1
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Bogdanove AJ, Bohm A, Miller JC, Morgan RD, Stoddard BL. Engineering altered protein-DNA recognition specificity. Nucleic Acids Res 2018; 46:4845-4871. [PMID: 29718463 PMCID: PMC6007267 DOI: 10.1093/nar/gky289] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/03/2018] [Accepted: 04/06/2018] [Indexed: 02/07/2023] Open
Abstract
Protein engineering is used to generate novel protein folds and assemblages, to impart new properties and functions onto existing proteins, and to enhance our understanding of principles that govern protein structure. While such approaches can be employed to reprogram protein-protein interactions, modifying protein-DNA interactions is more difficult. This may be related to the structural features of protein-DNA interfaces, which display more charged groups, directional hydrogen bonds, ordered solvent molecules and counterions than comparable protein interfaces. Nevertheless, progress has been made in the redesign of protein-DNA specificity, much of it driven by the development of engineered enzymes for genome modification. Here, we summarize the creation of novel DNA specificities for zinc finger proteins, meganucleases, TAL effectors, recombinases and restriction endonucleases. The ease of re-engineering each system is related both to the modularity of the protein and the extent to which the proteins have evolved to be capable of readily modifying their recognition specificities in response to natural selection. The development of engineered DNA binding proteins that display an ideal combination of activity, specificity, deliverability, and outcomes is not a fully solved problem, however each of the current platforms offers unique advantages, offset by behaviors and properties requiring further study and development.
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Affiliation(s)
- Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Andrew Bohm
- Sackler School of Graduate Biomedical Sciences, Tufts University, 136 Harrison Avenue, Boston, MA 02111, USA
| | - Jeffrey C Miller
- Sangamo Therapeutics Inc. 501 Canal Blvd., Richmond, CA 94804, USA
| | - Richard D Morgan
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98019, USA
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2
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Krauss IR, Merlino A, Vergara A, Sica F. An overview of biological macromolecule crystallization. Int J Mol Sci 2013; 14:11643-91. [PMID: 23727935 PMCID: PMC3709751 DOI: 10.3390/ijms140611643] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/08/2013] [Accepted: 05/20/2013] [Indexed: 12/11/2022] Open
Abstract
The elucidation of the three dimensional structure of biological macromolecules has provided an important contribution to our current understanding of many basic mechanisms involved in life processes. This enormous impact largely results from the ability of X-ray crystallography to provide accurate structural details at atomic resolution that are a prerequisite for a deeper insight on the way in which bio-macromolecules interact with each other to build up supramolecular nano-machines capable of performing specialized biological functions. With the advent of high-energy synchrotron sources and the development of sophisticated software to solve X-ray and neutron crystal structures of large molecules, the crystallization step has become even more the bottleneck of a successful structure determination. This review introduces the general aspects of protein crystallization, summarizes conventional and innovative crystallization methods and focuses on the new strategies utilized to improve the success rate of experiments and increase crystal diffraction quality.
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Affiliation(s)
- Irene Russo Krauss
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
- Institute of Biostructures and Bioimages, C.N.R, Via Mezzocannone 16, Napoli I-80134, Italy
| | - Alessandro Vergara
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
- Institute of Biostructures and Bioimages, C.N.R, Via Mezzocannone 16, Napoli I-80134, Italy
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, Napoli I-80126, Italy; E-Mails: (I.R.K.); (A.M.); (A.V.)
- Institute of Biostructures and Bioimages, C.N.R, Via Mezzocannone 16, Napoli I-80134, Italy
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +39-81-674-479; Fax: +39-81-674-090
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3
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Pryor EE, Wozniak DJ, Hollis T. Crystallization of Pseudomonas aeruginosa AmrZ protein: development of a comprehensive method for obtaining and optimization of protein-DNA crystals. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:985-993. [PMID: 22869139 PMCID: PMC3412790 DOI: 10.1107/s1744309112025316] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 06/04/2012] [Indexed: 06/01/2023]
Abstract
The AmrZ protein from the pathogenic bacterium Pseudomonas aeruginosa is a transcription factor that activates and represses the genes for several potent virulence factors, which gives the bacteria a selective advantage in infection. AmrZ was crystallized in complex with DNA containing the amrZ1 repressor binding site. Obtaining crystals of the complex required the integration of a number of well known techniques along with the development of new methods. Here, these processes are organized and combined into a comprehensive method which yielded diffraction-quality crystals. Part of this method included thorough data mining of the crystallization conditions of protein-DNA complexes to create a new directed crystallization screen. An optimized technique for the verification of protein-DNA complexes in crystals is also presented. Taken together, the methods described in this article attempt to streamline the difficult process of obtaining diffraction-quality crystals of protein-DNA complexes through the organization of older methods combined with the introduction of new techniques.
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Affiliation(s)
- Edward E. Pryor
- Department of Biochemistry and Center for Structural Biology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA
| | - Daniel J. Wozniak
- Department of Microbiology, The Ohio State University, 1018 BRT, 460 West 12th Avenue, Columbus, OH 43210, USA
| | - Thomas Hollis
- Department of Biochemistry and Center for Structural Biology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA
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4
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Abstract
DNA self-assembly has crucial implications in reading out the genetic information in the cell and in nanotechnological applications. In a recent paper, self-assembled DNA crystals displaying spectacular triangular motifs have been described (Zheng et al., 2009). The authors claimed that their data demonstrate the possibility to rationally design well-ordered macromolecular 3D DNA lattice with precise spatial control using sticky ends. However, the authors did not recognize the fundamental features that control DNA self-assembly in the lateral direction. By analysing available crystallographic data and simulating a DNA triangle, we show that the double helix geometry, sequence-specific cytosine–phosphate interactions and divalent cations are in fact responsible for the precise spatial assembly of DNA.
