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Panneerselvam S, Shehzad A, Mueller-Dieckmann J, Wilmanns M, Bocola M, Davari MD, Schwaneberg U. Crystallographic insights into a cobalt (III) sepulchrate based alternative cofactor system of P450 BM3 monooxygenase. Biochim Biophys Acta Proteins Proteom 2017; 1866:134-140. [PMID: 28739446 DOI: 10.1016/j.bbapap.2017.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/15/2017] [Accepted: 07/18/2017] [Indexed: 12/26/2022]
Abstract
P450 BM3 is a multi-domain heme-containing soluble bacterial monooxygenase. P450 BM3 and variants are known to oxidize structurally diverse substrates. Crystal structures of individual domains of P450 BM3 are available. However, the spatial organization of the full-length protein is unknown. In this study, crystal structures of the P450 BM3 M7 heme domain variant with and without cobalt (III) sepulchrate are reported. Cobalt (III) sepulchrate acts as an electron shuttle in an alternative cofactor system employing zinc dust as the electron source. The crystal structure shows a binding site for the mediator cobalt (III) sepulchrate at the entrance of the substrate access channel. The mediator occupies an unusual position which is far from the active site and distinct from the binding of the natural redox partner (FAD/NADPH binding domain).
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Affiliation(s)
| | - Aamir Shehzad
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany; Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, Pakistan
| | | | - Matthias Wilmanns
- European Molecular Biology Laboratory-Hamburg, c/o DESY, Hamburg, Germany
| | - Marco Bocola
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Mehdi D Davari
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany; DWI-Leibniz Institut für Interaktive Materialien, Forckenbeckstraße 50, 52056 Aachen, Germany.
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2
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Kundu P, Biswas R, Mukherjee S, Reinhard L, Dutta A, Mueller-Dieckmann J, Weiss MS, Pal NK, Das AK. Structure-based Epitope Mapping of Mycobacterium tuberculosis Secretary Antigen MTC28. J Biol Chem 2016; 291:13943-13954. [PMID: 27189947 DOI: 10.1074/jbc.m116.726422] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Indexed: 11/06/2022] Open
Abstract
Secretary proteins of Mycobacterium tuberculosis are key players of the mycobacterial infection pathway. MTC28 is a 28-kDa proline-rich secretary antigen of Mycobacterium tuberculosis and is only conserved in pathogenic strains of mycobacteria. Here we report the crystal structure of MTC28 at 2.8- and 2.15-Å resolutions for the structure-based epitope design. MTC28 shares a "mog1p"-fold consisting of seven antiparallel β strands stacked between α helices. Five probable epitopes have been located on a solvent-accessible flexible region by computational analysis of the structure of MTC28. Simultaneously, the protein is digested with trypsin and the resulting fragments are purified by HPLC. Such 10 purified peptide fragments are screened against sera from patients infected with pulmonary tuberculosis (PTB). Two of these 10 fragments, namely (127)ALDITLPMPPR(137) and (138)WTQVPDPNVPDAFVVIADR(156),are found to be major immunogenic epitopes that are localized on the outer surface of the protein molecule and are part of a single continuous epitope that have been predicted in silico Mutagenesis and antibody inhibition studies are in accordance with the results obtained from epitope mapping.
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Affiliation(s)
- Prasun Kundu
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Rupam Biswas
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Somnath Mukherjee
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Linda Reinhard
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden,; Röntgen-Ångström-Cluster, Karolinska Institutet Outstation, Centre for Structural Systems Biology, c/o DESY, D-22607 Hamburg, Germany,; European Molecular Biology Laboratory, Hamburg Unit, 22603 Hamburg, Germany
| | - Anirudha Dutta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Jochen Mueller-Dieckmann
- Abteilung für Mikrobiologie und Biotechnologie, Biozentrum Klein Flottbek, Universität Hamburg, Ohnhorststraße18, 22609 Hamburg, Germany
| | - Manfred S Weiss
- Macromolecular Crystallography (HZB-MX), Helmholtz-Zentrum Berlin für Materialien und Energie, D-12489 Berlin, Germany
| | - Nishit Kumar Pal
- Nil Ratan Sirkar Medical College and Hospital,138 AJC Bose Road, Sealdah, Raja Bazar, Kolkata, West Bengal 700014, India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal 721302, India,.
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Meyer NH, Mayerhofer H, Tripsianes K, Blindow S, Barths D, Mewes A, Weimar T, Köhli T, Bade S, Madl T, Frey A, Haas H, Mueller-Dieckmann J, Sattler M, Schramm G. A Crystallin Fold in the Interleukin-4-inducing Principle of Schistosoma mansoni Eggs (IPSE/α-1) Mediates IgE Binding for Antigen-independent Basophil Activation. J Biol Chem 2015; 290:22111-26. [PMID: 26163514 DOI: 10.1074/jbc.m115.675066] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Indexed: 11/06/2022] Open
Abstract
The IL-4-inducing principle from Schistosoma mansoni eggs (IPSE/α-1), the major secretory product of eggs from the parasitic worm S. mansoni, efficiently triggers basophils to release the immunomodulatory key cytokine interleukin-4. Activation by IPSE/α-1 requires the presence of IgE on the basophils, but the detailed molecular mechanism underlying activation is unknown. NMR and crystallographic analysis of IPSEΔNLS, a monomeric IPSE/α-1 mutant, revealed that IPSE/α-1 is a new member of the βγ-crystallin superfamily. We demonstrate that this molecule is a general immunoglobulin-binding factor with highest affinity for IgE. NMR binding studies of IPSEΔNLS with the 180-kDa molecule IgE identified a large positively charged binding surface that includes a flexible loop, which is unique to the IPSE/α-1 crystallin fold. Mutational analysis of amino acids in the binding interface showed that residues contributing to IgE binding are important for IgE-dependent activation of basophils. As IPSE/α-1 is unable to cross-link IgE, we propose that this molecule, by taking advantage of its unique IgE-binding crystallin fold, activates basophils by a novel, cross-linking-independent mechanism.
