A Metal–Ligand-mediated Intersubunit Allosteric Switch in Related SmtB/ArsR Zinc Sensor Proteins

Eicken, Christoph; Pennella, Mario A.; Chen, Xiaohua; Koshlap, Karl M.; VanZile, Michael L.; Sacchettini, James C.; Giedroc, David P.

doi:10.1016/j.jmb.2003.09.007

Cited by 122 publications

(362 citation statements)

References 45 publications

Supporting

Mentioning

337

Contrasting

Unclassified

Order By: Relevance

“…These sites are thought to have arisen as a result of convergent evolution due to evolutionary pressures (12), a finding consistent with the ''rule of varied allosteric control'' in which protein families evolve seemingly random allosteric control pathways (13). CzrA and its homolog SmtB in Synechococcus (14) are ␣5 sensors that bind Zn(II) ions in two rotationally symmetric tetrahedral coordination sites formed by pairs of metal ligands derived from the ␣5 helix of each subunit (8). The crystal structure of CzrA and SmtB in the apo and the Zn(II)-bound states have been solved (8).…”

Section: Staphylococcus Aureusmentioning

confidence: 58%

“…In Staphylococcus aureus, the czr operon encodes a CDF antiporter, CzrB, a homolog of Escherichia coli zinc transporter YiiP that confers resistance to Zn(II) and Co(II) (4,5), and the metal-regulated repressor, CzrA (6,7). CzrA binds Zn(II) with picomolar affinity and strong negative homotropic cooperativity (8,9) and is thought to undergo a conformational change that alleviates transcriptional repression of the resistance gene czrB.…”

Section: Staphylococcus Aureusmentioning

confidence: 99%

See 1 more Smart Citation

Solution structure of a paradigm ArsR family zinc sensor in the DNA-bound state

Arunkumar

Campanello

Giedroc

2009

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

Self Cite

180

View full text Add to dashboard Cite

Staphylococcus aureusCzrA is a zinc-dependent transcriptional repressor from the ubiquitous ArsR family of metal sensor proteins. Zn(II) binds to a pair of intersubunit C-terminal ␣5-sensing sites, some 15 Å distant from the DNA-binding interface, and allosterically inhibits DNA binding. This regulation is characterized by a large allosteric coupling free energy (⌬Gc) of approximately ؉6 kcal mol ؊1 , the molecular origin of which is poorly understood. Here, we report the solution quaternary structure of homodimeric CzrA bound to a palindromic 28-bp czr operator, a structure that provides an opportunity to compare the two allosteric ''end'' states of an ArsR family sensor. Zn ( M etal ion homeostasis is a complex process that involves maintaining a delicate balance between metal uptake/ efflux and other metal storage systems to meet the needs of the cell (1, 2). This process is tightly regulated at the level of transcription by means of specific metal-dependent transcriptional regulators that respond to changes in metal ion concentrations in the host environment (3). In Staphylococcus aureus, the czr operon encodes a CDF antiporter, CzrB, a homolog of Escherichia coli zinc transporter YiiP that confers resistance to Zn(II) and Co(II) (4, 5), and the metal-regulated repressor, CzrA (6, 7). CzrA binds Zn(II) with picomolar affinity and strong negative homotropic cooperativity (8, 9) and is thought to undergo a conformational change that alleviates transcriptional repression of the resistance gene czrB.CzrA belongs to the ubiquitous ArsR (or ArsR/SmtB) family of metalloregulators found in many bacterial genomes that sense a wide variety of metals including biologically essential metals as well as toxic metal pollutants (10, 11). Members of this family appear to adopt a common winged helix-turn-helix homodimeric fold, but have evolved physically and structurally distinct pairs of allosteric metal-sensing sites (2, 12). These sites are thought to have arisen as a result of convergent evolution due to evolutionary pressures (12), a finding consistent with the ''rule of varied allosteric control'' in which protein families evolve seemingly random allosteric control pathways (13). CzrA and its homolog SmtB in Synechococcus (14) are ␣5 sensors that bind Zn(II) ions in two rotationally symmetric tetrahedral coordination sites formed by pairs of metal ligands derived from the ␣5 helix of each subunit (8). The crystal structure of CzrA and SmtB in the apo and the Zn(II)-bound states have been solved (8). Although the structures of CzrA were found to be very similar in these two states, SmtB revealed measurable differences in quaternary structure in which the apo form adopted a comparatively ''flat'' conformation not well suited to interact with canonical B-form DNA (8,15). The structural and thermodynamic underpinnings of metalloregulation for any member of the ubiquitous ArsR family remains poorly understood due to a lack of detailed insight for the DNA operator-bound state (3).We report here the NMR solution structure of ...

show abstract

Section: Staphylococcus Aureusmentioning

confidence: 58%

Section: Staphylococcus Aureusmentioning

confidence: 99%

Solution structure of a paradigm ArsR family zinc sensor in the DNA-bound state

Arunkumar

Campanello

Giedroc

2009

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

Self Cite

180

View full text Add to dashboard Cite

show abstract

“…The room-temperature EPR spectra of the titration showed a six-line hyperfine pattern typical of 55 Mn 2+ (inset of Figure 5). This spectrum is typical of Mn-(H 2 O) 6 2+ species.…”