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Affiliation(s)
- Youri Timsit
- Information Génomique et Structurale, CNRS-UPR2589, Institut de Microbiologie de la Méditerranée, Parc Scientifique de Luminy, Marseille, 13288, France.
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5
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Ferré-D'Amaré AR. Use of the spliceosomal protein U1A to facilitate crystallization and structure determination of complex RNAs. Methods 2010; 52:159-67. [PMID: 20554048 PMCID: PMC2974902 DOI: 10.1016/j.ymeth.2010.06.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Accepted: 06/03/2010] [Indexed: 01/05/2023] Open
Abstract
The structure determination of complex RNA molecules such as ribozymes, riboswitches and aptamers by X-ray crystallography hinges on the preparation of well-ordered crystals. Success usually results from molecular engineering to facilitate crystallization. An approach that has resulted in 10 new RNA structures in the past decade is the use of the U1A crystallization module. In this approach, the cognate site for the U1A spliceosomal protein is introduced into a functionally dispensable location in the RNA of interest, and the RNA is cocrystallized with the basic RNA-binding protein. In addition to facilitating crystallization, the presence of U1A can be useful for de novo phase determination. In this paper, some general considerations for the use of this approach to RNA crystallization are presented, and specifics of the application of the U1A module to the crystallization of the hairpin ribozyme and the tetracycline aptamer are reviewed.
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Affiliation(s)
- Adrian R Ferré-D'Amaré
- Howard Hughes Medical Institute and Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA.
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6
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Abstract
A number of RNAs ranging from small helices to large megadalton ribonucleoprotein complexes have been solved to atomic resolution using X-ray crystallography. As with proteins, RNA crystallography involves a number of screening trials in which the concentration of macromolecule, precipitant, salt, and temperature are varied, an approach known as searching "condition space." In contrast to proteins, the nature of base pairing in nucleic acids creates predictable secondary structure that facilitates the rational design of RNA variants, allowing "sequence space" to be screened in parallel. This chapter reviews RNA-specific techniques and considerations for RNA crystallography and presents a complete workflow used by our laboratory for solving RNA structures starting with initial library construction, methods to investigate and improve RNA crystal quality, and finally phase determination and structure solution.
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Affiliation(s)
- Francis E Reyes
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado, USA
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7
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Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton NC. Alteration of sequence specificity of the type II restriction endonuclease HincII through an indirect readout mechanism. J Biol Chem 2006; 281:23852-69. [PMID: 16675462 DOI: 10.1074/jbc.m512339200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The functional and structural consequences of a mutation of the DNA intercalating residue of HincII, Q138F, are presented. Modeling has suggested that the DNA intercalation by Gln-138 results in DNA distortions potentially used by HincII in indirect readout of its cognate DNA, GTYRAC (Y = C or T, R = A or G) (Horton, N. C., Dorner, L. F., and Perona, J. J. (2002) Nat. Struct. Biol. 9, 42-47). Kinetic data presented here indicate that the mutation of glutamine 138 to phenylalanine (Q138F) results in a change in sequence specificity at the center two base pairs of the cognate recognition site. We show that the preference of HincII for cutting, but not binding, the three cognate sites differing in the center two base pairs has been altered by the mutation Q138F. Five new crystal structures are presented including Q138F HincII bound to GTTAAC and GTCGAC both with and without Ca2+ as well as the structure of wild type HincII bound to GTTAAC. The Q138F HincII/DNA structures show conformational changes in the protein, bound DNA, and at the protein-DNA interface, consistent with the formation of adaptive complexes. Analysis of these structures and the effect of Ca2+ binding on the protein-DNA interface illuminates the origin of the altered specificity by the mutation Q138F in the HincII enzyme.
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Affiliation(s)
- Hemant K Joshi
- Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA
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8
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Batey RT, Sagar MB, Doudna JA. Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle. J Mol Biol 2001; 307:229-46. [PMID: 11243816 DOI: 10.1006/jmbi.2000.4454] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The signal recognition particle (SRP) is a ribonucleoprotein complex responsible for targeting proteins to the endoplasmic reticulum in eukarya or to the inner membrane in prokarya. The crystal structure of the universally conserved RNA-protein core of the Escherichia coli SRP, refined here to 1.5 A resolution, revealed minor groove recognition of the 4.5 S RNA component by the M domain of the Ffh protein. Within the RNA, nucleotides comprising two phylogenetically conserved internal loops create a unique surface for protein recognition. To determine the energetic importance of conserved nucleotides for SRP assembly, we measured the affinity of the M domain for a series of RNA mutants. This analysis reveals how conserved nucleotides within the two internal loop motifs establish the architecture of the macromolecular interface and position essential functional groups for direct recognition by the protein.