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Affiliation(s)
- N Helge Meyer
- From the Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, the Munich Center for Integrated Protein Science and Biomolecular NMR, Department of Chemie, Technische Universität München, 85747 Garching
| | | | - Konstantinos Tripsianes
- From the Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, the Munich Center for Integrated Protein Science and Biomolecular NMR, Department of Chemie, Technische Universität München, 85747 Garching
| | | | | | | | - Thomas Weimar
- the Institute of Chemistry, University of Lübeck, 23562 Lübeck, Germany
| | - Thies Köhli
- the Institute of Chemistry, University of Lübeck, 23562 Lübeck, Germany
| | - Steffen Bade
- Mucosal Immunology and Diagnostic Section, Research Center Borstel, 23845 Borstel, and
| | - Tobias Madl
- From the Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, the Munich Center for Integrated Protein Science and Biomolecular NMR, Department of Chemie, Technische Universität München, 85747 Garching
| | - Andreas Frey
- Mucosal Immunology and Diagnostic Section, Research Center Borstel, 23845 Borstel, and
| | | | | | - Michael Sattler
- From the Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, the Munich Center for Integrated Protein Science and Biomolecular NMR, Department of Chemie, Technische Universität München, 85747 Garching,
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Mayerhofer H, Panneerselvam S, Kaljunen H, Tuukkanen A, Mertens HDT, Mueller-Dieckmann J. Structural model of the cytosolic domain of the plant ethylene receptor 1 (ETR1). J Biol Chem 2015; 290:2644-58. [PMID: 25451923 PMCID: PMC4317023 DOI: 10.1074/jbc.m114.587667] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 11/24/2014] [Indexed: 11/06/2022] Open
Abstract
Ethylene initiates important aspects of plant growth and development through disulfide-linked receptor dimers located in the endoplasmic reticulum. The receptors feature a small transmembrane, ethylene binding domain followed by a large cytosolic domain, which serves as a scaffold for the assembly of large molecular weight complexes of different ethylene receptors and other cellular participants of the ethylene signaling pathway. Here we report the crystallographic structures of the ethylene receptor 1 (ETR1) catalytic ATP-binding and the ethylene response sensor 1 dimerization histidine phosphotransfer (DHp) domains and the solution structure of the entire cytosolic domain of ETR1, all from Arabidopsis thaliana. The isolated dimeric ethylene response sensor 1 DHp domain is asymmetric, the result of different helical bending angles close to the conserved His residue. The structures of the catalytic ATP-binding, DHp, and receiver domains of ethylene receptors and of a homologous, but dissimilar, GAF domain were refined against experimental small angle x-ray scattering data, leading to a structural model of the entire cytosolic domain of the ethylene receptor 1. The model illustrates that the cytosolic domain is shaped like a dumbbell and that the receiver domain is flexible and assumes a position different from those observed in prokaryotic histidine kinases. Furthermore the cytosolic domain of ETR1 plays a key role, interacting with all other receptors and several participants of the ethylene signaling pathway. Our model, therefore, provides the first step toward a detailed understanding of the molecular mechanics of this important signal transduction process in plants.
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Affiliation(s)
- Hubert Mayerhofer
- From the European Molecular Biology Laboratory (EMBL) Hamburg, c/o Deutsches Elektronen-Synchrotron (DESY), Building 25A, Notkestrasse 85, 22603 Hamburg, Germany
| | - Saravanan Panneerselvam
- From the European Molecular Biology Laboratory (EMBL) Hamburg, c/o Deutsches Elektronen-Synchrotron (DESY), Building 25A, Notkestrasse 85, 22603 Hamburg, Germany
| | - Heidi Kaljunen
- From the European Molecular Biology Laboratory (EMBL) Hamburg, c/o Deutsches Elektronen-Synchrotron (DESY), Building 25A, Notkestrasse 85, 22603 Hamburg, Germany
| | - Anne Tuukkanen
- From the European Molecular Biology Laboratory (EMBL) Hamburg, c/o Deutsches Elektronen-Synchrotron (DESY), Building 25A, Notkestrasse 85, 22603 Hamburg, Germany
| | - Haydyn D T Mertens
- From the European Molecular Biology Laboratory (EMBL) Hamburg, c/o Deutsches Elektronen-Synchrotron (DESY), Building 25A, Notkestrasse 85, 22603 Hamburg, Germany
| | - Jochen Mueller-Dieckmann
- From the European Molecular Biology Laboratory (EMBL) Hamburg, c/o Deutsches Elektronen-Synchrotron (DESY), Building 25A, Notkestrasse 85, 22603 Hamburg, Germany
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5
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Kaljunen H, Chow J, Streit WR, Mueller-Dieckmann J. Cloning, expression, purification and preliminary X-ray analysis of EstN2, a novel archaeal α/β-hydrolase from Candidatus Nitrososphaera gargensis. Acta Crystallogr F Struct Biol Commun 2014; 70:1394-7. [PMID: 25286947 PMCID: PMC4188087 DOI: 10.1107/s2053230x14018482] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 08/13/2014] [Indexed: 11/10/2022] Open
Abstract
EstN2 is a novel α/β-hydrolase originating from the ammonia-oxidizing thaumarchaeon Candidatus Nitrososphaera gargensis. The genome of the organism was sequenced and genes conferring putative lipolytic activity were amplified and cloned into Escherichia coli as a heterologous host. Through function-based screening, esterase and lipase activity was detected. A recombinant enzyme designated EstN2 was successfully expressed, purified and crystallized. The crystals belonged to space group I2, with one molecule per asymmetric unit, and diffracted X-rays to 1.5 Å resolution.
