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Benini S, Haouz A, Proux F, Alzari P, Wilson K. The crystal structure of Rv2991 from Mycobacterium tuberculosis: An F 420 binding protein with unknown function. J Struct Biol 2019; 206:216-224. [PMID: 30890426 DOI: 10.1016/j.jsb.2019.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/13/2019] [Accepted: 03/14/2019] [Indexed: 11/25/2022]
Abstract
The crystal structure of the conserved hypothetical protein Rv2991 from Mycobacterium tuberculosis has been solved by SAD using seleno-methionine substituted protein. The dimeric biological assembly and the sequence and fold conservation are typical of F420 cofactor binding enzymes. Despite Rv2991 still being of unknown function, sequence and structural comparison with similar proteins enable a role to be proposed for its C-terminal stretch of residues in recognizing and orienting the substrate. In addition, the C-terminus is involved in both protein folding and determining the size of the active site cavity.
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Affiliation(s)
- Stefano Benini
- Bioorganic Chemistry and Bio-Crystallography Laboratory (B(2)Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, Bolzano 39100, Italy.
| | - Ahmed Haouz
- C2RT-Plateforme de cristallographie, Institut Pasteur, CNRS UMR 3528, 75724 Paris Cedex 15, France
| | - Florence Proux
- C2RT-Plateforme de cristallographie, Institut Pasteur, CNRS UMR 3528, 75724 Paris Cedex 15, France
| | - Pedro Alzari
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, Université Paris Diderot, Sorbonne Paris Cité, 75724 Paris Cedex 15, France
| | - Keith Wilson
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
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Abstract
Experimental phasing by single- or multi-wavelength anomalous dispersion (SAD or MAD) has become the most popular method of de novo macromolecular structure determination. Continuous advances at third-generation synchrotron sources have enabled the deployment of rapid data collection protocols that are capable of recording SAD or MAD data sets. However, procedural simplifications driven by the pursuit of high throughput have led to a loss of sophistication in data collection strategies, adversely affecting measurement accuracy from the viewpoint of anomalous phasing. In this chapter, we detail optimized strategies for collecting high-quality data for experimental phasing, with particular emphasis on minimizing errors from radiation damage as well as from the instrument. This chapter also emphasizes data processing for "on-the-fly" decision-making during data collection, a critical process when data quality depends directly on information gathered while at the synchrotron.
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Abdur R, Gerlits OO, Gan J, Jiang J, Salon J, Kovalevsky AY, Chumanevich AA, Weber IT, Huang Z. Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:354-61. [PMID: 24531469 PMCID: PMC3940196 DOI: 10.1107/s1399004713027922] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 10/11/2013] [Indexed: 11/11/2022]
Abstract
The crystal structures of protein-nucleic acid complexes are commonly determined using selenium-derivatized proteins via MAD or SAD phasing. Here, the first protein-nucleic acid complex structure determined using selenium-derivatized nucleic acids is reported. The RNase H-RNA/DNA complex is used as an example to demonstrate the proof of principle. The high-resolution crystal structure indicates that this selenium replacement results in a local subtle unwinding of the RNA/DNA substrate duplex, thereby shifting the RNA scissile phosphate closer to the transition state of the enzyme-catalyzed reaction. It was also observed that the scissile phosphate forms a hydrogen bond to the water nucleophile and helps to position the water molecule in the structure. Consistently, it was discovered that the substitution of a single O atom by a Se atom in a guide DNA sequence can largely accelerate RNase H catalysis. These structural and catalytic studies shed new light on the guide-dependent RNA cleavage.
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Affiliation(s)
- Rob Abdur
- Department of Chemistry and Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Oksana O. Gerlits
- Department of Chemistry and Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Jianhua Gan
- Department of Chemistry and Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Jiansheng Jiang
- Department of Chemistry and Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Jozef Salon
- Department of Chemistry and Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Andrey Y. Kovalevsky
- Department of Chemistry and Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Alexander A. Chumanevich
- Department of Chemistry and Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Irene T. Weber
- Department of Chemistry and Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Zhen Huang
- Department of Chemistry and Department of Biology, Georgia State University, Atlanta, GA 30303, USA
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Duke EMH, Johnson LN. Macromolecular crystallography at synchrotron radiation sources: current status and future developments. Proc Math Phys Eng Sci 2010. [DOI: 10.1098/rspa.2010.0448] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
X-ray diffraction with synchrotron radiation (SR) has revealed the atomic structures of numerous biological macromolecules including proteins and protein complexes, nucleic acids and their protein complexes, viruses, membrane proteins and drug targets. The bright SR X-ray beam with its small divergence has made the study of weakly diffracting crystals of large biological molecules possible. The ability to tune the wavelength of the SR beam to the absorption edge of certain elements has allowed anomalous scattering to be exploited for phase determination. We review the developments at synchrotron sources and beamlines from the early days to the present time, and discuss the significance of the results in providing a deeper understanding of the biological function, the design of new therapeutic molecules and time-resolved studies of dynamic events using pump–probe techniques. Radiation damage, a problem with bright X-ray sources, has been partially alleviated by collecting data at low temperature (100 K) but work is ongoing. In the most recent development, free electron laser sources can offer a peak brightness of hard X-rays approximately 10
8
times brighter than that achieved at SR sources. We describe briefly how early experiments at FLASH and Linear Coherent Light Source have shown exciting possibilities for the future.