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Affiliation(s)
- R T Batey
- Department of Molecular Biophysics and Biochemistry and Howard Hughes Medical Institute, Yale University, P.O. Box 208114, New Haven, CT 06520-8814, USA
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9
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Davies DR, Goryshin IY, Reznikoff WS, Rayment I. Three-dimensional structure of the Tn5 synaptic complex transposition intermediate. Science 2000; 289:77-85. [PMID: 10884228 DOI: 10.1126/science.289.5476.77] [Citation(s) in RCA: 298] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Genomic evolution has been profoundly influenced by DNA transposition, a process whereby defined DNA segments move freely about the genome. Transposition is mediated by transposases, and similar events are catalyzed by retroviral integrases such as human immunodeficiency virus-1 (HIV-1) integrase. Understanding how these proteins interact with DNA is central to understanding the molecular basis of transposition. We report the three-dimensional structure of prokaryotic Tn5 transposase complexed with Tn5 transposon end DNA determined to 2.3 angstrom resolution. The molecular assembly is dimeric, where each double-stranded DNA molecule is bound by both protein subunits, orienting the transposon ends into the active sites. This structure provides a molecular framework for understanding many aspects of transposition, including the binding of transposon end DNA by one subunit and cleavage by a second, cleavage of two strands of DNA by a single active site via a hairpin intermediate, and strand transfer into target DNA.
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Affiliation(s)
- D R Davies
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
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10
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Tan S, Hunziker Y, Pellegrini L, Richmond TJ. Crystallization of the yeast MATalpha2/MCM1/DNA ternary complex: general methods and principles for protein/DNA cocrystallization. J Mol Biol 2000; 297:947-59. [PMID: 10736229 DOI: 10.1006/jmbi.2000.3606] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We describe our efforts to crystallize binary MCM1/DNA and ternary MATalpha2/MCM1/DNA complexes, including the unsuccessful attempts to crystallize MCM1/DNA complexes and the successful design of DNA crystal packing that resulted in high-resolution crystals of the MATalpha2/MCM1/DNA complex. We detail general procedures useful for preparing protein/DNA cocrystals, including improved methods for producing and purifying DNA-binding proteins and DNA fragments, for purifying protein/DNA complexes, and for controlling pH conditions during crystallization. We also describe the rational design of DNA for protein/DNA cocrystallization attempts, based on our analysis of how straight and bent DNA with single base-pair overhangs can pack end-to-end in a crystal.
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MESH Headings
- Base Pairing/genetics
- Base Sequence
- Binding Sites
- Crystallization
- Crystallography, X-Ray
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Fungal/isolation & purification
- DNA, Fungal/metabolism
- DNA, Recombinant/genetics
- DNA-Binding Proteins/chemistry
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/isolation & purification
- DNA-Binding Proteins/metabolism
- Escherichia coli/genetics
- Fungal Proteins/chemistry
- Fungal Proteins/genetics
- Fungal Proteins/isolation & purification
- Fungal Proteins/metabolism
- Genes, Fungal/genetics
- Homeodomain Proteins/chemistry
- Homeodomain Proteins/genetics
- Homeodomain Proteins/isolation & purification
- Homeodomain Proteins/metabolism
- Hydrogen-Ion Concentration
- Minichromosome Maintenance 1 Protein
- Models, Molecular
- Molecular Weight
- Oligodeoxyribonucleotides/chemistry
- Oligodeoxyribonucleotides/genetics
- Oligodeoxyribonucleotides/isolation & purification
- Oligodeoxyribonucleotides/metabolism
- Operator Regions, Genetic/genetics
- Peptide Fragments/chemistry
- Peptide Fragments/genetics
- Peptide Fragments/metabolism
- Plasmids/genetics
- Protein Structure, Tertiary
- Receptors, Mating Factor
- Receptors, Peptide/genetics
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/isolation & purification
- Recombinant Proteins/metabolism
- Repressor Proteins/chemistry
- Repressor Proteins/genetics
- Repressor Proteins/isolation & purification
- Repressor Proteins/metabolism
- Saccharomyces cerevisiae/chemistry
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae Proteins
- Sepharose/analogs & derivatives
- Sepharose/metabolism
- Transcription Factors/chemistry
- Transcription Factors/genetics
- Transcription Factors/isolation & purification
- Transcription Factors/metabolism
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Affiliation(s)
- S Tan
- Institut für Molekularbiologie und Biophysik, ETH-Hönggerberg, ETH-Zürich, CH-8093, Switzerland
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11
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Kwong PD, Wyatt R, Desjardins E, Robinson J, Culp JS, Hellmig BD, Sweet RW, Sodroski J, Hendrickson WA. Probability analysis of variational crystallization and its application to gp120, the exterior envelope glycoprotein of type 1 human immunodeficiency virus (HIV-1). J Biol Chem 1999; 274:4115-23. [PMID: 9933605 DOI: 10.1074/jbc.274.7.4115] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The extensive glycosylation and conformational mobility of gp120, the envelope glycoprotein of type 1 human immunodeficiency virus (HIV-1), pose formidable barriers for crystallization. To surmount these difficulties, we used probability analysis to determine the most effective crystallization approach and derive equations which show that a strategy, which we term variational crystallization, substantially enhances the overall probability of crystallization for gp120. Variational crystallization focuses on protein modification as opposed to crystallization screening. Multiple variants of gp120 were analyzed with an iterative cycle involving a limited set of crystallization conditions and biochemical feedback on protease sensitivity, glycosylation status, and monoclonal antibody binding. Sources of likely conformational heterogeneity such as N-linked carbohydrates, flexible or mobile N and C termini, and variable internal loops were reduced or eliminated, and ligands such as CD4 and antigen-binding fragments (Fabs) of monoclonal antibodies were used to restrict conformational mobility as well as to alter the crystallization surface. Through successive cycles of manipulation involving 18 different variants, we succeeded in growing six different types of gp120 crystals. One of these, a ternary complex composed of gp120, its receptor CD4, and the Fab of the human neutralizing monoclonal antibody 17b, diffracts to a minimum Bragg spacing of at least 2.2 A and is suitable for structural analysis.