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Affiliation(s)
- Heidi Kaljunen
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Jennifer Chow
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststrasse 18, 22609 Hamburg, Germany
| | - Wolfgang R. Streit
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststrasse 18, 22609 Hamburg, Germany
| | - Jochen Mueller-Dieckmann
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststrasse 18, 22609 Hamburg, Germany
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Panneerselvam S, Shehzad A, Mueller-Dieckmann J, Schwaneberg U. Structural insights of mediated electron transfer by P450 BM3 monooxygenase. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314088305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
P450 BM3 is a 119-kDa water-soluble heme monooxygenase originating from Bacillus megaterium. P450 BM3 and variants are known to oxidize structurally diverse substrates. However, the requirement for the natural cofactor, NADPH, limits cell-free applications of P450 BM3 in drug synthesis, fuelling efforts to establish alternative cofactor system. Hence, P450 BM3 variants have been generated which circumvent the requirement for NADPH, and enabled P450 BM3 to be driven with alternative electron sources. In this study, crystal structures of the P450 BM3 M7 heme domain variant (F87A, V281G, M354S) with and without cobalt (III) sepulchrate are reported. Cobalt (III) sepulchrate acts as an electron shuttle in an alternative cofactor system employing zinc dust as the electron source. The crystal structure shows a binding site for the mediator cobalt (III) sepulchrate at the entrance of the substrate access channel. The mediator occupies a position which is far from the active site and distinct from the binding of the natural redox partner (FAD/NADPH binding domain). The unusual binding position suggests that the mediator shuttles electrons to the heme-centre through new routes. Electron transfer could occur by a `through-protein' or a `substrate-relayed' pathway. The latter seems more plausible since it would ensure efficient use of electrons only in the presence of a substrate in the active site. The structural evidence also indicates that the use of a positively charged mediator is important to effectively reduce the catalytic heme domain. Understanding the mediator-monooxygenase interface opens new avenues for tailoring P450 BM3 to match application demands. Structural and molecular understanding of mediated electron transfer enables a paradigm shift from a mediator acceptance screening to a rational mediator design which considers only stability and electron transfer performance parameters.
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Kaljunen H, Panneerselvam S, Mueller-Dieckmann J. Cloning, overexpression, purification and preliminary X-ray analysis of the protein kinase domain of enhanced disease resistance 1 (EDR1) from Arabidopsis thaliana. Acta Crystallogr F Struct Biol Commun 2014; 70:959-62. [PMID: 25005098 PMCID: PMC4089541 DOI: 10.1107/s2053230x14011844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 05/21/2014] [Indexed: 11/10/2022] Open
Abstract
Enhanced disease resistance 1 is a member of the Raf-like mitogen-activated protein kinase kinase kinase (MAPKKK) family that negatively regulates disease resistance, ethylene-induced senescence and programmed cell death in response to both abiotic and biotic stresses. A catalytically inactive form of the EDR1 kinase domain was successfully cloned, expressed, purified and crystallized. Crystallization was conducted in the presence of the ATP analogue AMP-PNP. The crystals belonged to space group P3221 and contained two molecules in the asymmetric unit. The crystals diffracted X-rays to 2.55 Å resolution.
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Abstract
Crystallization remains the bottleneck in the crystallographic process leading from a gene to a three-dimensional model of the encoded protein or RNA. Automation of the individual steps of a crystallization experiment, from the preparation of crystallization cocktails for initial or optimization screens to the imaging of the experiments, has been the response to address this issue. Today, large high-throughput crystallization facilities, many of them open to the general user community, are capable of setting up thousands of crystallization trials per day. It is thus possible to test multiple constructs of each target for their ability to form crystals on a production-line basis. This has improved success rates and made crystallization much more convenient. High-throughput crystallization, however, cannot relieve users of the task of producing samples of high quality. Moreover, the time gained from eliminating manual preparations must now be invested in the careful evaluation of the increased number of experiments. The latter requires a sophisticated data and laboratory information-management system. A review of the current state of automation at the individual steps of crystallization with specific attention to the automation of optimization is given.
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Affiliation(s)
- Patrick Shaw Stewart
- Douglas Instruments Ltd, Douglas House, East Garston, Hungerford, Berkshire RG17 7HD, England
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9
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Pietrzyk AJ, Bujacz A, Mueller-Dieckmann J, Łochynska M, Jaskolski M, Bujacz G. Crystallographic identification of an unexpected protein complex in silkworm haemolymph. Acta Crystallogr D Biol Crystallogr 2013; 69:2353-64. [PMID: 24311577 DOI: 10.1107/s0907444913021823] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 08/05/2013] [Indexed: 11/10/2022]
Abstract
The first crystal structure of a complex formed by two storage proteins, SP2 and SP3, isolated from their natural source, mulberry silkworm (Bombyx mori L.) haemolymph, has been determined. The structure was solved by molecular replacement using arylphorin, a protein rich in aromatic amino-acid residues, from oak silkworm as the initial model. The quality of the electron-density maps obtained from the X-ray diffraction experiment allowed the authors to detect that the investigated crystal structure was composed of two different arylphorins: SP2 and SP3. This discovery was confirmed by N-terminal sequencing. SP2 has been extensively studied previously, whereas only a few reports on SP3 are available. However, to date no structural studies have been reported for these proteins. These studies revealed that SP2 and SP3 exist in the silkworm body as a heterohexamer formed by one SP2 trimer and one SP3 trimer. The overall fold, consisting of three haemocyanin-like subdomains, of SP2 and SP3 is similar. Both proteins contain a conserved N-glycosylation motif in their structures.
