1
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Fan C, Sukomon N, Flood E, Rheinberger J, Allen TW, Nimigean CM. Ball-and-chain inactivation in a calcium-gated potassium channel. Nature 2020; 580:288-293. [PMID: 32269335 PMCID: PMC7153497 DOI: 10.1038/s41586-020-2116-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 01/15/2020] [Indexed: 01/21/2023]
Abstract
Inactivation is the process by which ion channels terminate ion flux through their pores while the opening stimulus is still present1. In neurons, inactivation of both sodium and potassium channels is crucial for the generation of action potentials and regulation of firing frequency1,2. A cytoplasmic domain of either the channel or an accessory subunit is thought to plug the open pore to inactivate the channel via a 'ball-and-chain' mechanism3-7. Here we use cryo-electron microscopy to identify the molecular gating mechanism in calcium-activated potassium channels by obtaining structures of the MthK channel from Methanobacterium thermoautotrophicum-a purely calcium-gated and inactivating channel-in a lipid environment. In the absence of Ca2+, we obtained a single structure in a closed state, which was shown by atomistic simulations to be highly flexible in lipid bilayers at ambient temperature, with large rocking motions of the gating ring and bending of pore-lining helices. In Ca2+-bound conditions, we obtained several structures, including multiple open-inactivated conformations, further indication of a highly dynamic protein. These different channel conformations are distinguished by rocking of the gating rings with respect to the transmembrane region, indicating symmetry breakage across the channel. Furthermore, in all conformations displaying open channel pores, the N terminus of one subunit of the channel tetramer sticks into the pore and plugs it, with free energy simulations showing that this is a strong interaction. Deletion of this N terminus leads to functionally non-inactivating channels and structures of open states without a pore plug, indicating that this previously unresolved N-terminal peptide is responsible for a ball-and-chain inactivation mechanism.
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Affiliation(s)
- Chen Fan
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Nattakan Sukomon
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Emelie Flood
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - Jan Rheinberger
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Department of Structural Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Toby W Allen
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA.
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2
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Attri P, Han J, Choi S, Choi EH, Bogaerts A, Lee W. CAP modifies the structure of a model protein from thermophilic bacteria: mechanisms of CAP-mediated inactivation. Sci Rep 2018; 8:10218. [PMID: 29977069 PMCID: PMC6033864 DOI: 10.1038/s41598-018-28600-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 06/19/2018] [Indexed: 12/14/2022] Open
Abstract
Cold atmospheric plasma (CAP) has great potential for sterilization in the food industry, by deactivation of thermophilic bacteria, but the underlying mechanisms are largely unknown. Therefore, we investigate here whether CAP is able to denature/modify protein from thermophilic bacteria. We focus on MTH1880 (MTH) from Methanobacterium thermoautotrophicum as model protein, which we treated with dielectric barrier discharge (DBD) plasma operating in air for 10, 15 and 20 mins. We analysed the structural changes of MTH using circular dichroism, fluorescence and NMR spectroscopy, as well as the thermal and chemical denaturation, upon CAP treatment. Additionally, we performed molecular dynamics (MD) simulations to determine the stability, flexibility and solvent accessible surface area (SASA) of both the native and oxidised protein.
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Affiliation(s)
- Pankaj Attri
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium
| | - Jeongmin Han
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, 134 Shinchon-Dong, Seodaemoon-Gu, Seoul, 120-749, Korea
| | - Sooho Choi
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, 134 Shinchon-Dong, Seodaemoon-Gu, Seoul, 120-749, Korea
| | - Eun Ha Choi
- Department of Electrical and Biological Physics, Kwangwoon University, Seoul, 01897, Korea
| | - Annemie Bogaerts
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium.
| | - Weontae Lee
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, 134 Shinchon-Dong, Seodaemoon-Gu, Seoul, 120-749, Korea.
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3
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Pfoh R, Pai EF, Saridakis V. Nicotinamide mononucleotide adenylyltransferase displays alternate binding modes for nicotinamide nucleotides. Acta Crystallogr D Biol Crystallogr 2015; 71:2032-9. [PMID: 26457427 PMCID: PMC4601368 DOI: 10.1107/s1399004715015497] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 08/18/2015] [Indexed: 11/10/2022]
Abstract
Nicotinamide mononucleotide adenylyltransferase (NMNAT) catalyzes the biosynthesis of NAD(+) and NaAD(+). The crystal structure of NMNAT from Methanobacterium thermoautotrophicum complexed with NAD(+) and SO4(2-) revealed the active-site residues involved in binding and catalysis. Site-directed mutagenesis was used to further characterize the roles played by several of these residues. Arg11 and Arg136 were implicated in binding the phosphate groups of the ATP substrate. Both of these residues were mutated to lysine individually. Arg47 does not interact with either NMN or ATP substrates directly, but was deemed to play a role in binding as it is proximal to Arg11 and Arg136. Arg47 was mutated to lysine and glutamic acid. Surprisingly, when expressed in Escherichia coli all of these NMNAT mutants trapped a molecule of NADP(+) in their active sites. This NADP(+) was bound in a conformation that was quite different from that displayed by NAD(+) in the native enzyme complex. When NADP(+) was co-crystallized with wild-type NMNAT, the same structural arrangement was observed. These studies revealed a different conformation of NADP(+) in the active site of NMNAT, indicating plasticity of the active site.
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Affiliation(s)
- Roland Pfoh
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - Emil F. Pai
- Campbell Family Institute for Cancer Research, Princess Margaret Cancer Center, University Health Network, Toronto Medical Discovery Tower–MaRS Centre, 101 College Street, Toronto, ON M5G 1L7, Canada
- Departments of Biochemistry, Medical Biophysics and Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Vivian Saridakis
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
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4
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Knappy CS, Chong JPJ, Keely BJ. Rapid discrimination of archaeal tetraether lipid cores by liquid chromatography-tandem mass spectrometry. J Am Soc Mass Spectrom 2009; 20:51-59. [PMID: 18922702 DOI: 10.1016/j.jasms.2008.09.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Revised: 09/12/2008] [Accepted: 09/12/2008] [Indexed: 05/26/2023]
Abstract
Atmospheric pressure chemical ionization liquid chromatography-tandem mass spectrometry (APCI LC-MS/MS) of tetraether lipid cores of archaeal origin reveals distinct dissociation pathways for three classes of core lipid extracted from Methanobacter thermautotrophicus. Within these classes, two isobaric tetraether lipids, one a scarcely reported lipid constituent of M. thermautotrophicus and the other an artefact formed during extraction from cultured cells, were identified and distinguished via their MS(2) spectra. APCI LC-MS/MS discriminates different tetraether core lipid types and isobaric species and reveals the mass of the constituent biphytanyl chains within the tetraether cores, albeit without full elucidation of their structures. Furthermore, the method allows direct estimation of the relative proportions of tetraether core lipids from chromatographic peak area measurement, allowing rapid profiling of these compounds in microbiological and environmental extracts.
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5
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Kuszewski JJ, Thottungal RA, Clore GM, Schwieters CD. Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: improved robustness and performance of the PASD algorithm. J Biomol NMR 2008; 41:221-39. [PMID: 18668206 PMCID: PMC2575051 DOI: 10.1007/s10858-008-9255-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Accepted: 07/02/2008] [Indexed: 05/05/2023]
Abstract
We report substantial improvements to the previously introduced automated NOE assignment and structure determination protocol known as PASD (Kuszewski et al. (2004) J Am Chem Soc 26:6258-6273). The improved protocol includes extensive analysis of input spectral data to create a low-resolution contact map of residues expected to be close in space. This map is used to obtain reasonable initial guesses of NOE assignment likelihoods which are refined during subsequent structure calculations. Information in the contact map about which residues are predicted to not be close in space is applied via conservative repulsive distance restraints which are used in early phases of the structure calculations. In comparison with the previous protocol, the new protocol requires significantly less computation time. We show results of running the new PASD protocol on six proteins and demonstrate that useful assignment and structural information is extracted on proteins of more than 220 residues. We show that useful assignment information can be obtained even in the case in which a unique structure cannot be determined.