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Affiliation(s)
- P D Kwong
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
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12
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Albright RA, Matthews BW. Crystal structure of lambda-Cro bound to a consensus operator at 3.0 A resolution. J Mol Biol 1998; 280:137-51. [PMID: 9653037 DOI: 10.1006/jmbi.1998.1848] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The structure of the Cro protein from bacteriophage lambda in complex with a 19 base-pair DNA duplex that includes the 17 base-pair consensus operator has been determined at 3.0 A resolution. The structure confirms the large changes in the protein and DNA seen previously in a crystallographically distinct low-resolution structure of the complex and, for the first time, reveals the detailed interactions between the side-chains of the protein and the base-pairs of the operator. Relative to the crystal structure of the free protein, the subunits of Cro rotate 53 degrees with respect to each other on binding DNA. At the same time the DNA is bent by 40 degrees through the 19 base-pairs. The intersubunit connection includes a region within the protein core that is structurally reminiscent of the "ball and socket" motif seen in the immunoglobulins and T-cell receptors. The crystal structure of the Cro complex is consistent with virtually all available biochemical and related data. Some of the interactions between Cro and DNA proposed on the basis of model-building are now seen to be correct, but many are different. Tests of the original model by mutagenesis and biochemical analysis corrected some but not all of the errors. Within the limitations of the crystallographic resolution it appears that operator recognition is achieved almost entirely by direct hydrogen-bonding and van der Waals contacts between the protein and the exposed bases within the major groove of the DNA. The discrimination of Cro between the operators OR3 and OR1, which differ in sequence at just three positions, is inferred to result from a combination of small differences, both favorable and unfavorable. A van der Waals contact at one of the positions is of primary importance, while the other two provide smaller, indirect effects. Direct hydrogen bonding is not utilized in this distinction.
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Affiliation(s)
- R A Albright
- Institute of Molecular Biology Howard Hughes Medical Institute and Department of Physics, University of Oregon, Eugene, OR, 97403-1229, USA
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13
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Jacobson EM, Li P, Rosenfeld MG, Aggarwal AK. Crystallization and preliminary X-ray analysis of Pit-1 POU domain complexed to a 28 base pair DNA element. Proteins 1996; 24:263-5. [PMID: 8820493 DOI: 10.1002/(sici)1097-0134(199602)24:2<263::aid-prot14>3.0.co;2-l] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The POU domain, representing an approximately 150 amino acid conserved region, serves as the DNA-recognition domain for a large number of eukaryotic transcription factors. Bipartite in nature, the POU domain is comprised of a N-terminal POU-specific domain connected by a linker of variable length to a C-terminal homeodomain. We report here co-crystals of pituitary-specific factor Pit-1 POU domain bound as a dimer to a 28 bp DNA fragment. The crystals diffract to at least 2.3 angstroms in resolution and belong to space group P1 with unit cell dimensions of a = 42.5 angstroms, b = 50.1 angstroms, c = 55.8 angstroms, alpha = 76.7 degrees, beta = 79.3 degrees, and gamma = 67.2 degrees.
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Affiliation(s)
- E M Jacobson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York 10032, USA
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14
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Pio F, Ni CZ, Mitchell RS, Knight J, McKercher S, Klemsz M, Lombardo A, Maki RA, Ely KR. Co-crystallization of an ETS domain (PU.1) in complex with DNA. Engineering the length of both protein and oligonucleotide. J Biol Chem 1995; 270:24258-63. [PMID: 7592633 DOI: 10.1074/jbc.270.41.24258] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The PU.1 transcription factor is a member of the ets gene family of regulatory proteins. These molecules play a role in normal development and also have been implicated in malignant processes such as the development of erythroid leukemia. The Ets proteins share a conserved DNA-binding domain (the ETS domain) that recognizes a purine-rich sequence with the core sequence: 5'-C/AGGAA/T-3'. This domain binds to DNA as a monomer, unlike many other DNA-binding proteins. The ETS domain of the PU.1 transcription factor has been crystallized in complex with a 16-base pair oligonucleotide that contains the recognition sequence. The crystals formed in the space group C2 with a = 89.1, b = 101.9, c = 55.6 A, and beta = 111.2 degrees and diffract to at least 2.3 A. There are two complexes in the asymmetric unit. Production of large usable crystals was dependent on the length of both protein and DNA components, the use of oligonucleotides with unpaired A and T bases at the termini, and the presence of polyethylene glycol and zinc acetate in the crystallization solutions. This is the first ETS domain to be crystallized, and the strategy used to crystallize this complex may be useful for other members of the ets family.