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Affiliation(s)
- Agnieszka J Pietrzyk
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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Panneerselvam S, Kaljunen H, Mueller-Dieckmann J. Cloning, overexpression, purification and preliminary X-ray analysis of the catalytic domain of the ethylene receptor ETR1 from Arabidopsis thaliana. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1307-1309. [PMID: 24192376 PMCID: PMC3818060 DOI: 10.1107/s174430911302842x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 10/16/2013] [Indexed: 06/02/2023]
Abstract
Ethylene is a gaseous plant hormone which controls many aspects of plant growth and development. It is perceived by membrane-bound receptors with a similarity to bacterial two-component systems. The catalytic and ATP-binding domain of the histidine kinase domain of ETR1 from Arabidopsis thaliana has been cloned, overexpressed and crystallized. The protein was crystallized together with various nucleotides. Crystals obtained in the presence of ADP belonged to space group I222 or I2(1)2(1)2(1) with one molecule per asymmetric unit. They diffracted X-ray radiation to beyond 1.85 Å resolution.
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Affiliation(s)
| | - Heidi Kaljunen
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
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Mayerhofer H, Mueller-Dieckmann J. Cloning, expression, purification and preliminary X-ray analysis of the dimerization domain of ethylene response sensor 1 (ERS1) from Arabidopsis thaliana. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1029-32. [PMID: 23989156 PMCID: PMC3758156 DOI: 10.1107/s1744309113021751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 08/04/2013] [Indexed: 11/10/2022]
Abstract
Ethylene signalling is initiated by a group of membrane-bound receptors with similarity to two-component systems. ERS1 belongs, together with ETR1, to subfamily 1, which plays a predominant role in ethylene signalling. The dimerization domain of ERS1 was crystallized in space groups C222(1) and P2(1)2(1)2, with two and four molecules per asymmetric unit, respectively. The crystals diffracted X-ray radiation to 1.9 Å resolution.
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Affiliation(s)
- Hubert Mayerhofer
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
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Pietrzyk AJ, Bujacz A, Mueller-Dieckmann J, Lochynska M, Jaskolski M, Bujacz G. Two crystal structures of Bombyx mori lipoprotein 3 - structural characterization of a new 30-kDa lipoprotein family member. PLoS One 2013; 8:e61303. [PMID: 23613829 PMCID: PMC3628942 DOI: 10.1371/journal.pone.0061303] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 03/07/2013] [Indexed: 11/19/2022] Open
Abstract
The 30-kDa family of lipoproteins from insect hemolymph has been the focus of a number of studies over the last few years. Recently, four crystal structures of Bombyx mori lipoprotein 7 have been determined. Here we report two crystal structures of another member of the 30-kDa lipoprotein family, Bombyx mori lipoprotein 3 (Bmlp3). The protein was isolated from its natural source, mulberry silkworm hemolymph. It crystallized in two different crystal forms, Bmlp3-p21 (space group P21) and Bmlp3-c2 (space group C2). The crystal structures were solved by molecular replacement using the coordinates of Bmlp7 as a starting model. The crystals of Bmlp3-p21 diffracted X-rays to 2.4 Å resolution and of Bmlp3-c2 to 2.1 Å resolution. Bmlp3 has an overall fold characteristic of 30-kDa lipoproteins, with a VHS-type N-terminal domain and β-trefoil C-terminal domain. Structural comparison of Bmlp3 and Bmlp7 shows that the loops present in the C-terminal domain are flexible and participate in dimer formation. Additionally, new putative binding sites of Bmlp3 have been analyzed in detail and the electrostatic potential of the protein surface at physiological pH 7.4 conditions has been calculated. The results of these calculations are the starting point for an explanation of the recently reported cell-penetrating properties of the 30-kDa lipoproteins.
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Affiliation(s)
- Agnieszka J. Pietrzyk
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Anna Bujacz
- Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
| | | | | | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Grzegorz Bujacz
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
- * E-mail:
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Reinhard L, Mayerhofer H, Geerlof A, Mueller-Dieckmann J, Weiss MS. Optimization of protein buffer cocktails using Thermofluor. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:209-14. [PMID: 23385769 PMCID: PMC3564630 DOI: 10.1107/s1744309112051858] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 12/25/2012] [Indexed: 11/10/2022]
Abstract
The stability and homogeneity of a protein sample is strongly influenced by the composition of the buffer that the protein is in. A quick and easy approach to identify a buffer composition which increases the stability and possibly the conformational homogeneity of a protein sample is the fluorescence-based thermal-shift assay (Thermofluor). Here, a novel 96-condition screen for Thermofluor experiments is presented which consists of buffer and additive parts. The buffer screen comprises 23 different buffers and the additive screen includes small-molecule additives such as salts and nucleotide analogues. The utilization of small-molecule components which increase the thermal stability of a protein sample frequently results in a protein preparation of higher quality and quantity and ultimately also increases the chances of the protein crystallizing.