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Affiliation(s)
- John J Kuszewski
- Imaging Sciences Laboratory, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892-5624, USA
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6
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Kuo MMC, Baker KA, Wong L, Choe S. Dynamic oligomeric conversions of the cytoplasmic RCK domains mediate MthK potassium channel activity. Proc Natl Acad Sci U S A 2007; 104:2151-6. [PMID: 17287352 PMCID: PMC1892972 DOI: 10.1073/pnas.0609085104] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [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: 10/16/2006] [Indexed: 12/21/2022] Open
Abstract
The crystal structure of the RCK-containing MthK provides a molecular framework for understanding the ligand gating mechanisms of K+ channels. Here we examined the macroscopic currents of MthK in enlarged Escherichia coli membrane by patch clamp and rapid perfusion techniques and showed that the channel undergoes desensitization in seconds after activation by Ca2+ or Cd2+. Additionally, MthK is inactivated by slightly acidic pH only from the cytoplasmic side. Examinations of isolated RCK domain by size-exclusion chromatography, static light scattering, analytical sedimentation, and stopped-flow spectroscopy show that Ca2+ rapidly converts isolated RCK monomers to multimers at alkaline pH. In contrast, the RCK domain at acidic pH remains firmly dimeric regardless of Ca2+ but restores predominantly to multimer or monomer at basic pH with or without Ca2+, respectively. These functional and biochemical analyses correlate the four functional states of the MthK channel with distinct oligomeric states of its RCK domains and indicate that the RCK domains undergo oligomeric conversions in modulating MthK activities.
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Affiliation(s)
- Mario Meng-Chiang Kuo
- Structural Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Kent A. Baker
- Structural Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Lee Wong
- Structural Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Senyon Choe
- Structural Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037
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7
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Julien O, Gignac I, Hutton A, Yee A, Arrowsmith CH, Gagné SM. MTH187 from Methanobacterium thermoautotrophicum has three HEAT-like repeats. J Biomol NMR 2006; 35:149-54. [PMID: 16819590 DOI: 10.1007/s10858-006-0029-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2006] [Accepted: 03/07/2006] [Indexed: 05/10/2023]
Abstract
With the completion of genome sequencing projects, there are a large number of proteins for which we have little or no functional information. Since protein function is closely related to three-dimensional conformation, structural proteomics is one avenue where the role of proteins with unknown function can be investigated. In the present structural project, the structure of MTH187 has been determined by solution-state NMR spectroscopy. This protein of 12.4 kDa is one of the 424 non-membrane proteins that were cloned and purified for the structural proteomic project of Methanobacterium thermoautotrophicum [Christendat, D., Yee, A., Dharamsi, A., Kluger, Y., Gerstein, M., Arrowsmith, C.H. and Edwards, A.M. (2000) Prog. Biophys. Mol. Biol., 73, 339-345]. Methanobacterium thermoautotrophicum is a thermophilic archaeon that grows optimally at 65 degrees C. A particular characteristic of this microorganism is its ability to generate methane from carbon dioxide and hydrogen [Smith, D.R., Doucette-Stamm, L.A., Deloughery, C., Lee, H., Dubois, J., Aldredge, T., Bashirzadeh, R., Blakely, D., Cook, R., Gilbert, K., Harrison, D., Hoang, L., Keagle, P., Lumm, W., Pothier, B., Qiu, D., Spadafora, R., Vicaire, R., Wang, Y., Wierzbowski, J., Gibson, R., Jiwani, N., Caruso, A., Bush, D., Reeve, J. N. et al. (1997) J. Bacteriol., 179, 7135-7155].
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Affiliation(s)
- Olivier Julien
- Département de biochimie et de microbiologie and CREFSIP, Université Laval, 3255 pav. Marchand, Québec, G1K 7P4, Canada
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8
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Grishaev A, Steren CA, Wu B, Pineda-Lucena A, Arrowsmith C, Llinás M. ABACUS, a direct method for protein NMR structure computation via assembly of fragments. Proteins 2006; 61:36-43. [PMID: 16080153 DOI: 10.1002/prot.20457] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The ABACUS algorithm obtains the protein NMR structure from unassigned NOESY distance restraints. ABACUS works as an integrated approach that uses the complete set of available NMR experimental information in parallel and yields spin system typing, NOE spin pair identities, sequence specific resonance assignments, and protein structure, all at once. The protocol starts from unassigned molecular fragments (including single amino acid spin systems) derived from triple-resonance (1)H/(13)C/(15)N NMR experiments. Identifications of connected spin systems and NOEs precede the full sequence specific resonance assignments. The latter are obtained iteratively via Monte Carlo-Metropolis and/or probabilistic sequence selections, molecular dynamics structure computation and BACUS filtering (A. Grishaev and M. Llinás, J Biomol NMR 2004;28:1-10). ABACUS starts from scratch, without the requirement of an initial approximate structure, and improves iteratively the NOE identities in a self-consistent fashion. The procedure was run as a blind test on data recorded on mth1743, a 70-amino acid genomic protein from M. thermoautotrophicum. It converges to a structure in ca. 15 cycles of computation on a 3-GHz processor PC. The calculated structures are very similar to the ones obtained via conventional methods (1.22 A backbone RMSD). The success of ABACUS on mth1743 further validates BACUS as a NOESY identification protocol.
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Affiliation(s)
- A Grishaev
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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9
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Abstract
Minichromosomal maintenance proteins (MCMs) are considered to be the replicative helicase. Methanobacterium thermoautotrophicum has a single MCM gene (mtMCM). The crystal structure of the mtMCM N-terminal region is a double hexamer. Structure-guided sequence alignment indicates a structural conservation of this fragment across archaeal and eukaryotic MCMs. The mtMCM structure was successfully used to analyze a Saccharomyces cerevisiae MCM5 mutant, called BOB1, which contains a single residue change from Pro to Leu and bypasses a kinase normally required for initiation of DNA replication. A domain-push model was proposed to explain the BOB1 bypass activity. Here we investigate the effects of BOB1 mutation on the biochemical activities of mtMCM. Surprisingly, the BOB1 mutation (P62L) had a major effect on the helicase activity but had no significant impact on DNA binding and ATPase activities. These results will contribute to a more detailed understanding of the BOB1 bypass activity and other aspects of DNA replication control.
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Affiliation(s)
- Ryan J Fletcher
- Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
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10
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Abstract
Potassium channels play an essential role in a wide range of biological processes, including cell volume regulation and the maintenance and control of electrical signals. With the advent of the structural era of ion channel biology, it has become critical to learn more about the functional properties of the prokaryotic channels, and this is the area in which genetic screens have become an increasingly useful approach. Here, we describe a bacteria-based complementation assay that we applied to investigate gating mutants of the prokaryotic K+ channel MthK, which was cloned from the archeon Methanobacterium thermoautotrophicum. The results demonstrated that heterologously expressed MthK is fully assembled and functional in Escherichia coli. This complementation assay should be useful in the initial identification of prokaryotic K+ channel mutants that result in altered channel function.
