Journal of Biological Chemistry

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OmpR is the response regulator of a two-component regulatory system that controls the expression of the porin genes ompF and ompC in Escherichia coli. This regulator consists of two domains joined by a flexible linker region. The amino-terminal domain is phosphorylated by the sensor kinase EnvZ, and the carboxylterminal domain binds DNA via a winged helix-turn-helix motif. In vitro studies have shown that amino-terminal phosphorylation enhances the DNA binding affinity of OmpR and, conversely, that DNA binding by the carboxyl terminus increases OmpR phosphorylation. In the present work, we demonstrate that the linker region contributes to this communication between the two domains of OmpR. Changing the specific amino acid composition of the linker alters OmpR function, as does increasing or decreasing its length. Three linker mutants give rise to an OmpF ؉ OmpC ؊ phenotype, but the defects are not due to a shared molecular mechanism. Currently, functional homology between response regulators is predicted based on similarities in the amino and carboxylterminal domains. The results presented here indicate that linker length and composition should also be considered. Furthermore, classification of response regulators in the same subfamily does not necessarily imply that they share a common response mechanism.

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Section: Methodsmentioning

confidence: 99%

“…For example, two highly homologous regulators from the same subfamily, OmpR and PhoB, have linker regions of 15 and 6 amino acid residues, respectively (20,21,34). An understanding of the molecular mechanism for transmitting information between the two domains will depend upon understanding the interface that con-nects them.…”

mentioning

confidence: 99%

The Linker Region Plays an Important Role in the Interdomain Communication of the Response Regulator OmpR

Mattison¹,

Oropeza²,

Kenney

2002

Journal of Biological Chemistry

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“…19 ArcA is a member of the OmpR/PhoB subfamily of RR transcription factors, by far the largest subfamily of RRs, accounting for 15 of the 34 RRs presently identified in E. coli. 20,21 RRs of this subfamily are distinguished by a C-terminal winged helix-turn-helix DNA-binding motif 22,23 and the most extensively characterized members of this subfamily are known to bind as tandem dimers to DNA direct repeat recognition sequences. [24][25][26] Phosphorylation of the regulatory domain enhances DNA binding, ultimately resulting in regulation of transcription, but a detailed mechanism of this process has not been elucidated.…”

Section: Introductionmentioning

confidence: 99%

Structural Analysis and Solution Studies of the Activated Regulatory Domain of the Response Regulator ArcA: A Symmetric Dimer Mediated by the α4-β5-α5 Face

Toro-Roman

Mack²,

Stock

2005

Journal of Molecular Biology

119

137

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SUMMARYEscherichia coli react to changes from aerobic to anaerobic conditions of growth using the ArcAArcB two-component signal transduction system. This system, in conjunction with other proteins, regulates the respiratory metabolic pathways in the organism. ArcA is a member of the OmpR/ PhoB subfamily of response regulator transcription factors that are known to regulate transcription by binding in tandem to target DNA direct repeats. It is still unclear in this subfamily how activation by phosphorylation of the regulatory domain of response regulators stimulates DNA binding by the effector domain and how dimerization and domain orientation, as well as intra-and intermolecular interactions, affect this process. In order to address these questions we have solved the crystal structure of the regulatory domain of ArcA in the presence and absence of the phosphoryl analog, BeF 3 − . In the crystal structures, the regulatory domain of ArcA forms a symmetric dimer mediated by the α4-β5-α5 face of the protein and involving a number of residues that are highly conserved in the OmpR/PhoB subfamily. It is hypothesized that members of this subfamily use a common mechanism of regulation by dimerization. Additional biophysical studies were employed to probe the oligomerization state of ArcA, as well as its individual domains, in solution. The solution studies show the propensity of the individual domains to associate into oligomers larger than the dimer observed for the intact protein, and suggest that the C-terminal DNA-binding domain also plays a role in oligomerization.

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“…RRs are typically found at the ends of autophosphotransfer pathways where they regulate transcription functioning as phosphorylation-activated switches that regulate output responses. The majority of RRs are transcription factors with effector domains that can be divided into three major subfamilies based on their DNA-binding domains: the OmpR/PhoB winged-helix domains (Kondo et al, 1997;Martinez-Hackert and Stock, 1997;Okamura et al, 2000), the NarL/FixJ four-helix domains (Baikalov et al, 1996;, and NtrC ATPase-coupled transcription factors (Pelton et al, 1999). The HP-RR is grouped into the OmpR/PhoB subfamily of response regulators, which shares structural similarities on its C-terminal effector domain with these proteins.…”

Section: Introductionmentioning

confidence: 99%

Backbone Dynamics of an Atypical Orphan Response Regulator Protein, Helicobacter pylori 1043

Jeong

Lee

et al. 2013

Molecules and Cells

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An atypical orphan response regulator protein, HP1043 (HP-RR) in Helicobacter pylori, is proven to be essential for cell growth and does not require the well known phosphorelay scheme. HP-RR was identified as a symmetric dimer with two functional domains, an N-terminal regulatory domain (HP-RR r ) and a C-terminal effector domain (HP-RR e ). HP-RR is a new class of response regulator, as a phosphorylation-independent regulator. Previously, we have presented a detailed three-dimensional structure of HP-RR using NMR spectroscopy and X-ray crystallography. In this study, in order to understand the functional importance of flexibilities in HP-RR r and HP-RR e , T 1 , T 2 , heteronuclear NOE experiments have been performed and backbone dynamics of HP-RR r and HP-RR e were investigated. HP-RR r is a symmetric dimer and the interface region, α4-β5-α5 of dimer, showed high rigidity (high S 2 values). Site of rearrangements associated with phosphorylation of HP-RR r (Ser 75 : R ex = 3.382, Ile 95 : R ex = 5.228) showed slow chemical exchanges. HP-RR e is composed of three α-helices flanked on two sides by anti-parallel β-sheets. Low order parameters as well as conformational exchanges in the centers of loop regions known as the DNA binding site and transcription site of HP-RR e suggested that flexibility of HP-RR e is essential for interaction with DNA. In conclusion, backbone dynamics information for HP-RR implies that structural flexibilities in HP-RR r are necessary for the phosphorylation site and the dynamic nature of HP-RR e is essential for the regulation of interaction between protein and DNA.

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The DNA-binding domain of OmpR: crystal structures of a winged helix transcription factor

Cited by 227 publications

References 71 publications

The Linker Region Plays an Important Role in the Interdomain Communication of the Response Regulator OmpR

The Linker Region Plays an Important Role in the Interdomain Communication of the Response Regulator OmpR

Structural Analysis and Solution Studies of the Activated Regulatory Domain of the Response Regulator ArcA: A Symmetric Dimer Mediated by the α4-β5-α5 Face

Backbone Dynamics of an Atypical Orphan Response Regulator Protein, Helicobacter pylori 1043

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