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Affiliation(s)
- Linda Reinhard
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
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14
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Shehzad A, Panneerselvam S, Linow M, Bocola M, Roccatano D, Mueller-Dieckmann J, Wilmanns M, Schwaneberg U. P450 BM3 crystal structures reveal the role of the charged surface residue Lys/Arg184 in inversion of enantioselective styrene epoxidation. Chem Commun (Camb) 2013; 49:4694-6. [DOI: 10.1039/c3cc39076d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Chow J, Kovacic F, Dall Antonia Y, Krauss U, Fersini F, Schmeisser C, Lauinger B, Bongen P, Pietruszka J, Schmidt M, Menyes I, Bornscheuer UT, Eckstein M, Thum O, Liese A, Mueller-Dieckmann J, Jaeger KE, Streit WR. The metagenome-derived enzymes LipS and LipT increase the diversity of known lipases. PLoS One 2012; 7:e47665. [PMID: 23112831 PMCID: PMC3480424 DOI: 10.1371/journal.pone.0047665] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 09/13/2012] [Indexed: 11/18/2022] Open
Abstract
Triacylglycerol lipases (EC 3.1.1.3) catalyze both hydrolysis and synthesis reactions with a broad spectrum of substrates rendering them especially suitable for many biotechnological applications. Most lipases used today originate from mesophilic organisms and are susceptible to thermal denaturation whereas only few possess high thermotolerance. Here, we report on the identification and characterization of two novel thermostable bacterial lipases identified by functional metagenomic screenings. Metagenomic libraries were constructed from enrichment cultures maintained at 65 to 75 °C and screened resulting in the identification of initially 10 clones with lipolytic activities. Subsequently, two ORFs were identified encoding lipases, LipS and LipT. Comparative sequence analyses suggested that both enzymes are members of novel lipase families. LipS is a 30.2 kDa protein and revealed a half-life of 48 h at 70 °C. The lipT gene encoded for a multimeric enzyme with a half-life of 3 h at 70 °C. LipS had an optimum temperature at 70 °C and LipT at 75 °C. Both enzymes catalyzed hydrolysis of long-chain (C(12) and C(14)) fatty acid esters and additionally hydrolyzed a number of industry-relevant substrates. LipS was highly specific for (R)-ibuprofen-phenyl ester with an enantiomeric excess (ee) of 99%. Furthermore, LipS was able to synthesize 1-propyl laurate and 1-tetradecyl myristate at 70 °C with rates similar to those of the lipase CalB from Candida antarctica. LipS represents the first example of a thermostable metagenome-derived lipase with significant synthesis activities. Its X-ray structure was solved with a resolution of 1.99 Å revealing an unusually compact lid structure.
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Affiliation(s)
- Jennifer Chow
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Filip Kovacic
- Institute of Molecular Enzyme Technology, Heinrich Heine University Duesseldorf, Research Center Juelich, Juelich, Germany
| | - Yuliya Dall Antonia
- European Molecular Biology Laboratory (EMBL) Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Ulrich Krauss
- Institute of Molecular Enzyme Technology, Heinrich Heine University Duesseldorf, Research Center Juelich, Juelich, Germany
| | - Francesco Fersini
- European Molecular Biology Laboratory (EMBL) Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Christel Schmeisser
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
| | - Benjamin Lauinger
- Institute of Bioorganic Chemistry, Heinrich Heine University Duesseldorf, Research Center Juelich, Juelich, Germany
| | - Patrick Bongen
- Institute of Bioorganic Chemistry, Heinrich Heine University Duesseldorf, Research Center Juelich, Juelich, Germany
| | - Joerg Pietruszka
- Institute of Bioorganic Chemistry, Heinrich Heine University Duesseldorf, Research Center Juelich, Juelich, Germany
| | - Marlen Schmidt
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Greifswald, Germany
| | - Ina Menyes
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Greifswald, Germany
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Greifswald, Germany
| | - Marrit Eckstein
- Bioprocess Development Consumer Specialties and Biocatalysis Biotechnology, Evonik Industries AG, Essen, Germany
| | - Oliver Thum
- Bioprocess Development Consumer Specialties and Biocatalysis Biotechnology, Evonik Industries AG, Essen, Germany
| | - Andreas Liese
- Institute of Technical Biocatalysis, Hamburg University of Technology, Hamburg, Germany
| | - Jochen Mueller-Dieckmann
- European Molecular Biology Laboratory (EMBL) Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Duesseldorf, Research Center Juelich, Juelich, Germany
| | - Wolfgang R. Streit
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Hamburg, Germany
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Reinhard L, Mueller-Dieckmann J, Weiss MS. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of succinyl-diaminopimelate desuccinylase (Rv1202, DapE) from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1089-93. [PMID: 22949202 PMCID: PMC3433205 DOI: 10.1107/s174430911203062x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Accepted: 07/04/2012] [Indexed: 11/10/2022]
Abstract
Succinyl-diaminopimelate desuccinylase from Mycobacterium tuberculosis (DapE, Rv1202) has been cloned, heterologously expressed in Escherichia coli and purified using standard chromatographic techniques. Diffraction-quality crystals were obtained at acidic pH from ammonium sulfate and PEG and diffraction data were collected from two crystals to resolutions of 2.40 and 2.58 Å, respectively. The crystals belonged to the monoclinic space group P2(1), with unit-cell parameters a = 79.7, b = 76.0, c = 82.9 Å, β = 119°. The most probable content of the asymmetric unit was two molecules of DapE, which would correspond to a solvent content of 56%. Both examined crystals turned out to be pseudo-merohedrally twinned, with twin operator -h, -k, h + l and twin fractions of approximately 0.46 and 0.16, respectively.
