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Roggenbauer H, Seifritz W, Lindmo T, Stout RB, Robinson AH, List F, Knudsen P, Zorzoli GB, Wrona BJ, Roberts JTA, Johanson E, Tuohig WD, Menlove HO, Forster RA, Parker JL, Smith DB, Bates JF, Paxton MM, Straalsund JL. Authors. NUCL TECHNOL 2017. [DOI: 10.13182/nt73-a31340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Affiliation(s)
- F. List
- Danish Atomic Energy Commission Research Establishment Risø, Roskilde, Denmark
| | - P. Knudsen
- Danish Atomic Energy Commission Research Establishment Risø, Roskilde, Denmark
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Schreiber T, Sorgatz A, List F, Blüher D, Thieme S, Wilmanns M, Bonas U. Refined requirements for protein regions important for activity of the TALE AvrBs3. PLoS One 2015; 10:e0120214. [PMID: 25781334 PMCID: PMC4363659 DOI: 10.1371/journal.pone.0120214] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [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: 07/29/2014] [Accepted: 01/20/2015] [Indexed: 11/25/2022] Open
Abstract
AvrBs3, the archetype of the family of transcription activator-like (TAL) effectors from phytopathogenic Xanthomonas bacteria, is translocated by the type III secretion system into the plant cell. AvrBs3 localizes to the plant cell nucleus and activates the transcription of target genes. Crucial for this is the central AvrBs3 region of 17.5 34-amino acid repeats that functions as a DNA-binding domain mediating recognition in a “one-repeat-to-one base pair” manner. Although AvrBs3 forms homodimers in the plant cell cytosol prior to nuclear import, it binds DNA as a monomer. Here, we show that complex formation of AvrBs3 proteins negatively affects their DNA-binding affinity in vitro. The conserved cysteine residues at position 30 of each repeat facilitate AvrBs3 complexes via disulfide bonds in vitro but are also required for the gene-inducing activity of the AvrBs3 monomer, i.e., activation of plant gene promoters. Our data suggest that the latter is due to a contribution to protein plasticity and that cysteine substitutions to alanine or serine result in a different DNA-binding mode. In addition, our studies revealed that extended parts of both the N-terminal and C-terminal regions of AvrBs3 contribute to DNA binding and, hence, gene-inducing activity in planta.
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Affiliation(s)
- Tom Schreiber
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Anika Sorgatz
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Felix List
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- European Molecular Biology Laboratory, Hamburg Unit, Notkestraße 85, Hamburg, Germany
| | - Doreen Blüher
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Sabine Thieme
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Notkestraße 85, Hamburg, Germany
| | - Ulla Bonas
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- * E-mail:
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List F, Vega M, Razeto A, Häger M, Sterner R, Wilmanns M. Catalysis Uncoupling in a Glutamine Amidotransferase Bienzyme by Unblocking the Glutaminase Active Site. ACTA ACUST UNITED AC 2012; 19:1589-99. [DOI: 10.1016/j.chembiol.2012.10.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Revised: 10/02/2012] [Accepted: 10/11/2012] [Indexed: 11/30/2022]
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Reisinger B, Bocola M, List F, Claren J, Rajendran C, Sterner R. A sugar isomerization reaction established on various (βα)₈-barrel scaffolds is based on substrate-assisted catalysis. Protein Eng Des Sel 2012; 25:751-60. [PMID: 23109729 DOI: 10.1093/protein/gzs080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In the course of tryptophan biosynthesis, the isomerization of phosphoribosylanthranilate (PRA) is catalyzed by the (βα)₈-barrel enzyme TrpF. The reaction occurs via a general acid-base mechanism with an aspartate and a cysteine residue acting as acid and base, respectively. PRA isomerase activity could be established on two (βα)₈-barrel enzymes involved in histidine biosynthesis, namely HisA and HisF, and on a HisAF chimera, by introducing two aspartate-to-valine substitutions. We have analyzed the reaction mechanism underlying this engineered activity by measuring its pH dependence, solving the crystal structure of a HisF variant with bound product analogue, and applying molecular dynamics simulations and mixed quantum and molecular mechanics calculations. The results suggest that PRA is anchored by the C-terminal phosphate-binding sites of HisA, HisF and HisAF. As a consequence, a conserved aspartate residue, which is equivalent to Cys7 from TrpF, is properly positioned to act as catalytic base. However, no obvious catalytic acid corresponding to Asp126 from TrpF could be identified in the three proteins. Instead, this role appears to be carried out by the carboxylate group of the anthranilate moiety of PRA. Thus, the engineered PRA isomerization activity is based on a reaction mechanism including substrate-assisted catalysis and thus differs substantially from the naturally evolved reaction mechanism used by TrpF.