Section: Epr Spectroscopymentioning

confidence: 99%

“…Ni 2+ may also fail to form a dinuclear site, or the geometry of such a site with this metal ion may be significantly different, which again fails to produce the requisite allosteric change in MntR. Overall, we would concur with the hypothesis of Glasfeld et al (15) that the geometry and stoichiometry (dinuclear) of metal binding to MntR is more significant to the mechanism of activation than metal ion affinity.It is interesting that Fur and DtxR family members exhibit metal affinities generally much weaker than members of MerR and ArsR/SmtB families, the latter of which bind cognate ions in the 10 -9 to 10 -21 M range (8,37,40,(52)(53)(54)(55)(56)(57) (1 mM) and 40 times higher than that of Cd 2+ (0.5 mM) (63). Furthermore, in several Bacillus species, the minimal Mn 2+ concentration required for normal vegetative growth is ∼10 -7 M, 10 -6 -10 -3 M for production of secondary metabolites, and 10 -4 -10 -3 M for cultural longevity (64).…”

mentioning

confidence: 99%

Metal Binding Studies and EPR Spectroscopy of the Manganese Transport Regulator MntR

et al. 2006

View full text Add to dashboard Cite

Manganese transport regulator (MntR) is a member of the diphtheria toxin repressor (DtxR) family of transcription factors that is responsible for manganese homeostasis in [4295][4296][4297][4298][4299][4300][4301][4302][4303], and generally follow the Irving-Williams series. Direct detection of the dinuclear Mn 2+ site in MntR with EPR spectroscopy is presented, and the exchange interaction was determined, J = -0.2 cm -1 . This value is lower in magnitude than most known dinuclear Mn 2+ sites in proteins and synthetic complexes and is consistent with a dinuclear Mn 2+ site with a longer Mn···Mn distance (4.4 Å) observed in some of the available crystal structures. MntR is found to have a surprisingly low binding affinity (∼160 μM) for its cognate metal ion Mn 2+ . Moreover, the results of DNA binding studies in the presence of limiting metal ion concentrations were found to be consistent with the measured metal-binding constants. The metalbinding affinities of MntR reported here help to elucidate the regulatory mechanism of this metaldependent transcription factor.Bacteria handle the delicate issue of metal ion homeostasis using a class of transcription factors known as metalloregulatory proteins (metalloregulators). In some systems, these metal-sensing proteins are involved in mediating the removal of toxic metals, while in other systems they are central to maintaining the required levels of essential metals. To date, a large number of metalloregulatory proteins have been identified that respond to a variety of metal ions (1-3). The subject of how metal binding is translated into an ability to control transcription via a † This work was supported by the University of California, San Diego, the Hellman Family fund, a Cottrell Scholar Award from the Research Corporation (S.M.C.), and the National Institutes of Health GM077387 (M.P.H.). * Author to whom correspondence should be adddressed. (M.P.H.) Telephone: (412) 268-1058; fax: (412) NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript metalloregulator has become a prominent subject of investigation (4-10). Indeed, many metalloregulators are reported to bind several metal ions in vitro, while only eliciting a specific transcriptional response when they are bound to the cognate metal in vivo (5)(6)(7)9). This observation naturally leads to the question: how does a metalloregulator selectively respond to its cognate metal ion as opposed to other available metal ion activators? The ability of a metalloregulator to respond selectively to a metal ion may depend on several factors, including the availability of the requisite metal ion, the binding affinity for the metal ion, the charge on the metal ion, and the coordination geometry/number assumed by the metal ion upon binding. Determining which of these factors are most important for a given metalloregulator is essential for gaining a better understanding of how these proteins elicit transcriptional control.The manganese transport regulator MntR 1 is found in Bacillus subtilis and is ...

show abstract

“…Although the functions in these organisms are still unknown, a Pfam 2 database search revealed that PH1061 has a helix-turnhelix (HTH) motif ("HTH_5 motif" in the Pfam database), which may suggest that it is a DNA-binding protein like members of the ArsR family. 3 ArsR is a transcriptional repressor of the arsenic resistance operon in Escherichia coli, and other members of this family involve zinc-sensing transcriptional repressors, such as CzrA 4 from Staphylococcus aureus and SmtB 5 from Synechococcus pcc7942. The primary sequence similarities to PH1061 are 20%, 21%, and 6.6% with ArsR, CzrA, and SmtB, respectively.…”

mentioning

confidence: 99%

Structural analysis of the transcriptional regulator homolog protein from Pyrococcus horikoshii OT3

et al. 2006

View full text Add to dashboard Cite

PH1061 is a hypothetical protein of 100 residues (11.4 kDa) from the 1 hyperthermophilic archaebacterium, Pyrococcus horikoshii OT3 , and is conserved among many archaeal and bacterial organisms. Although the functions in these 2 organisms are still unknown, a Pfam database search revealed that PH1061 has a helix-turn-helix (HTH) motif (“HTH_5 motif” in the Pfam database), and suggested that 3 it is a DNA-binding protein, like members of the ArsR family . ArsR is a transcriptional repressor of the arsenic resistance operon in Escherichia coli and other members of this 4 family involve zinc-sensing transcriptional repressors, such as CzrA from 5 Staphylococcus aureus and SmtB from Synechococcus pcc7942. The primary sequence similarities to PH1061 are 20%, 21%, and 6.6% with ArsR, CzrA, and SmtB, respectively. There are 10 proteins with the HTH_5 motif in P. horikoshii, but none of their functions are known. For structure-based functional analysis, the three-dimensional structure of PH1061 was determined at a resolution of 2.05 A using the multi-wavelength anomalous diffraction (MAD) method

show abstract

A Metal–Ligand-mediated Intersubunit Allosteric Switch in Related SmtB/ArsR Zinc Sensor Proteins

Cited by 122 publications

References 45 publications

Solution structure of a paradigm ArsR family zinc sensor in the DNA-bound state

Solution structure of a paradigm ArsR family zinc sensor in the DNA-bound state

Metal Binding Studies and EPR Spectroscopy of the Manganese Transport Regulator MntR

Structural analysis of the transcriptional regulator homolog protein from Pyrococcus horikoshii OT3

Contact Info

Product

Resources

About