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Affiliation(s)
- Linda Reinhard
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany.
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17
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Pietrzyk AJ, Panjikar S, Bujacz A, Mueller-Dieckmann J, Lochynska M, Jaskolski M, Bujacz G. High-resolution structure of Bombyx mori lipoprotein 7: crystallographic determination of the identity of the protein and its potential role in detoxification. Acta Crystallogr D Biol Crystallogr 2012; 68:1140-51. [PMID: 22948915 DOI: 10.1107/s0907444912021555] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 05/11/2012] [Indexed: 11/11/2022]
Abstract
Three crystal structures of a lipoprotein (Bmlp7) of unknown function, a member of the 30 kDa lipoprotein family from mulberry silkworm (Bombyx mori L.) haemolymph, have been determined. The 1.33 Å resolution structure is an excellent example of how a precise crystallographic study can contribute to protein identification. The correct sequence of this haemolymph-isolated protein was assigned thanks to superb-quality electron-density maps. Two unexpected cadmium cations were found in this crystal structure [Bmlp7-I(Cd)] and their presence may be connected to a detoxification mechanism in this insect. For a comparison of the metal-binding sites, the crystal structure of a platinum complex (Bmlp7-Pt) was also solved at 1.94 Å resolution. The third (2.50 Å resolution) structure, of the native protein harvested in a different season (Bmlp7-II), corresponds to a different polymorph with an altered pattern of intermolecular interactions and with a total absence of cadmium ions and highlights the possible involvement of Bmlp7 in the response to environmental pollution. The N-terminal domain of Bmlp7 has a fold resembling a clockwise spiral created by six helices and can be classified as a VHS domain. The C-terminal domain is folded as a β-trefoil. The biological function of Bmlp7 is unknown, but its structural homology to sugar-binding proteins suggests that, in analogy to other 30 kDa haemolymph lipoproteins, it could play a role as an anti-apoptotic factor or function in the immune response of the insect to fungal infections.
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Affiliation(s)
- Agnieszka J Pietrzyk
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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18
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Fersini F, Dall’Antonia Y, Chow J, Streit WR, Mueller-Dieckmann J. Cloning, expression, purification and preliminary X-ray analysis of a putative metagenome-derived lipase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:923-6. [PMID: 22869123 PMCID: PMC3412774 DOI: 10.1107/s1744309112025651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 06/05/2012] [Indexed: 03/22/2024]
Abstract
LipS is a novel thermostable putative lipase that was isolated from a metagenomic library using functional screening methods. The corresponding gene shows high similarity to that encoding a putative but uncharacterized esterase from Symbiobacterium thermophilum IAM14863 (99% nucleotide-sequence similarity). Two different constructs of the recombinant lipase were crystallized. Crystals belonging to space group P4(2)2(1)2 diffracted X-ray radiation to 2.8 Å resolution and crystals belonging to space group P4 diffracted to 2.0 Å resolution. The most probable content of their asymmetric units were two molecules (P4(2)2(1)2) and four or five molecules (P4), respectively.
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Affiliation(s)
- Francesco Fersini
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | | | - Jennifer Chow
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststrasse 18, 22609 Hamburg, Germany
| | - Wolfgang R. Streit
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststrasse 18, 22609 Hamburg, Germany
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19
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Mayerhofer H, Panneerselvam S, Mueller-Dieckmann J. Protein kinase domain of CTR1 from Arabidopsis thaliana promotes ethylene receptor cross talk. J Mol Biol 2011; 415:768-79. [PMID: 22155294 DOI: 10.1016/j.jmb.2011.11.046] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 11/24/2011] [Accepted: 11/29/2011] [Indexed: 11/25/2022]
Abstract
Ethylene controls many aspects of plant growth and development. Signaling by the gaseous phytohormone is initiated by disulfide-linked membrane-bound receptors, and the formation of heteromeric receptor clusters contributes to the broad range of ethylene responsiveness. In Arabidopsis thaliana, the TCS-like ethylene receptors interact with the cytosolic serine/threonine kinase constitutive triple response 1 (CTR1), a proposed mitogen-activated protein kinase kinase kinase. In the absence of the hormone, the receptor and therefore CTR1 are active. Hence, ethylene acts as an inverse agonist of its signaling pathway. The three-dimensional structures of the active, triphosphorylated and the unphosphorylated, inactive kinase domain of CTR1 in complex with staurosporine illustrate the conformational rearrangements that form the basis of activity regulation. Additionally, in analytical ultracentrifugation experiments, active kinase domains form back-to-back dimers, while inactive and activation loop variants are monomers. Together with a front-to-front activation interface, the active protein kinase dimers thereby engage in interactions that promote CTR1-mediated cross talk between ethylene receptor clusters. This model provides a structural foundation for the observed high sensitivity of plants to ethylene.
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20
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Schuldt L, Suchowersky R, Veith K, Mueller-Dieckmann J, Weiss MS. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the regulatory domain of aspartokinase (Rv3709c) from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:380-5. [PMID: 21393848 PMCID: PMC3053168 DOI: 10.1107/s1744309111000030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 01/03/2011] [Indexed: 03/04/2023]
Abstract
The regulatory domain of Mycobacterium tuberculosis aspartokinase (Mtb-AK, Mtb-Ask, Rv3709c) has been cloned, heterologously expressed in Escherichia coli and purified using standard chromatographic techniques. Screening for initial crystallization conditions using the regulatory domain (AK-β) in the presence of the potential feedback inhibitor threonine identified four conditions which yielded crystals suitable for X-ray diffraction analysis. From these four conditions five different crystal forms of Mtb-AK-β resulted, three of which belonged to the orthorhombic system, one to the tetragonal system and one to the monoclinic system. The highest resolution (1.6 Å) was observed for a crystal form belonging to space group P2(1)2(1)2(1), with unit-cell parameters a=53.70, b=63.43, c=108.85 Å and two molecules per asymmetric unit.