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Affiliation(s)
- F Pio
- Cancer Research Center, La Jolla Cancer Research Foundation, California 92037, USA
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15
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Oubridge C, Ito N, Teo CH, Fearnley I, Nagai K. Crystallisation of RNA-protein complexes. II. The application of protein engineering for crystallisation of the U1A protein-RNA complex. J Mol Biol 1995; 249:409-23. [PMID: 7783201 DOI: 10.1006/jmbi.1995.0306] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The hairpin is one of the most commonly found structural motifs of RNA and is often a binding site for proteins. Crystallisation of U1A spliceosomal protein bound to a RNA hairpin, its natural binding site on U1snRNA, is described. RNA oligonucleotides were synthesised either chemically or by in vitro transcription using T7 RNA polymerase and purified to homogeneity by gel electrophoresis. Crystallisation trials with the wild-type protein sequence and RNA hairpins containing various stem sequences and overhanging nucleotides only resulted in a cubic crystal form which diffracted to 7-8 A resolution. A new crystal form was grown by using a protein variant containing mutations of two surface residues. The N-terminal sequence of the protein was also varied to reduce heterogeneity which was detected by protein mass spectrometry. A further crystallisation search using the double mutant protein and varying the RNA hairpins resulted in crystals diffracting to beyond 1.7 A. The methods and strategy described in this paper may be applicable to crystallisation of other RNA-protein complexes.
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Affiliation(s)
- C Oubridge
- MRC Laboratory of Molecular Biology, Cambridge, UK
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16
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Li T, Stark M, Johnson AD, Wolberger C. Crystallization and preliminary X-ray diffraction studies of an a1/alpha 2/DNA ternary complex. Proteins 1995; 21:161-4. [PMID: 7777491 DOI: 10.1002/prot.340210210] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Crystals have been obtained of a ternary complex containing the yeast a1/alpha 2 homeodomain heterodimer bound to a 21-base pair DNA site containing two 5' overhanging bases at each end. The crystals are grown from cobaltic hexamine and form in space group P6(1) or P6(5) with a = b = 133 A, c = 45.4 A. Crystals that are flash-frozen at -179 degrees C diffract to 2.7 A along the c-axis and to 2.4 A in perpendicular directions. The crystals contain one protein-DNA complex in the crystallographic asymmetric unit.
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Affiliation(s)
- T Li
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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17
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Ma PC, Rould MA, Weintraub H, Pabo CO. Crystal structure of MyoD bHLH domain-DNA complex: perspectives on DNA recognition and implications for transcriptional activation. Cell 1994; 77:451-9. [PMID: 8181063 DOI: 10.1016/0092-8674(94)90159-7] [Citation(s) in RCA: 373] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The crystal structure of a MyoD basic-helix-loop-helix (bHLH) domain-DNA complex has been solved and refined at 2.8 A resolution. This structure proves that bHLH and bHLH-leucine zipper (bHLH-ZIP) proteins are remarkably similar; it helps us understand subtle differences in binding preferences for these proteins; and it has surprising implications for our understanding of transcription. Specifically, Ala-114 and Thr-115, which are required for positive control in the myogenic proteins, are buried at the protein-DNA interface. These residues are not available for direct protein-protein contacts, but they may determine the conformation of Arg-111. Comparisons with Max suggest that the conformation of this arginine, which is different in the two structures, may play an important role in myogenic transcription.
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Affiliation(s)
- P C Ma
- Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge 02139
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18
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Abstract
The crystal structure of the lambda repressor-operator complex has been refined to an R-factor of 18.9% at 1.8 A resolution. This refinement, using data collected at low temperature, has revealed the structure of the N-terminal arm and shows that the interactions of repressor with the two halves of the pseudo-symmetric operator site are significantly different. The two halves of the complex are most similar near the outer edge of the operator site (in a region where the lambda and 434 repressors make similar contacts), but they become increasingly different toward the center of the operator. There are striking differences near the center of the site where it appears that the arm makes significant contacts to only one half of the DNA site. This suggested a new way of aligning the operator sites in phage lambda. The high resolution structure confirms many of the previously noted features of the complex, but also reveals a number of new protein-DNA contacts. It also gives a better view of the extensive H-bonding networks that couple contacts made by different residues and different regions of the protein, and reveals important new details about the helix-turn-helix (HTH) region, and the positions of many water molecules in the complex.
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Affiliation(s)
- L J Beamer
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205
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19
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Mehta P, Bussiere D, Hoffman D, Bastia D, White S. Crystallization and preliminary structural analysis of the replication terminator protein of Bacillus subtilis. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(19)37043-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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20
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Schultz SC, Shields GC, Steitz TA. Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science 1991; 253:1001-7. [PMID: 1653449 DOI: 10.1126/science.1653449] [Citation(s) in RCA: 870] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The 3 angstrom resolution crystal structure of the Escherichia coli catabolite gene activator protein (CAP) complexed with a 30-base pair DNA sequence shows that the DNA is bent by 90 degrees. This bend results almost entirely from two 40 degrees kinks that occur between TG/CA base pairs at positions 5 and 6 on each side of the dyad axis of the complex. DNA sequence discrimination by CAP derives both from sequence-dependent distortion of the DNA helix and from direct hydrogen-bonding interactions between three protein side chains and the exposed edges of three base pairs in the major groove of the DNA. The structure of this transcription factor--DNA complex provides insights into possible mechanisms of transcription activation.
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Affiliation(s)
- S C Schultz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
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21
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Affiliation(s)
- P S Freemont
- Protein Structure Laboratory, Imperial Cancer Research Fund, Lincoln's Inn Fields, London, U.K
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22
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Abstract
The crystal structure of phage 434 Cro protein in complex with a 20 base-pair DNA fragment has been determined to 2.5 A resolution. The DNA fragment contains the sequence of the OR1 operator site. The structure shows a bent conformation for the DNA, straighter at the center and more bent at the ends. The central base-pairs adopt conformations with significant deviations from coplanarity. The two molecules interact extensively along their common interface, both through hydrogen bonds and van der Waals interactions. The significance of these interactions for operator binding and recognition is discussed.