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Affiliation(s)
- Bernd Reisinger
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Germany
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Carstensen L, Sperl JM, Bocola M, List F, Schmid FX, Sterner R. Conservation of the Folding Mechanism between Designed Primordial (βα)8-Barrel Proteins and Their Modern Descendant. J Am Chem Soc 2012; 134:12786-91. [DOI: 10.1021/ja304951v] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Linn Carstensen
- Institut für Biophysik
und physikalische Biochemie, Universität Regensburg, D-93040 Regensburg, Germany
| | - Josef M. Sperl
- Institut für Biophysik
und physikalische Biochemie, Universität Regensburg, D-93040 Regensburg, Germany
| | - Marco Bocola
- Institut für Biophysik
und physikalische Biochemie, Universität Regensburg, D-93040 Regensburg, Germany
| | - Felix List
- Institut für Biophysik
und physikalische Biochemie, Universität Regensburg, D-93040 Regensburg, Germany
| | - Franz X. Schmid
- Laboratorium für Biochemie
und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Reinhard Sterner
- Institut für Biophysik
und physikalische Biochemie, Universität Regensburg, D-93040 Regensburg, Germany
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List F, Bocola M, Haeger MC, Sterner R. Constitutively active glutaminase variants provide insights into the activation mechanism of anthranilate synthase. Biochemistry 2012; 51:2812-8. [PMID: 22432907 DOI: 10.1021/bi201618v] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The glutamine amidotransferase (GATase) family comprises enzyme complexes which consist of glutaminase and synthase subunits that catalyze in a concerted reaction the incorporation of nitrogen within various metabolic pathways. An important feature of GATases is the strong stimulation of glutaminase activity by the associated synthase. To understand the mechanism of this tight activity regulation, we probed by site-directed mutagenesis four residues of the glutaminase subunit TrpG from anthranilate synthase that are located between the catalytic Cys-His-Glu triad and the synthase subunit TrpE. In order to minimize structural perturbations induced by the introduced exchanges, the amino acids from TrpG were substituted with the corresponding residues of the closely related glutaminase HisH from imidazole glycerol phosphate synthase. Steady-state kinetic characterization showed that, in contrast to wild-type TrpG, two TrpG variants with single exchanges constitutively hydrolyzed glutamine in the absence of TrpE. A reaction assay performed with hydroxylamine as a stronger nucleophile replacing water and a filter assay with radiolabeled glutamine indicated that the formation of the thioester intermediate is the rate-limiting step of constitutive glutamine hydrolysis. Molecular dynamics simulations with wild-type TrpG and constitutively active TrpG variants suggest that the introduced amino acid exchanges result in a distance reduction between the active site Cys-His pair, which facilitates the deprotonation of the sulfhydryl group of the catalytic cysteine and thus enables its nucleophilic attack onto the carboxamide group of the glutamine side chain. We propose that native TrpG in the anthranilate synthase complex is activated by a similar mechanism.