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Affiliation(s)
- Linda Schuldt
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany.
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21
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Mayerhofer H, Mueller-Dieckmann C, Mueller-Dieckmann J. Cloning, expression, purification and preliminary X-ray analysis of the protein kinase domain of constitutive triple response 1 (CTR1) from Arabidopsis thaliana. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:117-20. [PMID: 21206040 PMCID: PMC3079988 DOI: 10.1107/s1744309110047640] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 11/16/2010] [Indexed: 11/10/2022]
Abstract
Ethylene, a gaseous plant hormone, is perceived by a group of membrane-bound receptors. Constitutive triple response 1 (CTR1) from Arabidopsis thaliana directly interacts with ethylene receptors and thus links signal reception to the intracellular signalling pathway. The C-terminal protein kinase domain of CTR1 has been crystallized in its wild-type form and as a kinase-dead mutant. The wild-type crystals diffracted X-ray radiation to 3 Å resolution and the crystals of the kinase-dead mutant diffacted to 2.5 Å resolution. The crystals belonged to space groups P4(1)2(1)2 and P4(2)2(1)2, respectively, with two molecules per asymmetric unit in both cases.
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Affiliation(s)
- Hubert Mayerhofer
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
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22
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Panjikar S, Mayerhofer H, Tucker PA, Mueller-Dieckmann J, de Sanctis D. Single isomorphous replacement phasing of selenomethionine-containing proteins using UV-induced radiation damage. Acta Crystallogr D Biol Crystallogr 2010; 67:32-44. [DOI: 10.1107/s090744491004299x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Accepted: 10/21/2010] [Indexed: 11/10/2022]
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23
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Hatzopoulos GN, Mueller-Dieckmann J. Structure of translation initiation factor 1 from Mycobacterium tuberculosis and inferred binding to the 30S ribosomal subunit. FEBS Lett 2010; 584:1011-5. [PMID: 20132820 DOI: 10.1016/j.febslet.2010.01.051] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Revised: 01/22/2010] [Accepted: 01/25/2010] [Indexed: 11/24/2022]
Abstract
The crystal structure of the free form of IF1 from Mycobacterium tuberculosis has been determined at 1.47 A resolution. The structure adopts the expected OB fold and matches the high structural conservation among IF1 orthologues. In order to further explore the function of Mtb-IF1, we built a model of its interaction with the 30S ribosomal subunit based on the crystal structure of the complex from Thermus thermophilus. The model suggests that several functionally important side chain residues undergo large movements while the rest of the protein in complex shows only very limited conformational change as compared to its form in solution.
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24
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Mayerhofer H, Schramm G, Hatzopoulos GN, Mueller-Dieckmann C, Haas H, Mueller-Dieckmann J. Cloning, expression, purification, crystallization and preliminary X-ray crystallographic analysis of interleukin-4-inducing principle from Schistosoma mansoni eggs (IPSE/alpha-1). Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:594-6. [PMID: 19478439 PMCID: PMC2688418 DOI: 10.1107/s1744309109015899] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Accepted: 04/28/2009] [Indexed: 11/10/2022]
Abstract
The interleukin-4-inducing principle from Schistosoma mansoni eggs (IPSE/alpha-1) triggers the release of large amounts of interleukin-4 from human blood basophils, thus presumably playing an immunomodulatory role during schistosome infection. IPSE/alpha-1 was crystallized and a native X-ray data set was collected to 1.66 A resolution from a single crystal at 100 K using synchrotron radiation. The crystal belonged to space group P6(1) or P6(5), with one molecule per asymmetric unit.
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Affiliation(s)
- Hubert Mayerhofer
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
| | | | | | | | - Helmut Haas
- Research Center Borstel, D-23845 Borstel, Germany
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25
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Kernstock S, Koch-Nolte F, Mueller-Dieckmann J, Weiss MS, Mueller-Dieckmann C. Cloning, expression, purification and crystallization as well as X-ray fluorescence and preliminary X-ray diffraction analyses of human ADP-ribosylhydrolase 1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:529-32. [PMID: 19407395 PMCID: PMC2675603 DOI: 10.1107/s1744309109014067] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Accepted: 04/15/2009] [Indexed: 11/10/2022]
Abstract
Human ADP-ribosylhydrolase 1 (hARH1, ADPRH) cleaves the glycosidic bond of ADP-ribose attached to an Arg residue of a protein. hARH1 has been cloned, expressed heterologously in Escherichia coli, purified and crystallized in complex with K(+) and ADP. The orthorhombic crystals contained one monomer per asymmetric unit, exhibited a solvent content of 43% and diffracted X-rays to a resolution of 1.9 A. A prerequisite for obtaining well diffracting crystals was the performance of X-ray fluorescence analysis on poorly diffracting apo hARH1 crystals, which revealed the presence of trace amounts of K(+) in the crystal. Adding K-ADP to the crystallization cocktail then resulted in a crystal of different morphology and with dramatically improved diffraction properties.