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Affiliation(s)
- A Mondragón
- Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, MA 02138
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23
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Wolberger C, Pabo CO, Vershon AK, Johnson AD. Crystallization and preliminary X-ray diffraction studies of a MAT alpha 2-DNA complex. J Mol Biol 1991; 217:11-3. [PMID: 1988673 DOI: 10.1016/0022-2836(91)90605-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Crystals have been obtained of the DNA-binding domain of the yeast MAT alpha 2 repressor bound to a 21 base-pair DNA site. The crystals are grown from polyethylene glycol and CaCl2 and form in space group P2(1) with a = 60.1 A, b = 39.4 A, c = 68.7 A and beta = 98 degrees. They diffract to 2.9 A resolution and contain one protein-DNA complex in the crystallographic asymmetric unit.
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Affiliation(s)
- C Wolberger
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205
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24
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25
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26
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Kissinger CR, Liu BS, Martin-Blanco E, Kornberg TB, Pabo CO. Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution: a framework for understanding homeodomain-DNA interactions. Cell 1990; 63:579-90. [PMID: 1977522 DOI: 10.1016/0092-8674(90)90453-l] [Citation(s) in RCA: 807] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The crystal structure of a complex containing the engrailed homeodomain and a duplex DNA site has been determined at 2.8 A resolution and refined to a crystallographic R factor of 24.4%. In this complex, two separate regions of the 61 amino acid polypeptide contact a TAAT subsite. An N-terminal arm fits into the minor groove, and the side chains of Arg-3 and Arg-5 make contacts near the 5' end of this "core consensus" binding site. An alpha helix fits into the major groove, and the side chains of IIe-47 and Asn-51 contact base pairs near the 3' end of the TAAT site. This "recognition helix" is part of a structurally conserved helix-turn-helix unit, but these helices are longer than the corresponding helices in the lambda repressor, and the relationship between the helix-turn-helix unit and the DNA is significantly different.
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Affiliation(s)
- C R Kissinger
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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27
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Liu B, Kissinger CR, Pabo CO. Crystallization and preliminary X-ray diffraction studies of the engrailed homeodomain and of an engrailed homeodomain/DNA complex. Biochem Biophys Res Commun 1990; 171:257-9. [PMID: 1975495 DOI: 10.1016/0006-291x(90)91385-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The homeodomain from the engrailed protein of Drosophila has been crystallized from ammonium phosphate at pH 6.8. The crystals form in space group P6(1)22 (or P6(5)22), with cell dimensions a = b = 44.8 A and c = 118.2 A. These crystals diffract to 1.8 A resolution. A complex containing the engrailed homeodomain and a duplex DNA site also has been crystallized. The cocrystals form in space group C2 with a = 131.2 A, b = 45.5 A, c = 72.9 A and beta = 119.0 degrees. These crystals diffract to 2.6 A resolution.
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Affiliation(s)
- B Liu
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205
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28
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Wang AHJ, Gao YG. Crystallization of oligonucleotides and their complexes with antitumor drugs. Methods 1990. [DOI: 10.1016/s1046-2023(05)80151-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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29
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30
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Steitz TA. Structural studies of protein-nucleic acid interaction: the sources of sequence-specific binding. Q Rev Biophys 1990; 23:205-80. [PMID: 2204954 DOI: 10.1017/s0033583500005552] [Citation(s) in RCA: 460] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Structural studies of DNA-binding proteins and their complexes with DNA have proceeded at an accelerating pace in recent years due to important technical advances in molecular genetics, DNA synthesis, protein crystallography and nuclear magnetic resonance. The last major review on this subject by Pabo & Sauer (1984) summarized the structural and functional studies of the three sequence-specific DNA-binding proteins whose crystal structures were then known, theE. colicatabolite gene activator protein (CAP) (McKay & Steitz, 1981; McKayet al.1982; Weber & Steitz, 1987), acrorepressor from phage λ (Andersonet al.1981), and the DNA-binding proteolytic fragment ofλcIrepressor protein (Pabo & Lewis, 1982) Although crystallographic studies of theE. coli lacrepressor protein were initiated as early as 1971 when it was the only regulatory protein available in sufficient quantities for structural studies (Steitzet al.1974), little was established about the structural aspects of DNA-binding proteins until the structure of CAP was determined in 1980 followed shortly thereafter by the structure ofλcrorepressor and subsequently that of the λ repressor fragment. There are now determined at high resolution the crystal structures of seven prokaryotic gene regulatory proteins or fragments [CAP,λcro,λcIrepressor fragment, 434 repressor fragment (Andersonet al.1987), 434crorepressor (Wolbergeret al.1988),E. coli trprepressor (Schevitzet al.1985),E. coli metrepressor (Raffertyet al.1989)],EcoRI restriction endonuclease (McClarinet al.1986), DNAse I (Suck & Ofner, 1986), the catalytic domain of γδ resolvase (Hatfullet al.1989) and two sequence-independent double-stranded DNA-binding proteins [the Klenow fragment ofE. coliDNA polymerase I (Olliset al.1985) and theE. coliHu protein (Tanakaet al., 1984)].