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Affiliation(s)
- Lyubov V Parfenova
- Department of Physiology, University of Texas Health Science Center, San Antonio, USA
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11
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Arluison V, Mura C, Guzmán MR, Liquier J, Pellegrini O, Gingery M, Régnier P, Marco S. Three-dimensional structures of fibrillar Sm proteins: Hfq and other Sm-like proteins. J Mol Biol 2005; 356:86-96. [PMID: 16337963 DOI: 10.1016/j.jmb.2005.11.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [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: 08/26/2005] [Revised: 11/02/2005] [Accepted: 11/03/2005] [Indexed: 10/25/2022]
Abstract
Hfq is a nucleic acid-binding protein that functions as a global regulator of gene expression by virtue of its interactions with several small, non-coding RNA species. Originally identified as an Escherichia coli host factor required for RNA phage Qbeta replication, Hfq is now known to post-transcriptionally regulate bacterial gene expression by modulating both mRNA stability and translational activity. Recently shown to be a member of the diverse Sm protein family, Hfq adopts the OB-like fold typical of other Sm and Sm-like (Lsm) proteins, and also assembles into toroidal homo-oligomers that bind single-stranded RNA. Similarities between the structures, functions, and evolution of Sm/Lsm proteins and Hfq are continually being discovered, and we now report an additional, unexpected biophysical property that is shared by Hfq and other Sm proteins: E.coli Hfq polymerizes into well-ordered fibres whose morphologies closely resemble those found for Sm-like archaeal proteins (SmAPs). However, the hierarchical assembly of these fibres is dissimilar: whereas SmAPs polymerize into polar tubes (and striated bundles of such tubes) by head-to-tail stacking of individual homo-heptamers, helical Hfq fibres are formed by cylindrical slab-like layers that consist of 36 subunits arranged as a hexamer of Hfq homo-hexamers (i.e. protofilaments in a 6 x 6 arrangement). The different fibrillar ultrastructures formed by Hfq and SmAP are presented and examined herein, with the overall goal of elucidating another similarity amongst the diverse members of the Sm protein family.
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Affiliation(s)
- Véronique Arluison
- Institut de Biologie Physico-Chimique, CNRS UPR 9073 conventionnée avec l'université Paris 7, 13 rue P. et M. Curie, 75005 Paris, France.
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12
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Amegbey G, Stothard P, Kuznetsova E, Yee A, Arrowsmith CH, Wishart DS. Solution Structure of MTH0776 from Methanobacterium thermoautotrophicum. J Biomol NMR 2005; 33:51-6. [PMID: 16222557 DOI: 10.1007/s10858-005-1275-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2005] [Accepted: 07/11/2005] [Indexed: 05/04/2023]
Affiliation(s)
- Godwin Amegbey
- Department of Computing Science and Biological Sciences, University of Alberta, Edmonton, Alberta, Canada, T6G 2E8
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13
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Blanco FJ, Yee A, Campos-Olivas R, Ortiz AR, Devos D, Valencia A, Arrowsmith CH, Rico M. Solution structure of the hypothetical protein Mth677 from Methanobacterium thermoautotrophicum: a novel alpha+beta fold. Protein Sci 2005; 13:1458-65. [PMID: 15152082 PMCID: PMC2279996 DOI: 10.1110/ps.04620504] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The structure of Mth677, a hypothetical protein from Methanobacterium thermoautotrophicum (Mth), has been determined by using heteronuclear nuclear magnetic resonance (NMR) methods on a double-labeled (15)N-(13)C sample. Mth677 adopts a novel alpha+beta fold, consisting of two alpha-helices (one N terminal and one C terminal) packed on the same side of a central beta-hairpin. This structure is likely shared by its three orthologs, detected in three other Archaebacteria. There are no clear features in the sequences of these proteins or in the genome organization of Mth to make a reliable functional assignment to this protein. However, the structural similarity to Escherichia coli MinE, the protein which controls that division occurs at the midcell site, lends support to the proposal that Mth677 might be, in Mth, the counterpart of the topological specificity domain of MinE in E. coli.
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Affiliation(s)
- Francisco J Blanco
- NMR Group, Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
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14
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Amegbey G, Chang Z, Stothard P, Yee A, Arrowsmith C, Wishart DS. Complete 1H, 13C and 15N NMR assignments of MTH0776 from Methanobacterium thermoautotrophicum. J Biomol NMR 2004; 30:459-460. [PMID: 15630567 DOI: 10.1007/s10858-004-4341-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2004] [Accepted: 09/28/2004] [Indexed: 05/24/2023]
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15
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Gutiérrez P, Osborne MJ, Siddiqui N, Trempe JF, Arrowsmith C, Gehring K. Structure of the archaeal translation initiation factor aIF2 beta from Methanobacterium thermoautotrophicum: implications for translation initiation. Protein Sci 2004; 13:659-67. [PMID: 14978306 PMCID: PMC2286745 DOI: 10.1110/ps.03506604] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
aIF2 beta is the archaeal homolog of eIF2 beta, a member of the eIF2 heterotrimeric complex, implicated in the delivery of Met-tRNA(i)(Met) to the 40S ribosomal subunit. We have determined the solution structure of the intact beta-subunit of aIF2 from Methanobacterium thermoautotrophicum. aIF2 beta is composed of an unfolded N terminus, a mixed alpha/beta core domain and a C-terminal zinc finger. NMR data shows the two folded domains display restricted mobility with respect to each other. Analysis of the aIF2 gamma structure docked to tRNA allowed the identification of a putative binding site for the beta-subunit in the ternary translation complex. Based on structural similarity and biochemical data, a role for the different secondary structure elements is suggested.
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MESH Headings
- Amino Acid Sequence
- Archaeal Proteins/chemistry
- Archaeal Proteins/genetics
- Archaeal Proteins/metabolism
- Binding Sites/genetics
- Cloning, Molecular
- Databases, Protein
- Guanosine Triphosphate/chemistry
- Guanosine Triphosphate/metabolism
- Methanobacterium/chemistry
- Methanobacterium/genetics
- Models, Molecular
- Molecular Sequence Data
- Nuclear Magnetic Resonance, Biomolecular
- Peptide Chain Initiation, Translational
- Peptide Initiation Factors/chemistry
- Peptide Initiation Factors/genetics
- Peptide Initiation Factors/metabolism
- Protein Binding
- Protein Conformation
- Protein Structure, Secondary
- RNA, Transfer, Met/chemistry
- RNA, Transfer, Met/metabolism
- Recombinant Proteins/chemistry
- Sequence Homology, Amino Acid
- Static Electricity
- Structural Homology, Protein
- Zinc Fingers/genetics
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Affiliation(s)
- Pablo Gutiérrez
- McGill University, Department of Biochemistry, McIntyre Medical Science Building, 3655 Promenade Sir William Osler, Montréal, Québec H3G 1Y6, Canada
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16
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Lee CH, Jung JW, Yee A, Arrowsmith CH, Lee W. Solution structure of a novel calcium binding protein, MTH1880, from Methanobacterium thermoautotrophicum. Protein Sci 2004; 13:1148-54. [PMID: 15044740 PMCID: PMC2280053 DOI: 10.1110/ps.03472104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
MTH1880 is a hypothetical protein from Methanobacterium thermoautotrophicum, a target organism of structural genomics. The solution structure determined by NMR spectroscopy demonstrates a typical alpha + beta-fold found in many proteins with different functions. The molecular surface of the protein reveals a small, highly acidic pocket comprising loop B (Asp36, Asp37, Asp38), the end of beta2 (Glu39), and loop D (Ser57, Ser58, Ser61), indicating that the protein would have a possible cation binding site. The NMR resonances of several amino acids within the acidic binding pocket in MTH1880, shifted upon addition of calcium ion. This calcium binding motif and overall topology of MTH1880 differ from those of other calcium binding proteins. MTH1880 did not show a calcium-induced conformational change typical of calcium sensor proteins. Therefore, we propose that the MTH1880 protein contains a novel motif for calcium-specific binding, and may function as a calcium buffering protein.
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Affiliation(s)
- Chang-Hun Lee
- Department of Biochemistry, College of Science, Yonsei University, 134 Seodaemoon-Gu, Shinchondong, Seoul, Korea 120-749
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17
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Abstract
Here we describe various methods currently under development aimed at identifying a protein's function from its three-dimensional structure. We are combining a number of these methods to create a pipeline of applications, called ProFunc, which will take a given 3D structure, run all the applications on it and compile and summarise the results obtained. The aim is to provide a best guess as to the protein's function from the evidence provided by the different methods. Here we present three examples, using structures solved by the Midwest Center for Structural Genomics consortium, illustrating the strengths and weaknesses of current approaches.
