The NIGMS structural biology facility at the NSLS

Allaire, Marc; Aslantaş, Mehmet; Berntson, A.; Berman, L. E.; Cheung, Stephanie; Clay, B.; Greene, Richard M.; Jakoncic, Jean; Johnson, E.; Kao, C.‐C.; Lenhard, A.; Pjerov, S.; Siddons, D. P.; Stober, W.; Venkatagiriyappa, V.; Yin, Zhiqi; Stojanoff, V.

doi:10.1080/08940880308603063

Cited by 8 publications

(6 citation statements)

References 3 publications

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“…Crystals that diffracted up to 1.85 Å resolution (Jakoncic, unpublished work) were obtained by further covering each well with mineral oil [9]. Diffraction data were recorded on beam line X6A at the National Synchrotron Light Source [10]. The 3D structure was determined by molecular replacement, using the α-subunit from naphthalene dioxygenase from Pseudomonas sp.…”

Section: Methodsmentioning

confidence: 99%

The catalytic pocket of the ring-hydroxylating dioxygenase from Sphingomonas CHY-1

Jakoncic

Jouanneau

Meyer

et al. 2007

Biochemical and Biophysical Research Communications

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Ring-hydroxylating dioxygenases are multicomponent bacterial enzymes that catalyze the first step in the oxidative degradation of aromatic hydrocarbons. The dioxygenase from Sphingomonas CHY-1 is unique in that it can oxidize a wide range of polycyclic aromatic hydrocarbons (PAHs). With a crystal structure similar to that of the seven other known dioxygenases, its catalytic domain features the largest hydrophobic substrate binding cavity characterized so far. Molecular modeling studies indicated that the catalytic cavity is large enough to accommodate a five-ring benzo [a]pyrene molecule. The predicted positions of this and other PAHs in the substrate binding pocket are consistent with the product regio-and stereo-selectivity of the enzyme. Keywordsdioxygenase; catalytic domain; mononuclear iron; bioremediation; high molecular weight polycyclic aromatic hydrocarbons The first step in the biodegradation of aromatic hydrocarbons by aerobic bacteria often involves a dihydroxylation on two adjacent carbon atoms of the aromatic ring, catalyzed by a ringhydroxylating dioxygenase (RHD). RHDs form a large family of enzymes, very diverse in terms of substrate specificity and protein sequence [1]. Their role is crucial in the degradation of many organic pollutants, including polycyclic aromatic hydrocarbons (PAHs), which are notorious for their resistance to biodegradation. Several bacteria were found to degrade PAHs but only a few have been reported to attack four and five ring PAHs [2,3]. In Sphingomonas strain CHY-1 a single RHD has been shown to be responsible for the oxidation of a wide range of PAHs [4]. This dioxygenase consists of three components, a NADH-dependent reductase (PhnA4), a ferredoxin containing a Rieske type [2Fe-2S] cluster (PhnA3), and a terminal oxygenase, PhnI, containing both a mononuclear iron [Fe 2+ ] and a [2Fe-2S] Rieske cluster [5]. Recent biochemical studies showed that the dioxygenase from strain CHY-1 was able to oxidize at least eight PAHs made of 2 to 5 aromatic rings, in contrast to most other dioxygenases, whose selectivity is limited to 2 and 3 ring PAHs [6,7,8]. A positive electron density observed in the PhnI refined three-dimensional structure served as probe in modeling different substrates in the catalytic pocket. This study presents evidence that the broad substrateCorresponding author: Vivian Stojanoff, Brookhaven National Laboratory, Upton NY 11973 US, Tel.: 1 631 344 8375; Fax: 1 631 344 3238, Email : vivian.stojanoff@gmail.gov. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. NIH Public AccessAuthor Manuscript Biochem Biophy...

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Section: Methodsmentioning

confidence: 99%

The catalytic pocket of the ring-hydroxylating dioxygenase from Sphingomonas CHY-1

Jakoncic

Jouanneau

Meyer

et al. 2007

Biochemical and Biophysical Research Communications

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“…The higher R merge values observed here are attributed to systematic and experimental errors and might be expected as this experiment was carried out on non-dedicated beamlines. To verify the quality of the data, a complete data set was collected at medium energy (12 keV) on a standard macromolecular crystallography beamline (Allaire et al, 2003) on a crystal grown under the same conditions and of the same size. Similar diffraction resolution with a 4 s exposure per oscillation resulted in similar statistics with an R merge of 4.5%, compatible with the values reported in the PDB for the structures mentioned above.…”

Section: Crystals and Diffraction Qualitymentioning

confidence: 99%

Anomalous diffraction at ultra-high energy for protein crystallography

et al. 2006

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Single-wavelength anomalous diffraction (SAD), multiwavelength anomalous diffraction (MAD) and single isomorphous replacement with anomalous scattering (SIRAS) phasing at ultra-high X-ray energy, 55 keV, are used successfully to determine a high-quality and high-resolution experimental electronic density map of hen egg-white lysozyme, a model protein. Several combinations, between single-and three-wavelength, with native data were exploited to demonstrate that standard phasing procedures with standard equipment and software can successfully be applied to three-dimensional crystal structure determination of a macromolecule, even at these very short wavelengths. For the first time, a high-quality three-dimensional molecular structure is reported from SAD phasing with ultra-high-energy X-rays. The quality of the crystallographic data and the experimental electron density maps meet current standards. The 2.7% anomalous signal from three Ho atoms, at the Ho K edge, was sufficient to obtain a remarkable electron density and build the first lanthanide structure for HEWL in its entirety. research papers J. Appl. Cryst. (2006). 39, 831-841 Jean Jakoncic et al. Anomalous diffraction at ultra-high energy 837

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“…Diffraction data were collected from one crystal of cocrystallized and one crystal of soaked Ba-derivatized xylanase at five different wavelengths, with the longest wavelength collected first, on beamline X6A (Allaire et al, 2003) at the National Synchrotron Light Source at Brookhaven National Laboratory (Upton, NY, USA) using an ADSC Q210 CCD detector. The wavelengths were chosen to cover a range of 7.3-12.7 keV.…”

Section: Methodsmentioning

confidence: 99%

Using barium ions for heavy-atom derivatization and phasing of xylanase II fromTrichoderma longibrachiatum

Moiseeva

Allaire

2007

Acta Crystallogr D Biol Cryst

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This paper describes the use of barium chloride to produce a heavy-atom derivative of xylanase II crystals from Trichoderma longibrachiatum, which was obtained either by cocrystallization or soaking. SAD phasing led to interpretable electron-density maps that allowed unambiguous chain tracing. In the best case, with a data set collected at 9.5 keV, 88% of the residues were built, with 83% of the side chains assigned. The barium ions are found to mainly interact with main-chain carbonyl groups and water molecules. It is suggested that barium ions could also be used as a potential anomalous scatterer in the quick cryosoaking procedure for phasing.

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The NIGMS structural biology facility at the NSLS

Cited by 8 publications

References 3 publications

The catalytic pocket of the ring-hydroxylating dioxygenase from Sphingomonas CHY-1

The catalytic pocket of the ring-hydroxylating dioxygenase from Sphingomonas CHY-1

Anomalous diffraction at ultra-high energy for protein crystallography

Using barium ions for heavy-atom derivatization and phasing of xylanase II fromTrichoderma longibrachiatum

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