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Affiliation(s)
- T A Steitz
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University
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31
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Schultz SC, Shields GC, Steitz TA. Crystallization of Escherichia coli catabolite gene activator protein with its DNA binding site. The use of modular DNA. J Mol Biol 1990; 213:159-66. [PMID: 2160019 DOI: 10.1016/s0022-2836(05)80128-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
To obtain crystals of the Escherichia coli catabolite gene activator protein (CAP) complexed with its DNA-binding site, we have searched for crystallization conditions with 26 different DNA segments greater than or equal to 28 base-pairs in length that explore a variety of nucleotide sequences, lengths, and extended 5' or 3' termini. In addition to utilizing uninterrupted asymmetric lac site sequences, we devised a novel approach of synthesizing half-sites that allowed us to efficiently generate symmetric DNA segments with a wide variety of extended termini and lengths in the large size range (greater than or equal to 28 bp) required by this protein. We report three crystal forms that are suitable for X-ray analysis, one of which (crystal form III) gives measurable diffraction amplitudes to 3 A resolution. Additives such as calcium, n-octyl-beta-D-glucopyranoside and spermine produce modest improvements in the quality of diffraction from crystal form III. Adequate stabilization of crystal form III is unexpectedly complex, requiring a greater than tenfold reduction in the salt concentration followed by addition of 2-methyl-2,4-pentanediol and then an increase in the concentration of polyethylene glycol.
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Affiliation(s)
- S C Schultz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
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32
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lac repressor: crystallization of intact tetramer and its complexes with inducer and operator DNA. Proc Natl Acad Sci U S A 1990; 87:1870-3. [PMID: 2408042 PMCID: PMC53585 DOI: 10.1073/pnas.87.5.1870] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The intact lac repressor tetramer, which regulates expression of the lac operon in Escherichia coli, has been crystallized in the native form, with an inducer, and in a ternary complex with operator DNA and an anti-inducer. The crystals without DNA diffract to better than 3.5 A. They belong to the monoclinic space group C2 and have cell dimensions a = 164.7 A, b = 75.6 A, and c = 161.2 A, with alpha = gamma = 90 degrees and beta = 125.5 degrees. Cocrystals have been obtained with a number of different lac operator-related DNA fragments. The complex with a blunt-ended 16-base-pair strand yielded tetragonal bipyramids that diffract to 6.5 A. These protein-DNA cocrystals crack upon exposure to the gratuitous inducer isopropyl beta-D-thiogalactoside, suggesting a conformational change in the repressor-operator complex.
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33
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Sauer RT, Jordan SR, Pabo CO. Lambda repressor: a model system for understanding protein-DNA interactions and protein stability. ADVANCES IN PROTEIN CHEMISTRY 1990; 40:1-61. [PMID: 2195849 DOI: 10.1016/s0065-3233(08)60286-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- R T Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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34
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35
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36
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Aggarwal AK, Rodgers DW, Drottar M, Ptashne M, Harrison SC. Recognition of a DNA operator by the repressor of phage 434: a view at high resolution. Science 1988; 242:899-907. [PMID: 3187531 DOI: 10.1126/science.3187531] [Citation(s) in RCA: 440] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The repressors of temperate bacteriophages such as 434 and lambda control transcription by binding to a set of DNA operator sites. The different affinity of repressor for each of these sites ensures efficient regulation. High-resolution x-ray crystallography was used to study the DNA-binding domain of phage 434 repressor in complex with a synthetic DNA operator. The structure shows recognition of the operator by direct interactions with base pairs in the major groove, combined with the sequence-dependent ability of DNA to adopt the required conformation on binding repressor. In particular, a network of three-centered bifurcated hydrogen bonds among base pairs in the operator helps explain why 434 repressor prefers certain sites over others. These bonds, which stabilize the conformation of the bound DNA, can form only with certain sequences.
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Affiliation(s)
- A K Aggarwal
- Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, MA 02138
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37
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Jordan SR, Pabo CO. Structure of the lambda complex at 2.5 A resolution: details of the repressor-operator interactions. Science 1988; 242:893-9. [PMID: 3187530 DOI: 10.1126/science.3187530] [Citation(s) in RCA: 421] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The crystal structure of a complex containing the DNA-binding domain of lambda repressor and a lambda operator site was determined at 2.5 A resolution and refined to a crystallographic R factor of 24.2 percent. The complex is stabilized by an extensive network of hydrogen bonds between the protein and the sugar-phosphate backbone. Several side chains form hydrogen bonds with sites in the major groove, and hydrophobic contacts also contribute to the specificity of binding. The overall arrangement of the complex is quite similar to that predicted from earlier modeling studies, which fit the protein dimer against linear B-form DNA. However, the cocrystal structure reveals important side chain-side chain interactions that were not predicted from the modeling or from previous genetic and biochemical studies.
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Affiliation(s)
- S R Jordan
- Department of Biophysics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205
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38
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Stearman RS, Frankel AD, Freire E, Liu BS, Pabo CO. Combining thermostable mutations increases the stability of lambda repressor. Biochemistry 1988; 27:7571-4. [PMID: 3061460 DOI: 10.1021/bi00419a059] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We have combined three mutations previously shown to stabilize lambda repressor against thermal denaturation. Two of these mutations are in helix 3, where Gly-46 and Gly-48 have been replaced by alanines [Hecht, M. H., et al. (1986) Proteins: Struct., Funct., Genet. 1, 43-46]. The other mutation, which replaces Tyr-88 with cysteine, allows the protein to form an intersubunit disulfide bond [Sauer, R. T., et al. (1986) Biochemistry 25, 5992-5998]. Calorimetric measurements show that the two alanine substitutions stabilize repressor by about 8 degrees C, that the disulfide bond stabilizes repressor by about 8 degrees C, and that the triple mutant is 16 degrees C more stable than wild-type repressor.