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Affiliation(s)
- Roman A Laskowski
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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18
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Wu B, Yee A, Pineda-Lucena A, Semesi A, Ramelot TA, Cort JR, Jung JW, Edwards A, Lee W, Kennedy M, Arrowsmith CH. Solution structure of ribosomal protein S28E from Methanobacterium thermoautotrophicum. Protein Sci 2004; 12:2831-7. [PMID: 14627743 PMCID: PMC2366991 DOI: 10.1110/ps.03358203] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The ribosomal protein S28E from the archaeon Methanobacterium thermoautotrophicum is a component of the 30S ribosomal subunit. Sequence homologs of S28E are found only in archaea and eukaryotes. Here we report the three-dimensional solution structure of S28E by NMR spectroscopy. S28E contains a globular region and a long C-terminal tail protruding from the core. The globular region consists of four antiparallel beta-strands that are arranged in a Greek-key topology. Unique features of S28E include an extended loop L2-3 that folds back onto the protein and a 12-residue charged C-terminal tail with no regular secondary structure and greater flexibility relative to the rest of the protein. The structural and surface resemblance to OB-fold family of proteins and the presence of highly conserved basic residues suggest that S28E may bind to RNA. A broad positively charged surface extending over one side of the beta-barrel and into the flexible C terminus may present a putative binding site for RNA.
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Affiliation(s)
- Bin Wu
- Northeast Structural Genomics Consortium, Division of Molecular and Structural Biology, Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2M9, Canada
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19
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Amegbey GY, Monzavi H, Habibi-Nazhad B, Bhattacharyya S, Wishart DS. Structural and functional characterization of a thioredoxin-like protein (Mt0807) from Methanobacterium thermoautotrophicum. Biochemistry 2003; 42:8001-10. [PMID: 12834352 DOI: 10.1021/bi030021g] [Citation(s) in RCA: 10] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mt0807 is an 85-residue thiol-redox protein from the anaerobic archaebacterium Methanobacterium thermoautotrophicum. Its small size, its participation in certain redox reactions, and the presence of a "classic" glutareodoxin active-site sequence have led to the suggestion that it might be a glutaredoxin. However, studies by previous workers indicated that it exhibited neither glutaredoxin-like nor thioredoxin-like properties. To clarify the true role of this protein and its structure/functional relationship with a paralogous thioredoxin (Mt0895, 28% sequence identity) and a recently characterized orthologous protein (Mj0307, 51% sequence identity), we undertook a series of biochemical and biophysical studies. Comparative enzymatic assays and thiol titration experiments were combined with NMR structural studies and detailed 3D structure comparisons. Structurally, our results show that Mt0807 has a glutaredoxin-like fold (central four-stranded beta-sheet core surrounded by two helices on one side and a third on the other). However, more detailed comparisons with other members of the thioredoxin superfamily indicate that Mt0807 actually has several key structural and active-site characteristics more common to a thioredoxin. Furthermore, biochemical tests show that Mt0807 actually behaves as true thioredoxin. Comparisons between Mt0807 and its paralogue, Mt0895, indicate these two archaebacterial thioredoxins share very similar folds, but exhibit very different activities and likely serve somewhat different roles. On the basis of its greater relative abundance and significantly stronger redox activity, we believe that Mt0807 is the primary thioredoxin for M. thermoautotrophicum, while Mt0895 plays a minor or supportive role. We also suggest that these two molecules (Mt0807 and Mt0895) may represent a group of ancient proteins that were ancestral to both thioredoxins and glutaredoxins.
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Affiliation(s)
- Godwin Y Amegbey
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Canada T6G 2N8
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Fletcher RJ, Bishop BE, Leon RP, Sclafani RA, Ogata CM, Chen XS. The structure and function of MCM from archaeal M. Thermoautotrophicum. Nat Struct Mol Biol 2003; 10:160-7. [PMID: 12548282 DOI: 10.1038/nsb893] [Citation(s) in RCA: 263] [Impact Index Per Article: 12.5] [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: 12/09/2002] [Accepted: 12/17/2002] [Indexed: 01/07/2023]
Abstract
Eukaryotic chromosomal DNA is licensed for replication precisely once in each cell cycle. The mini-chromosome maintenance (MCM) complex plays a role in this replication licensing. We have determined the structure of a fragment of MCM from Methanobacterium thermoautotrophicum (mtMCM), a model system for eukaryotic MCM. The structure reveals a novel dodecameric architecture with a remarkably long central channel. The channel surface has an unusually high positive charge and binds DNA. We also show that the structure of the N-terminal fragment is conserved for all MCMs proteins despite highly divergent sequences, suggesting a common architecture for a similar task: gripping/remodeling DNA and regulating MCM activity. An mtMCM mutant protein equivalent to a yeast MCM5 (CDC46) protein with the bob1 mutation at its N terminus has only subtle structural changes, suggesting a Cdc7-bypass mechanism by Bob1 in yeast. Yeast bypass experiments using MCM5 mutant proteins support the hypothesis for the bypass mechanism.
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Affiliation(s)
- Ryan J Fletcher
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Science Center, School of Medicine, Denver, Colorado 80262, USA
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21
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Martín-Benito J, Boskovic J, Gómez-Puertas P, Carrascosa JL, Simons C, Lewis SA, Bartolini F, Cowan NJ, Valpuesta JM. Structure of eukaryotic prefoldin and of its complexes with unfolded actin and the cytosolic chaperonin CCT. EMBO J 2002; 21:6377-86. [PMID: 12456645 PMCID: PMC136944 DOI: 10.1093/emboj/cdf640] [Citation(s) in RCA: 163] [Impact Index Per Article: 7.4] [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] [Indexed: 11/14/2022] Open
Abstract
The biogenesis of the cytoskeletal proteins actin and tubulin involves interaction of nascent chains of each of the two proteins with the oligomeric protein prefoldin (PFD) and their subsequent transfer to the cytosolic chaperonin CCT (chaperonin containing TCP-1). Here we show by electron microscopy that eukaryotic PFD, which has a similar structure to its archaeal counterpart, interacts with unfolded actin along the tips of its projecting arms. In its PFD-bound state, actin seems to acquire a conformation similar to that adopted when it is bound to CCT. Three-dimensional reconstruction of the CCT:PFD complex based on cryoelectron microscopy reveals that PFD binds to each of the CCT rings in a unique conformation through two specific CCT subunits that are placed in a 1,4 arrangement. This defines the phasing of the CCT rings and suggests a handoff mechanism for PFD.
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Affiliation(s)
| | | | | | | | - C.Torrey Simons
- Centro Nacional de Biotecnología, CSIC, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain and
Department of Biochemistry, NYU Medical Center, New York, NY 10016, USA Corresponding author e-mail: J.Martín-Benito and J.Boskovic contributed equally to this work
| | - Sally A. Lewis
- Centro Nacional de Biotecnología, CSIC, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain and
Department of Biochemistry, NYU Medical Center, New York, NY 10016, USA Corresponding author e-mail: J.Martín-Benito and J.Boskovic contributed equally to this work
| | - Francesca Bartolini
- Centro Nacional de Biotecnología, CSIC, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain and
Department of Biochemistry, NYU Medical Center, New York, NY 10016, USA Corresponding author e-mail: J.Martín-Benito and J.Boskovic contributed equally to this work
| | - Nicholas J. Cowan
- Centro Nacional de Biotecnología, CSIC, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain and
Department of Biochemistry, NYU Medical Center, New York, NY 10016, USA Corresponding author e-mail: J.Martín-Benito and J.Boskovic contributed equally to this work
| | - José M. Valpuesta
- Centro Nacional de Biotecnología, CSIC, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain and
Department of Biochemistry, NYU Medical Center, New York, NY 10016, USA Corresponding author e-mail: J.Martín-Benito and J.Boskovic contributed equally to this work
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22
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Abstract
Previous X-ray studies of have focused on the closed state of the potassium channel. Now the structure of a calcium-activated bacterial potassium channel has revealed the nature of the channel's open state. This provides a first view at high resolution of ion channel gating.