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Affiliation(s)
- E. M. H. Duke
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - L. N. Johnson
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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Kostelansky MS, Sun J, Lee S, Kim J, Ghirlando R, Hierro A, Emr SD, Hurley JH. Structural and functional organization of the ESCRT-I trafficking complex. Cell 2006; 125:113-26. [PMID: 16615894 PMCID: PMC1576341 DOI: 10.1016/j.cell.2006.01.049] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2005] [Revised: 12/06/2005] [Accepted: 01/12/2006] [Indexed: 11/21/2022]
Abstract
The endosomal sorting complex required for transport (ESCRT) complexes are central to receptor downregulation, lysosome biogenesis, and budding of HIV. The yeast ESCRT-I complex contains the Vps23, Vps28, and Vps37 proteins, and its assembly is directed by the C-terminal steadiness box of Vps23, the N-terminal half of Vps28, and the C-terminal half of Vps37. The crystal structures of a Vps23:Vps28 core subcomplex and the Vps23:Vps28:Vps37 core were solved at 2.1 and 2.8 A resolution. Each subunit contains a structurally similar pair of helices that form the core. The N-terminal domain of Vps28 has a hydrophobic binding site on its surface that is conformationally dynamic. The C-terminal domain of Vps28 binds the ESCRT-II complex. The structure shows how ESCRT-I is assembled by a compact core from which the Vps23 UEV domain, the Vps28 C domain, and other domains project to bind their partners.
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Affiliation(s)
- Michael S. Kostelansky
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, U. S. Department of Health and Human Services, Bethesda, MD 20892
| | - Ji Sun
- Department of Cellular and Molecular Medicine and Department of Chemistry and Biochemistry and Howard Hughes Medical Institute, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0668
| | - Sangho Lee
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, U. S. Department of Health and Human Services, Bethesda, MD 20892
| | - Jaewon Kim
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, U. S. Department of Health and Human Services, Bethesda, MD 20892
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, U. S. Department of Health and Human Services, Bethesda, MD 20892
| | - Aitor Hierro
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, U. S. Department of Health and Human Services, Bethesda, MD 20892
| | - Scott D. Emr
- Department of Cellular and Molecular Medicine and Department of Chemistry and Biochemistry and Howard Hughes Medical Institute, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0668
| | - James H. Hurley
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, U. S. Department of Health and Human Services, Bethesda, MD 20892
- *Corresponding author. , tel (301) 402-4703, fax (301) 480-0639
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Adams PD, Grosse-Kunstleve RW. Recent developments in software for the automation of crystallographic macromolecular structure determination. Curr Opin Struct Biol 2000; 10:564-8. [PMID: 11042455 DOI: 10.1016/s0959-440x(00)00132-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The automation of macromolecular structure determination by X-ray crystallography has long been a goal for many researchers. Recently, there have been improvements in the underlying algorithms, some of which have been implemented in software packages that deal with multiple stages of the structure determination process. These first steps towards complete automation have made X-ray crystallography more efficient.
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Affiliation(s)
- P D Adams
- Lawrence Berkeley National Laboratory, Mailstop 4-230, 1 Cyclotron Road, Berkeley, CA 94720, USA.
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Abstract
In only a few years, multiple wavelength anomalous diffraction (MAD) phasing has advanced from an esoteric technique used in only a few favorable cases to the method of choice for solving new macromolecular structures. Before 1994, MAD phasing had been used for fewer than a dozen new structure determinations. In 1999 alone, well over 100 new structures were determined by MAD phasing. The meteoric rise in MAD applications resulted from the availability of new synchrotron beamlines, equipped with low bandpass optics, fast readout detectors, cryogenic cooling and user-friendly interfaces. The power of MAD phasing has been amplified by the availability of new computer programs for locating the positions of the anomalous scattering atoms and for calculating phases from the experimental data. Phasing by anomalous scattering techniques has been applied to structures as large as 640 kDa and 120 selenium atoms in the asymmetric unit. The practical size limitation for application of MAD phasing techniques has not yet been encountered.
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Affiliation(s)
- S E Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA.
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