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Affiliation(s)
- R S Stearman
- Department of Biophysics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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39
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Abstract
Under phoA promoter control, TaqI endonuclease was overproduced to 5% of Escherichia coli cellular proteins. This was achieved by fusing the endonuclease gene to the first four codons of the alkaline phosphatase signal sequence. For maximal overproduction (30% of cellular proteins), a putative 14-bp hairpin within the endonuclease coding sequence was replaced with degenerate codons. In addition, TaqI methylase was required to protect host DNA. The endonuclease was purified in sufficient amounts for crystallization.
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Affiliation(s)
- F Barany
- Department of Microbiology, Hearst Microbiology Research Center, Cornell University Medical College, New York, NY 10021
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40
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Abstract
High resolution images of proteins bound to DNA can be achieved through the use of a simple inorganic chemical system that produces the hydroxyl radical.
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Affiliation(s)
- T D Tullius
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218
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41
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Rafferty JB, Phillips SE, Rojas C, Boulot G, Saint-Girons I, Guillou Y, Cohen GN. Crystallization of the met repressor from Escherichia coli. J Mol Biol 1988; 200:217-9. [PMID: 3288759 DOI: 10.1016/0022-2836(88)90348-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The met repressor from Escherichia coli has been crystallized in space group P21, with unit cell dimensions a = 35.6 A, b = 62.6 A, c = 44.5 A, beta = 102.4 degrees and one aporepressor dimer per asymmetric unit. Preliminary X-ray diffraction photographs show measurable intensities to beyond 1.5 A resolution, and the crystal form is ideally suited to high-resolution crystallographic analysis (1 A = 0.1 nm).
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Affiliation(s)
- J B Rafferty
- Astbury Department of Biophysics, University of Leeds, U.K
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42
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Joachimiak A, Marmorstein R, Schevitz R, Mandecki W, Fox J, Sigler P. Crystals of the trp repressor-operator complex suitable for X-ray diffraction analysis. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)61284-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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43
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Tullius TD, Dombroski BA, Churchill ME, Kam L. Hydroxyl radical footprinting: a high-resolution method for mapping protein-DNA contacts. Methods Enzymol 1987; 155:537-58. [PMID: 2828876 DOI: 10.1016/0076-6879(87)55035-2] [Citation(s) in RCA: 240] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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44
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Abstract
We use a new gel electrophoretic analysis to map the thermodynamically defined DNA binding domain of Escherichia coli CAP protein in the lac promoter. Strong binding interactions span a 28-30 bp duplex DNA region, substantially larger than that found for typical repressors. Sequence changes outside the central 28 bp of the binding site are found to affect the electrophoretically observed extent of bending. We also report a study of the DNA bending induced at a symmetrized CAP binding site, compared with the wild-type site; binding and bending are stronger at the upstream than at the downstream half of the wild-type site. Bends of the estimated 90 degrees - 180 degrees magnitude could play a vital regulatory role by producing tertiary structure in a local DNA domain, and by storing elastic energy for subsequent use in transcription or replication.
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45
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Sauer RT, Hehir K, Stearman RS, Weiss MA, Jeitler-Nilsson A, Suchanek EG, Pabo CO. An engineered intersubunit disulfide enhances the stability and DNA binding of the N-terminal domain of lambda repressor. Biochemistry 1986; 25:5992-8. [PMID: 3539184 DOI: 10.1021/bi00368a024] [Citation(s) in RCA: 118] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Site-directed mutagenesis has been used to replace Tyr-88 at the dimer interface of the N-terminal domain of lambda repressor with cysteine. Computer model building had suggested that this substitution would allow formation of an intersubunit disulfide without disruption of the dimer structure [Pabo, C. O., & Suchanek, E. G. (1986) Biochemistry (preceding paper in this issue)]. We find that the Cys-88 protein forms a disulfide-bonded dimer that is very stable to reduction by dithiothreitol and has increased operator DNA binding activity. The covalent Cys88-Cys88' dimer is also considerably more stable than the wild-type protein to thermal denaturation or urea denaturation. As a control, Tyr-85 was replaced with cysteine. A Cys85-Cys85' disulfide cannot form without disrupting the wild-type structure, and we find that this disulfide bond reduces the DNA binding activity and stability of the N-terminal domain.
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46
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Tullius TD, Dombroski BA. Hydroxyl radical "footprinting": high-resolution information about DNA-protein contacts and application to lambda repressor and Cro protein. Proc Natl Acad Sci U S A 1986; 83:5469-73. [PMID: 3090544 PMCID: PMC386308 DOI: 10.1073/pnas.83.15.5469] [Citation(s) in RCA: 386] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A method has been developed for making "footprints" of proteins bound to DNA. The hydroxyl radical, generated by reduction of hydrogen peroxide by iron(II), is the reagent used to cut the DNA. Hydroxyl radical breaks the backbone of DNA with almost no sequence dependence, so all backbone positions may be monitored for contact with protein. In addition to defining the DNA sequence in contact with the protein, hydroxyl radical footprints embody structural information about the DNA-protein complex. For example, hydroxyl radical footprints of the bacteriophage lambda repressor and Cro protein show directly that these proteins are bound to only one side of the DNA helix. Additional contacts of lambda repressor and Cro protein with DNA, not observed by other chemical footprinting methods, are revealed by hydroxyl radical footprinting.
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