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Affiliation(s)
- Mark S P Sansom
- Laboratory of Molecular Biophysics, Department of Biochemistry, The University of Oxford, The Rex Richards Building, South Parks Road, OX1 3QU, Oxford, UK.
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23
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Christendat D, Saridakis V, Kim Y, Kumar PA, Xu X, Semesi A, Joachimiak A, Arrowsmith CH, Edwards AM. The crystal structure of hypothetical protein MTH1491 from Methanobacterium thermoautotrophicum. Protein Sci 2002; 11:1409-14. [PMID: 12021439 PMCID: PMC2373630 DOI: 10.1110/ps.4720102] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
As part of our structural proteomics initiative, we have determined the crystal structure of MTH1491, a previously uncharacterized hypothetical protein from Methanobacterium thermoautotrophicum. MTH1491 is one of numerous structural genomics targets selected in a genome-wide survey of uncharacterized proteins. It belongs to a family of proteins whose biological function is not known. The crystal structure of MTH1491, the first structure for this family of proteins, consists of an overall five-stranded parallel beta-sheet with strand order 51234 and flanking helices. The oligomeric form of this molecule is a trimer as seen from both crystal contacts and gel filtration studies. Analysis revealed that the structure of MTH1491 is similar to that of dehydrogenases, amidohydrolases, and oxidoreductases. Using a combination of sequence and structural analyses, we showed that MTH1491 does not belong to either the dehydrogenase or the amidohydrolase superfamilies of proteins.
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Affiliation(s)
- Dinesh Christendat
- Clinical Genomics Center, University Health Network, Toronto, Ontario, M5G 1L7, Canada.
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Abstract
Ion channels exhibit two essential biophysical properties; that is, selective ion conduction, and the ability to gate-open in response to an appropriate stimulus. Two general categories of ion channel gating are defined by the initiating stimulus: ligand binding (neurotransmitter- or second-messenger-gated channels) or membrane voltage (voltage-gated channels). Here we present the structural basis of ligand gating in a K(+) channel that opens in response to intracellular Ca(2+). We have cloned, expressed, analysed electrical properties, and determined the crystal structure of a K(+) channel (MthK) from Methanobacterium thermoautotrophicum in the Ca(2+)-bound, opened state. Eight RCK domains (regulators of K(+) conductance) form a gating ring at the intracellular membrane surface. The gating ring uses the free energy of Ca(2+) binding in a simple manner to perform mechanical work to open the pore.
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Affiliation(s)
- Youxing Jiang
- Howard Hughes Medical Institute, Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
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26
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Abstract
Living cells regulate the activity of their ion channels through a process known as gating. To open the pore, protein conformational changes must occur within a channel's membrane-spanning ion pathway. KcsA and MthK, closed and opened K(+) channels, respectively, reveal how such gating transitions occur. Pore-lining 'inner' helices contain a 'gating hinge' that bends by approximately 30 degrees. In a straight conformation four inner helices form a bundle, closing the pore near its intracellular surface. In a bent configuration the inner helices splay open creating a wide (12 A) entryway. Amino-acid sequence conservation suggests a common structural basis for gating in a wide range of K(+) channels, both ligand- and voltage-gated. The open conformation favours high conduction by compressing the membrane field to the selectivity filter, and also permits large organic cations and inactivation peptides to enter the pore from the intracellular solution.
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Affiliation(s)
- Youxing Jiang
- Howard Hughes Medical Institute, Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
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Pineda-Lucena A, Yi GS, Chang X, Cort JR, Kennedy MA, Edwards AM, Arrowsmith CH. Solution structure of the hypothetical protein MTH0637 from Methanobacterium thermoautotrophicum. J Biomol NMR 2002; 22:291-294. [PMID: 11991357 DOI: 10.1023/a:1014908801766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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28
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Das K, Xiao R, Wahlberg E, Hsu F, Arrowsmith CH, Montelione GT, Arnold E. X-ray crystal structure of MTH938 from Methanobacterium thermoautotrophicum at 2.2 A resolution reveals a novel tertiary protein fold. Proteins 2001; 45:486-8. [PMID: 11746696 DOI: 10.1002/prot.1162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- K Das
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854, USA
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29
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Lee GM, Edwards AM, Arrowsmith CH, McIntosh LP. NMR-based structure of the conserved protein MTH865 from the archaeon Methanobacterium thermoautotrophicum. J Biomol NMR 2001; 21:63-66. [PMID: 11693569 DOI: 10.1023/a:1011928105928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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30
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Bertone P, Kluger Y, Lan N, Zheng D, Christendat D, Yee A, Edwards AM, Arrowsmith CH, Montelione GT, Gerstein M. SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics. Nucleic Acids Res 2001; 29:2884-98. [PMID: 11433035 PMCID: PMC55760 DOI: 10.1093/nar/29.13.2884] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
High-throughput structural proteomics is expected to generate considerable amounts of data on the progress of structure determination for many proteins. For each protein this includes information about cloning, expression, purification, biophysical characterization and structure determination via NMR spectroscopy or X-ray crystallography. It will be essential to develop specifications and ontologies for standardizing this information to make it amenable to retrospective analysis. To this end we created the SPINE database and analysis system for the Northeast Structural Genomics Consortium. SPINE, which is available at bioinfo.mbb.yale.edu/nesg or nesg.org, is specifically designed to enable distributed scientific collaboration via the Internet. It was designed not just as an information repository but as an active vehicle to standardize proteomics data in a form that would enable systematic data mining. The system features an intuitive user interface for interactive retrieval and modification of expression construct data, query forms designed to track global project progress and external links to many other resources. Currently the database contains experimental data on 985 constructs, of which 740 are drawn from Methanobacterium thermoautotrophicum, 123 from Saccharomyces cerevisiae, 93 from Caenorhabditis elegans and the remainder from other organisms. We developed a comprehensive set of data mining features for each protein, including several related to experimental progress (e.g. expression level, solubility and crystallization) and 42 based on the underlying protein sequence (e.g. amino acid composition, secondary structure and occurrence of low complexity regions). We demonstrate in detail the application of a particular machine learning approach, decision trees, to the tasks of predicting a protein's solubility and propensity to crystallize based on sequence features. We are able to extract a number of key rules from our trees, in particular that soluble proteins tend to have significantly more acidic residues and fewer hydrophobic stretches than insoluble ones. One of the characteristics of proteomics data sets, currently and in the foreseeable future, is their intermediate size ( approximately 500-5000 data points). This creates a number of issues in relation to error estimation. Initially we estimate the overall error in our trees based on standard cross-validation. However, this leaves out a significant fraction of the data in model construction and does not give error estimates on individual rules. Therefore, we present alternative methods to estimate the error in particular rules.
