SAD at home: solving the structure of oxalate decarboxylase with the anomalous signal from manganese using X-ray data collected on a home source

Stevenson, Clare E. M.; Tanner, Adam; Bowater, Laura; Bornemann, Stephen; Lawson, David M.

doi:10.1107/s0907444904023996

Cited by 7 publications

(6 citation statements)

References 24 publications

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“…Anomalous Fourier difference maps using calculated phases were used, when possible, to confirm the identity of bound metals. The anomalous signal of manganese is strong when using Cu Kα radiation and can be used to readily distinguish manganese from calcium and magnesium ions also present in the crystallization buffer (33). Also, a data set was collected from a crystal of the MntR•Zn 2+ complex at the zinc x-ray absorption edge in order to verify placement and identity of the bound zinc ions.…”

Section: Structure Determination and Refinementmentioning

confidence: 99%

Structural Basis for the Metal-Selective Activation of the Manganese Transport Regulator of Bacillus subtilis^,

et al. 2006

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The manganese transport regulator (MntR) of Bacillus subtilis is activated by Mn(2+) to repress transcription of genes encoding transporters involved in the uptake of manganese. MntR is also strongly activated by cadmium, both in vivo and in vitro, but it is poorly activated by other metal cations, including calcium and zinc. The previously published MntR.Mn(2+) structure revealed a binuclear complex of manganese ions with a metal-metal separation of 3.3 A (herein designated the AB conformer). Analysis of four additional crystal forms of MntR.Mn(2+) reveals that the AB conformer is only observed in monoclinic crystals at 100 K, suggesting that this conformation may be stabilized by crystal packing forces. In contrast, monoclinic crystals analyzed at room temperature (at either pH 6.5 or pH 8.5), and a second hexagonal crystal form (analyzed at 100 K), all reveal the shift of one manganese ion by 2.5 A, thereby leading to a newly identified conformation (the AC conformer) with an internuclear distance of 4.4 A. Significantly, the cadmium and calcium complexes of MntR also contain binuclear complexes with a 4.4 A internuclear separation. In contrast, the zinc complex of MntR contains only one metal ion per subunit, in the A site. Isothermal titration calorimetry confirms the stoichiometry of Mn(2+), Cd(2+), and Zn(2+) binding to MntR. We propose that the specificity of MntR activation is tied to productive binding of metal ions at two sites; the A site appears to act as a selectivity filter, determining whether the B or C site will be occupied and thereby fully activate MntR.

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Section: Structure Determination and Refinementmentioning

confidence: 99%

Structural Basis for the Metal-Selective Activation of the Manganese Transport Regulator of Bacillus subtilis^,

et al. 2006

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“…2a). We could find only four previous reports of phasing by Mn-SAD (Dauter et al, 2002;Ramagopal et al, 2003;Stevenson et al, 2004;Salgado et al, 2005), even though manganese is not uncommon in enzymes and has significant anomalous scattering at the Cu K wavelength.…”

Section: Data Collection Structure Solution and Refinementmentioning

confidence: 70%

Interaction of an echinomycin–DNA complex with manganese ions

2009

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The crystal structure of an echinomycin-d(ACGTACGT) duplex interacting with manganese(II) was solved by Mn-SAD using in-house data and refined to 1.1 Å resolution against synchrotron data. This complex crystallizes in a different space group compared with related complexes and shows a different mode of base pairing next to the bis-intercalation site, suggesting that the energy difference between Hoogsteen and Watson-Crick pairing is rather small. The binding of manganese to N7 of guanine is only possible because of DNA unwinding induced by the echinomycin, which might help to explain the mode of action of the drug.

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“…It has been pointed out that crystal decay can limit data quality, but in published S-SAD structure determinations data quality and phasing power always increase monotonically with increasing redundancy Dauter & Nagem, 2002;Debreczeni, Bunkó czi, Girmann et al, 2003;Olsen et al, 2004;Ramagopal et al, 2003;Roeser et al, 2005;Zwart, 2005;Dauter & Adamiak, 2001;Stevenson et al, 2004;Debreczeni, Bunkó czi, Ma et al, 2003). Here, this is not the case.…”

Section: Higher Multiplicity Does Not Necessarily Mean Better Datamentioning

confidence: 95%

In-house sulfur SAD phasing: a case study of the effects of data quality and resolution cutoffs

Sarma

Karplus

2006

Acta Crystallogr D Biol Crystallogr

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Single-wavelength anomalous diffraction (SAD) utilizing the weak signal of inherently present S atoms can be successfully used to solve macromolecular structures, although this is mostly performed with data from a synchrotron rather than a laboratory source. Using high redundancy, sufficiently accurate anomalous data may now often be collected in the laboratory using Cu Kalpha X-ray radiation. Systematic analyses of a laboratory-derived data set illuminate the effects of data quality, redundancy and resolution cutoffs on the ability to locate the S atoms and phase the structure of Ptr ToxA, a 13.2 kDa toxin secreted by the fungus Pyrenophora tritici-repentis. Three sulfurs contributed to the successful phasing of the structure and were located using the program SHELXD. It is observed that data quality improves with increasing redundancy, but after a certain point becomes worse owing to crystal decay, so that there is an optimal amount of data to include for the sulfur substructure solution. Further, the success rate in locating S atoms is dramatically improved at lower resolutions and in a manner similar to data quality, there exists an optimal resolution at which the likelihood of solving the substructure is maximized. Based on these observations, a strategy for SAD data collection and substructure solution is suggested.

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SAD at home: solving the structure of oxalate decarboxylase with the anomalous signal from manganese using X-ray data collected on a home source

Cited by 7 publications

References 24 publications

Structural Basis for the Metal-Selective Activation of the Manganese Transport Regulator of Bacillus subtilis^,

Structural Basis for the Metal-Selective Activation of the Manganese Transport Regulator of Bacillus subtilis^,

Interaction of an echinomycin–DNA complex with manganese ions

In-house sulfur SAD phasing: a case study of the effects of data quality and resolution cutoffs

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SAD at home: solving the structure of oxalate decarboxylase with the anomalous signal from manganese using X-ray data collected on a home source

Cited by 7 publications

References 24 publications

Structural Basis for the Metal-Selective Activation of the Manganese Transport Regulator of Bacillus subtilis,

Structural Basis for the Metal-Selective Activation of the Manganese Transport Regulator of Bacillus subtilis,

Interaction of an echinomycin–DNA complex with manganese ions

In-house sulfur SAD phasing: a case study of the effects of data quality and resolution cutoffs

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Product

Resources

About

Structural Basis for the Metal-Selective Activation of the Manganese Transport Regulator of Bacillus subtilis^,

Structural Basis for the Metal-Selective Activation of the Manganese Transport Regulator of Bacillus subtilis^,