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Affiliation(s)
- Stefan Kernstock
- Institut für Immunologie, Universitätsklinikum Eppendorf, D-20246 Hamburg, Germany
| | - Friedrich Koch-Nolte
- Institut für Immunologie, Universitätsklinikum Eppendorf, D-20246 Hamburg, Germany
| | | | - Manfred S. Weiss
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
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26
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Hatzopoulos GN, Kefala G, Mueller-Dieckmann J. Cloning, expression, purification, crystallization and preliminary X-ray crystallographic analysis of isocitrate dehydrogenase 2 (Rv0066c) from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:1139-42. [PMID: 19052369 PMCID: PMC2593698 DOI: 10.1107/s1744309108035343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Accepted: 10/29/2008] [Indexed: 11/11/2022]
Abstract
Isocitrate dehydrogenase 2 (Icd-2, Rv0066c) from Mycobacterium tuberculosis was cloned and heterologously expressed in Escherichia coli. The protein was purified by affinity and size-exclusion chromatography and crystallized. A complete data set has been collected and reduced to 3.25 A resolution in space group C2. Preliminary diffraction data analysis suggests a complex packing with at least six molecules in the asymmetric unit.
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Affiliation(s)
| | - Georgia Kefala
- Structural Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
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27
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Mueller-Dieckmann C, Kernstock S, Mueller-Dieckmann J, Weiss MS, Koch-Nolte F. Structure of mouse ADP-ribosylhydrolase 3 (mARH3). Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:156-62. [PMID: 18323597 PMCID: PMC2374154 DOI: 10.1107/s1744309108001413] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Accepted: 01/14/2008] [Indexed: 11/18/2022]
Abstract
ADP-ribosylation is a reversible and covalent post-translational modification in which the attachment of ADP-ribose is catalyzed by ADP-ribosyltransferases and the removal of ADP-ribose is catalyzed by ADP-ribosylhydrolases. ADP-ribosylhydrolase 3 from mouse, consisting of 347 amino-acid residues, has been cloned, purified and crystallized. The three-dimensional structure has been resolved at a resolution of 1.8 A. The structure constitutes a compact all-alpha-helical protein with two Mg(2+) ions located in the active-site crevice. A structural comparison of mouse ADP-ribosylhydrolase 3 with its human orthologue shows a high degree of structural similarity. Furthermore, four prokaryotic proteins deposited in the PDB could be identified as being structurally related.
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28
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Hatzopoulos GN, Mueller-Dieckmann J. Cloning, expression, purification, crystallization and preliminary X-ray crystallographic analysis of initiation factor 1 from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:183-6. [PMID: 17329809 PMCID: PMC2330178 DOI: 10.1107/s174430910700437x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Accepted: 01/26/2007] [Indexed: 11/11/2022]
Abstract
Initiation factor 1 (IF-1; Rv3462c) from Mycobacterium tuberculosis, a component of the 30S initiation complex, was cloned and heterologously expressed in Escherichia coli. The protein was purified by affinity and size-exclusion chromatography and crystallized. A complete data set has been collected to high resolution. The crystals belonged to space group P2(1)2(1)2, with two molecules per asymmetric unit which are related by translational symmetry.
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29
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Mueller-Dieckmann J. The open-access high-throughput crystallization facility at EMBL Hamburg. Acta Crystallogr D Biol Crystallogr 2006; 62:1446-52. [PMID: 17139079 DOI: 10.1107/s0907444906038121] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Accepted: 09/18/2006] [Indexed: 11/11/2022]
Abstract
Here, the establishment of Europe's largest high-throughput crystallization facility with open access to the general user community is reported. The facility covers every step in the crystallization process from the preparation of crystallization cocktails for initial or customized screens to the setup of hanging-drop vapour-diffusion experiments and their automatic imaging. In its first year of operation, 43 internal and 40 external users submitted over 500 samples for a total of 2985 crystallization plates. An electronic booking system for registration, the selection of experimental parameters (e.g. drop size, sample-to-reservoir ratio) and the reservation of time slots was developed. External users can choose from more than 1000 initial crystallization conditions. By default, experiments are kept for six months and are imaged 15 times during this time period. A remote viewing system is available to inspect experiments via the internet. Over 100 stock solutions are available for users wishing to design customized screens.
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30
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Kernstock S, Koch-Nolte F, Mueller-Dieckmann J, Weiss MS, Mueller-Dieckmann C. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of human ARH3, the first eukaryotic protein-ADP-ribosylhydrolase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:224-7. [PMID: 16511307 PMCID: PMC2197168 DOI: 10.1107/s1744309106003435] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2005] [Accepted: 01/27/2006] [Indexed: 11/10/2022]
Abstract
ADP-ribosylhydrolases catalyze the release of ADP-ribose from ADP-ribosylated proteins via hydrolysis of the glycosidic bond between ADP-ribose and a specific amino-acid residue in a target protein. Human ADP-ribosylhydrolase 3, consisting of 347 amino-acid residues, has been cloned and heterologously expressed in Escherichia coli, purified and crystallized in two different space groups. Preliminary X-ray diffraction studies yielded excellent diffraction data to a resolution of 1.6 A.
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Affiliation(s)
- Stefan Kernstock
- Institut für Immunologie, Universitätsklinikum Eppendorf, D-20246 Hamburg, Germany
| | - Friedrich Koch-Nolte
- Institut für Immunologie, Universitätsklinikum Eppendorf, D-20246 Hamburg, Germany
| | | | - Manfred S. Weiss
- EMBL Outstation Hamburg, c/o DESY Notkestrasse 85, D-22603 Hamburg, Germany
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