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Affiliation(s)
- P Bertone
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
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31
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Collins BM, Harrop SJ, Kornfeld GD, Dawes IW, Curmi PM, Mabbutt BC. Crystal structure of a heptameric Sm-like protein complex from archaea: implications for the structure and evolution of snRNPs. J Mol Biol 2001; 309:915-23. [PMID: 11399068 DOI: 10.1006/jmbi.2001.4693] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The Sm/Lsm proteins associate with small nuclear RNA to form the core of small nuclear ribonucleoproteins, required for processes as diverse as pre-mRNA splicing, mRNA degradation and telomere formation. The Lsm proteins from archaea are likely to represent the ancestral Sm/Lsm domain. Here, we present the crystal structure of the Lsm alpha protein from the thermophilic archaeon Methanobacterium thermoautotrophicum at 2.0 A resolution. The Lsm alpha protein crystallizes as a heptameric ring comprised of seven identical subunits interacting via beta-strand pairing and hydrophobic interactions. The heptamer can be viewed as a propeller-like structure in which each blade consists of a seven-stranded antiparallel beta-sheet formed from neighbouring subunits. There are seven slots on the inner surface of the heptamer ring, each of which is lined by Asp, Asn and Arg residues that are highly conserved in the Sm/Lsm sequences. These conserved slots are likely to form the RNA-binding site. In archaea, the gene encoding Lsm alpha is located next to the L37e ribosomal protein gene in a putative operon, suggesting a role for the Lsm alpha complex in ribosome function or biogenesis.
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Affiliation(s)
- B M Collins
- Department of Chemistry, Macquarie University, NSW 2109, Australia
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32
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Fändrich M, Tito MA, Leroux MR, Rostom AA, Hartl FU, Dobson CM, Robinson CV. Observation of the noncovalent assembly and disassembly pathways of the chaperone complex MtGimC by mass spectrometry. Proc Natl Acad Sci U S A 2000; 97:14151-5. [PMID: 11087821 PMCID: PMC18886 DOI: 10.1073/pnas.240326597] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have analyzed a newly described archaeal GimC/prefoldin homologue, termed MtGimC, by using nanoflow electrospray coupled with time-of-flight MS. The molecular weight of the complex from Methanobacterium thermoautotrophicum corresponds to a well-defined hexamer of two alpha subunits and four beta subunits. Dissociation of the complex within the gas phase reveals a quaternary arrangement of two central subunits, both alpha, and four peripheral beta subunits. By constructing a thermally controlled nanoflow device, we have monitored the thermal stability of the complex by MS. The results of these experiments demonstrate that a significant proportion of the MtGimC hexamer remains intact under low-salt conditions at elevated temperatures. This finding is supported by data from CD spectroscopy, which show that at physiological salt concentrations, the complex remains stable at temperatures above 65 degrees C. Mass spectrometric methods were developed to monitor in real time the assembly of the MtGimC hexamer from its component subunits. By using this methodology, the mass spectra recorded throughout the time course of the experiment showed the absence of any significantly populated intermediates, demonstrating that the assembly process is highly cooperative. Taken together, these data show that the complex is stable under the elevated temperatures that are appropriate for its hyperthermophile host and demonstrate that the assembly pathway leads exclusively to the hexamer, which is likely to be a structural unit in vivo.
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Affiliation(s)
- M Fändrich
- Oxford Centre for Molecular Sciences, New Chemistry Laboratory, University of Oxford, South Parks Road, OX1 3QT, United Kingdom
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33
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Affiliation(s)
- A D Miranker
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, P.O. Box 208114, New Haven, CT 06520, USA.
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Cort JR, Yee A, Edwards AM, Arrowsmith CH, Kennedy MA. Structure-based functional classification of hypothetical protein MTH538 from Methanobacterium thermoautotrophicum. J Mol Biol 2000; 302:189-203. [PMID: 10964569 DOI: 10.1006/jmbi.2000.4052] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The structure of MTH538, a previously uncharacterized hypothetical protein from Methanobacterium thermoautotrophicum, has been determined by NMR spectroscopy. MTH538 is one of numerous structural genomics targets selected in a genome-wide survey of uncharacterized sequences from this organism. MTH538 is a so-called singleton, a sequence not closely related to any other (known) sequences. The structure of MTH538 closely resembles the known structures of receiver domains from two component response regulator systems, such as CheY, and is similar to the structures of flavodoxins and GTP-binding proteins. Tests on MTH538 for characteristic activities of CheY and flavodoxin were negative. MTH538 did not become phosphorylated in the presence of acetyl phosphate and Mg(2+), although it appeared to bind Mg(2+). MTH538 also did not bind flavin mononucleotide (FMN) or coenzyme F(420). Nevertheless, sequence and structure parallels between MTH538/CheY and two families of ATPase/phosphatase proteins suggest that MTH538 may have a role in a phosphorylation-independent two-component response regulator system.
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Affiliation(s)
- J R Cort
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, EMSL 2569 K8-98, Richland, WA 99352, USA
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35
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Kozlov G, Ekiel I, Beglova N, Yee A, Dharamsi A, Engel A, Siddiqui N, Nong A, Gehring K. Rapid fold and structure determination of the archaeal translation elongation factor 1beta from Methanobacterium thermoautotrophicum. J Biomol NMR 2000; 17:187-194. [PMID: 10959626 DOI: 10.1023/a:1008363304977] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The tertiary fold of the elongation factor, aEF-1beta, from Methanobacterium thermoautotrophicum was determined in a high-throughput fashion using a minimal set of NMR experiments. NMR secondary structure prediction, deuterium exchange experiments and the analysis of chemical shift perturbations were combined to identify the protein fold as an alpha-beta sandwich typical of many RNA binding proteins including EF-G. Following resolution of the tertiary fold, a high resolution structure of aEF-1beta was determined using heteronuclear and homonuclear NMR experiments and a semi-automated NOESY assignment strategy. Analysis of the aEF-1beta structure revealed close similarity to its human analogue, eEF-1beta. In agreement with studies on EF-Ts and human EF-1beta, a functional mechanism for nucleotide exchange is proposed wherein Phe46 on an exposed loop acts as a lever to eject GDP from the associated elongation factor G-protein, aEF-1alpha. aEF-1beta was also found to bind calcium in the groove between helix alpha2 and strand beta4. This novel feature was not observed previously and may serve a structural function related to protein stability or may play a functional role in archaeal protein translation.
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Affiliation(s)
- G Kozlov
- McGill University, Department of Biochemistry, Montreal, PQ, Canada
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36
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Shechter DF, Ying CY, Gautier J. The intrinsic DNA helicase activity of Methanobacterium thermoautotrophicum delta H minichromosome maintenance protein. J Biol Chem 2000; 275:15049-59. [PMID: 10747908 DOI: 10.1074/jbc.m000398200] [Citation(s) in RCA: 126] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Minichromosome maintenance proteins (MCMs) form a family of conserved molecules that are essential for initiation of DNA replication. All eukaryotes contain six orthologous MCM proteins that function as heteromultimeric complexes. The sequencing of the complete genomes of several archaebacteria has shown that MCM proteins are also present in archaea. The archaea Methanobacterium thermoautotrophicum contains a single MCM-related sequence. Here we report on the expression and purification of the recombinant M. thermoautotrophicum MCM protein (MtMCM) in both Escherichia coli and baculovirus-infected cells. We show that purified MtMCM protein assembles in large macromolecular complexes consistent in size with being double hexamers. We demonstrate that MtMCM contains helicase activity that preferentially uses dATP and DNA-dependent dATPase and ATPase activities. The intrinsic helicase activity of MtMCM is abolished when a conserved lysine in the helicase domain I/nucleotide binding site is mutated. MtMCM helicase unwinds DNA duplexes in a 3' --> 5' direction and can unwind up to 500 base pairs in vitro. The kinetics, processivity, and directionality of MtMCM support its role as a replicative helicase in M. thermoautotrophicum. This strongly suggests that this function is conserved for MCM proteins in eukaryotes where a replicative helicase has yet to be identified.