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Affiliation(s)
- Felix List
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
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List F, Sterner R, Wilmanns M. Related (βα)8-barrel proteins in histidine and tryptophan biosynthesis: a paradigm to study enzyme evolution. Chembiochem 2011; 12:1487-94. [PMID: 21656890 DOI: 10.1002/cbic.201100082] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Indexed: 12/12/2022]
Affiliation(s)
- Felix List
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
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Liebold C, List F, Kalbitzer HR, Sterner R, Brunner E. The interaction of ammonia and xenon with the imidazole glycerol phosphate synthase from Thermotoga maritima as detected by NMR spectroscopy. Protein Sci 2011; 19:1774-82. [PMID: 20665694 DOI: 10.1002/pro.463] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The imidazole glycerol phosphate (ImGP) synthase from the hyperthermophilic bacterium Thermotoga maritima is a 1:1 complex of the glutaminase subunit HisH and the cyclase subunit HisF. It has been proposed that ammonia generated by HisH is transported through a channel to the active site of HisF, which generates intermediates of histidine (ImGP) and de novo biosynthesis of 5-aminoimidazole-4-carboxamideribotide. Solution NMR spectroscopy of ammonium chloride-titrated samples was used to study the interaction of NH(3) with amino acids inside this channel. Although numerous residues showed (15)N chemical shift changes, most of these changes were caused by nonspecific ionic strength effects. However, several interactions appeared to be specific. Remarkably, the amino acid residue Thr 78-which is located in the central channel-shows a large chemical shift change upon titration with ammonium chloride. This result and the reduced catalytic activity of the Thr78Met mutant indicate a special role of this residue in ammonia channeling. To detect and further characterize internal cavities in HisF, which might for example contribute to ammonia channeling, the interaction of HisF with the noble gas xenon was analyzed by solution NMR spectroscopy using (1)H-(15)N HSQC experiments. The results indicate that HisF contains three distinct internal cavities, which could be identified by xenon-induced chemical shift changes of the neighboring amino acid residues. Two of these cavities are located at the active site at opposite ends of the substrate N'-[(5'-phosphoribulosyl)formimino]-5-aminoimidazole-4-carboxamide-ribonucleotide (PRFAR) binding groove. The third cavity is located in the interior of the central β-barrel of HisF and overlaps with the putative ammonia transport channel.
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Affiliation(s)
- Christoph Liebold
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
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Wirth VF, List F, Diez G, Goldmann WH. Vinculin's C-terminal region facilitates phospholipid membrane insertion. Biochem Biophys Res Commun 2010; 398:433-7. [PMID: 20599708 DOI: 10.1016/j.bbrc.2010.06.094] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2010] [Accepted: 06/23/2010] [Indexed: 01/13/2023]
Abstract
The focal adhesion protein vinculin has been implicated in associating with soluble and membranous phospholipids. Here, we investigated the intermolecular interactions of two vinculin tail domains with membrane phospholipids. Previous studies have shown that the tail's unstructured C-terminus affects the mechanical behavior of cells, but not the H3 region. The aim of this work was to establish whether the C-terminal or the H3 region either associate favorably with or anchor in lipid membranes. This work characterizes the energetics and dynamics of phospholipid interactions using differential scanning calorimetry (DSC) as well as circular dichroism (CD) spectroscopy. Biochemical data from tryptophan quenching and SDS-PAGE experiments support calorimetric and CD spectroscopic findings insofar that only vinculin's C-terminus inserts into lipid membranes. These in vitro results provide further insight into the mechanical behavior of vinculin tail regions in cells and contribute to the understanding of their structure and function.
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Affiliation(s)
- Volker F Wirth
- Center for Medical Physics and Technology, Biophysics Group, Friedrich-Alexander-University, Erlangen-Nuremberg, Erlangen, Germany
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Wirth V, List F, Diez G, Ziegler WH, Goldmann WH. In vitro characterization of vinculin's lipid membrane-interacting domain, helix 3. Biophys J 2009. [DOI: 10.1016/j.bpj.2008.12.1655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Diez G, List F, Smith J, Ziegler WH, Goldmann WH. Direct evidence of vinculin tail–lipid membrane interaction in beta-sheet conformation. Biochem Biophys Res Commun 2008; 373:69-73. [DOI: 10.1016/j.bbrc.2008.05.182] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Accepted: 05/29/2008] [Indexed: 11/26/2022]
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Kolthoff JM, Hills FG, Lampe V, Beckurts H, Mayer F, Moser L, Singer J, Wynkoop G, Brukl A, Ruff O, Stephan E, Frommes M, Nie�ner M, Hillebrand WF, Lundell GEF, Fischer H, Leopoldi G, Cissarz A, Schneiderh�hn H, Zintl E, Kassler J, Knowles HB, Churchill HV, Bridges RW, Lee MF, Dittler E, Kirnbauer F, Dixon BE, Noyes, Bray, List F, Maxymowicz W, Spindeck F. Nachweis und Bestimmung des Berylliums und seine Trennung von anderen Elementen. Anal Bioanal Chem 1933. [DOI: 10.1007/bf01404774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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