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Affiliation(s)
- D F Shechter
- Department of Genetics and Development, Columbia University, New York, New York 10032, USA
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37
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Abstract
The membrane potential (delta psi) of whole cells of Methanobacterium thermoautotrophicum strain delta H was estimated under different external conditions using a TPP(+)-sensitive electrode. The results show that the delta psi values of M. thermoautotrophicum at alkaline pHout (8.5) are comparable with delta psi values under slightly acidic conditions (pH 6.8; 230 and 205 mV, respectively). On the other hand, the size of colonies on Petri dishes was remarkably smaller at pH 8.5 than at 6.8. The delta psi was insensitive to relevant ATPase inhibitors. At pH 6.8, the protonophore 3,3',4',5-tetrachlorosalicylanilide (TCS) strongly inhibited delta psi formation and ATP synthesis driven by methanogenic electron transport. On the other hand, at pH 8.5 the CH4 formation and ATP synthesis were insensitive to TCS and a protonophore-resistant delta psi of approximately 150 mV was determined. The finding of a protonophore-resistant delta psi at pH 8.5 indicates that at alkaline pHout these cells can switch from H(+)-energetics to Na(+)-energetics, when the delta [symbol: see text] H+ becomes limited. The results strongly support the hypothesis that at alkaline pHout Na+ ions might fully substitute for H+ in these cells as the coupling ions.
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Affiliation(s)
- P Polák
- Institute of Animal Biochemistry and Genetics, Slovak Academy of Sciences, 90 028 lvanka pri Dunaji, Slovakia.
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Leroux MR, Fändrich M, Klunker D, Siegers K, Lupas AN, Brown JR, Schiebel E, Dobson CM, Hartl FU. MtGimC, a novel archaeal chaperone related to the eukaryotic chaperonin cofactor GimC/prefoldin. EMBO J 1999; 18:6730-43. [PMID: 10581246 PMCID: PMC1171735 DOI: 10.1093/emboj/18.23.6730] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Group II chaperonins in the eukaryotic and archaeal cytosol assist in protein folding independently of the GroES-like cofactors of eubacterial group I chaperonins. Recently, the eukaryotic chaperonin was shown to cooperate with the hetero-oligomeric protein complex GimC (prefoldin) in folding actin and tubulins. Here we report the characterization of the first archaeal homologue of GimC, from Methanobacterium thermoautotrophicum. MtGimC is a hexamer of 87 kDa, consisting of two alpha and four beta subunits of high alpha-helical content that are predicted to contain extended coiled coils and represent two evolutionarily conserved classes of Gim subunits. Reconstitution experiments with MtGimC suggest that two subunits of the alpha class (archaeal Gimalpha and eukaryotic Gim2 and 5) form a dimer onto which four subunits of the beta class (archaeal Gimbeta and eukaryotic Gim1, 3, 4 and 6) assemble. MtGimalpha and beta can form hetero-complexes with yeast Gim subunits and MtGimbeta partially complements yeast strains lacking Gim1 and 4. MtGimC is a molecular chaperone capable of stabilizing a range of non-native proteins and releasing them for subsequent chaperonin-assisted folding. In light of the absence of Hsp70 chaperones in many archaea, GimC may fulfil an ATP-independent, Hsp70-like function in archaeal de novo protein folding.
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Affiliation(s)
- M R Leroux
- Max-Planck-Institut für Biochemie, Department of Cellular Biochemistry, Am Klopferspitz 18A, D-82152 Martinsried, Germany
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Ebert S, Rieger PG, Knackmuss HJ. Function of coenzyme F420 in aerobic catabolism of 2,4, 6-trinitrophenol and 2,4-dinitrophenol by Nocardioides simplex FJ2-1A. J Bacteriol 1999; 181:2669-74. [PMID: 10217752 PMCID: PMC93703 DOI: 10.1128/jb.181.9.2669-2674.1999] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2,4,6-Trinitrophenol (picric acid) and 2,4-dinitrophenol were readily biodegraded by the strain Nocardioides simplex FJ2-1A. Aerobic bacterial degradation of these pi-electron-deficient aromatic compounds is initiated by hydrogenation at the aromatic ring. A two-component enzyme system was identified which catalyzes hydride transfer to picric acid and 2,4-dinitrophenol. Enzymatic activity was dependent on NADPH and coenzyme F420. The latter could be replaced by an authentic preparation of coenzyme F420 from Methanobacterium thermoautotrophicum. One of the protein components functions as a NADPH-dependent F420 reductase. A second component is a hydride transferase which transfers hydride from reduced coenzyme F420 to the aromatic system of the nitrophenols. The N-terminal sequence of the F420 reductase showed high homology with an F420-dependent NADP reductase found in archaea. In contrast, no N-terminal similarity to any known protein was found for the hydride-transferring enzyme.
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Affiliation(s)
- S Ebert
- Institut für Mikrobiologie der Universität Stuttgart, Stuttgart, Germany
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Begley TJ, Cunningham RP. Methanobacterium thermoformicicum thymine DNA mismatch glycosylase: conversion of an N-glycosylase to an AP lyase. Protein Eng 1999; 12:333-40. [PMID: 10325404 DOI: 10.1093/protein/12.4.333] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The thymine DNA mismatch glycosylase from Methanobacterium thermoformicicum, a member of the endonuclease III family of repair proteins, excises the pyrimidine base from T-G and U-G mismatches. Unlike endonuclease III, it does not cleave the phosphodiester backbone by a beta-elimination reaction. This cleavage event has been attributed to a nucleophilic attack by the conserved Lys120 of endonuclease III on the aldehyde group at C1' of the deoxyribose and subsequent Schiff base formation. The inability of TDG to perform this beta-elimination event appears to be due to the presence of a tyrosine residue at the position equivalent to Lys120 in endonuclease III. The purpose of this work was to investigate the requirements for AP lyase activity. We replaced Tyr126 in TDG with a lysine residue to determine if this replacement would yield an enzyme with an associated AP lyase activity capable of removing a mismatched pyrimidine. We observed that this replacement abolishes the glycosylase activity of TDG but does not affect substrate recognition. It does, however, convert the enzyme into an AP lyase. Chemical trapping assays show that this cleavage proceeds through a Schiff base intermediate and suggest that the amino acid at position 126 interacts with C1' on the deoxyribose sugar.
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Affiliation(s)
- T J Begley
- Department of Biological Sciences, SUNY at Albany, Albany, NY 12222, USA
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Zhu W, Sandman K, Lee GE, Reeve JN, Summers MF. NMR structure and comparison of the archaeal histone HFoB from the mesophile Methanobacterium formicicum with HMfB from the hyperthermophile Methanothermus fervidus. Biochemistry 1998; 37:10573-80. [PMID: 9692946 DOI: 10.1021/bi973007a] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The solution-state structure of the recombinant archaeal histone rHFoB, from the mesophile Methanobacterium formicicum, has been determined by two- and three-dimensional (3D) proton homonuclear correlated nuclear magnetic resonance (NMR) methods. On the basis of 951 nuclear Overhauser effect (NOE)-derived distance restraints, rHFoB monomers form the histone fold and assemble into symmetric (rHFoB)2 dimers that have a structure consistent with assembly into archaeal nucleosomes. rHFoB exhibits approximately 78% sequence homology with rHMfB from the hyperthermophile Methanothermus fervidus, and the results obtained demonstrate that these two proteins have very similar 3D structures, with a root-mean-square deviation for backbone atoms of 0.65 +/- 0.13 A2. (rHFoB)2 dimers however unfold at lower temperatures and require a higher salt environment for stability than (rHMfB)2 dimers, and comparing the structures, we predict that these differences result from unfavorable surface-located ionic interactions and a larger, more solvent-accessible cavity adjacent to residue G36 in the hydrophobic core of (rHFoB)2.
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Affiliation(s)
- W Zhu
- Howard Hughes Medical Institute, Baltimore, Maryland 21250, USA
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42
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Abstract
The temperature, salt, and pH dependencies of unfolding of four recombinant (r) archaeal histones (rHFoB from the mesophile Methanobacterium formicicum, and rHMfA, rHMfB, and rHPyA1 from the hyperthermophiles Methanothermus fervidus and Pyrococcus strain GB-3a) have been determined by circular dichroism spectroscopy (CD) and differential scanning calorimetry (DSC). The thermal unfolding of these proteins is > 90% reversible, with concentration-dependent apparent Tm values and asymmetric unfolding transitions that are fit well by a two-state unfolding model in which a histone dimer unfolds to two random coil monomers. rHPyA1 dimers are stable in the absence of salt, whereas rHMfA, rHMfB, and rHFoB dimers unfold at 20 degrees C and pH 2 in solutions containing < 200 mM, < 400 mM, and < 1.5 M KCl, respectively. rHMfA, rHMfB, and rHFoB also experience significant cold denaturation in low salt concentrations and at low pH. The midpoint of thermal unfolding of a 1 M protein solution (T degree value) and the temperature dependency of the free energy of unfolding have been established for each histone, and both parameters correlate with the growth temperature of the originating archaeon. The changes in heat capacity upon unfolding are similar for the four histones, indicating that enhanced thermostability is not obtained by altering the curvature of the stability curve. Rather, the stability curves for the histones from the hyperthermophiles are displaced vertically to higher energies and laterally to higher Tmax values relative to the stability curve for rHFoB. The maximal free energies of unfolding for rHFoB, rHMfA, rHMfB, and rHPyA1 are 7.2, 15.5, 14.6, and 17.2 kcal/mol at 32, 35, 40, and 44 degrees C, respectively. T degree values for rHFoB, rHMfA, rHMfB, and rHPyA1 are 75, 104, 113, and 114 degrees C, respectively, at pH 5 in 0.2 M KCl. Structural features within the conserved histone fold that might confer these stability differences are discussed.
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Affiliation(s)
- W T Li
- Department of Microbiology, Ohio State University, Columbus 43210-1292, USA
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Abstract
The basic scheme for the biosynthesis of methanopterin (MPT) in Methanobacterium thermoautotrophicum strain DeltaH, and M. thermoautotrophicum strain Marburg, has been shown to be the same as that recently determined for Methanosarcina thermophila strain TM-1. This scheme has, as one of its unique steps, the condensation of 4-aminobenzoic acid with 5-phospho-alpha-d-ribosyl diphosphate (PRPP) to form 4-(beta-d-ribofuranosyl)aminobenzene 5'-phosphate (beta-RFA-P). Labeling experiments with each of these organisms have established that the sites in the overall sequence of reactions from beta-RFA-P to MPT, where the S-adenosylmethionine-dependent C-9 and C-7 methylations of the pterin-containing intermediates occur, are organism related. In this work, cell extracts of M. thermoautotrophicum strain DeltaH, and M. thermoautotrophicum strain Marburg were found to contain significant amounts of methanopterin lacking the phosphate and 2-hydroxyglutaric acid groups.
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Affiliation(s)
- R H White
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0308, USA.
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Harms U, Thauer RK. Identification of the active site histidine in the corrinoid protein MtrA of the energy-conserving methyltransferase complex from Methanobacterium thermoautotrophicum. Eur J Biochem 1997; 250:783-8. [PMID: 9461302 DOI: 10.1111/j.1432-1033.1997.00783.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The energy-conserving corrinoid-containing MtrA-H complex from Methanobacterium thermoautotrophicum is composed of eight different subunits of which MtrA harbors the corrinoid prosthetic group. EPR spectroscopic evidence has recently been presented for a histidine residue as a cobalt ligand of the cobamide [Harms, U. & Thauer, R. K. (1996a) Eur. J. Biochem. 241, 149-154]. This active site histidine was now identified by site-directed mutagenesis to be His84 in the MtrA sequence that contains three histidines. This result was substantiated by sequence comparison of MtrA from M. thermoautotrophicum, Methanococcus jannaschii, and Methanopyrus kandleri and of MtxA from Methanosarcina harkeri showing that only His84 is conserved. For comparison, the DNA sequences of the mtrEDCBAGH operon in M. kandleri and of the mtxXAH operon in M. barkeri were determined.
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Affiliation(s)
- U Harms
- Max-Planck-Institut für terrestrische Mikrobiologie and Laboratorium für Mikrobiologie des Fachbereichs Biologie der Philipps-Universität, Marburg, Germany
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Duboc P, Schill N, Menoud L, van Gulik W, von Stockar U. Measurements of sulfur, phosphorus and other ions in microbial biomass: influence on correct determination of elemental composition and degree of reduction. J Biotechnol 1995; 43:145-58. [PMID: 8562020 DOI: 10.1016/0168-1656(95)00135-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The elemental composition of microorganisms varies widely with respect to the N, S, P and ash content as well as many trace elements depending on microorganism and growth conditions. As a consequence, the mass of 1 C-mol of biomass can differ considerably from one microorganism to another. Experimental results show that sulfur is completely volatilized during combustion, so that the calculation of the mass fraction of oxygen is affected when S is not measured. However, its neglect does not seriously affect the elemental composition and the degree of reduction of biomass. Phosphorus is found in ash after combustion at the same degree of reduction as in biomass. Therefore, oxygen bound to it should be included in the elemental formula, so that the degree of reduction of biomass remains unchanged by inclusion of P into elemental formula. No external oxygen is incorporated into biomass during combustion and thus the measured ash fraction is correct.
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Affiliation(s)
- P Duboc
- Institut de Génie Chimique, Ecole Polytechnique Fédédrale de Lausanne, Switzerland
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Wasserfallen A, Huber K, Leisinger T. Purification and structural characterization of a flavoprotein induced by iron limitation in Methanobacterium thermoautotrophicum Marburg. J Bacteriol 1995; 177:2436-41. [PMID: 7730275 PMCID: PMC176902 DOI: 10.1128/jb.177.9.2436-2441.1995] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Cells of Methanobacterium thermoautotrophicum (strain Marburg) grown under iron-limiting conditions were found to synthesize a soluble polypeptide as one of the major cell proteins. This polypeptide purified as a homotetramer (170 kDa [subunit molecular mass, 43 kDa]) had a UV-visible spectrum typical of flavoproteins and contained 0.7 mol of flavin mononucleotide per mol of monomer. Quantitative analysis by immunoblotting with polyclonal antibodies indicated that the flavoprotein, which amounts to about 0.6% of soluble cell protein under iron-sufficient conditions (> or = 50 microM Fe2+), was induced fivefold by iron limitation (< 12 microM Fe2+). The flavoprotein-encoding gene, fprA, was cloned and sequenced. Sequence analysis revealed a well-conserved archaebacterial consensus promoter upstream of fprA, a flavodoxin signature within fprA, and 28% amino acid identity with a putative flavin mononucleotide-containing protein of Rhodobacter capsulatus which is found within an operon involved in nitrogen fixation. A possible physiological function for the flavoprotein is discussed.
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Affiliation(s)
- A Wasserfallen
- Mikrobiologisches Institut, Swiss Federal Institute of Technology, Zurich
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Abstract
The mesophilic methanogen Methanobacterium formicicum JF-1 has been shown to contain three members of the HMf family of archaeal histones, designated HFoA1, HFoA2, and HFoB, and their encodinig genes (hfoA1, hfoA2, and hfoB) have been cloned and sequenced. The HFo histones have primary sequences that are 75 to 82% identical to the HMf sequences and appear to share ancestry with the core histones that form the eukaryal nucleosome. The HFo proteins bind and compact DNA molecules into nucleosome-like structures apparently identical to those formed by the HMf proteins, but, in contrast to the HMf proteins, this activity of the HFo proteins is lost after incubation at 95 degrees C for 5 h.
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Affiliation(s)
- T J Darcy
- Department of Microbiology, Ohio State University, Columbus 43210
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Morii H, Koga Y. Asymmetrical topology of diether- and tetraether-type polar lipids in membranes of Methanobacterium thermoautotrophicum cells. J Biol Chem 1994; 269:10492-7. [PMID: 8144633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
We investigated the distribution of diether polar lipids between the inner and outer leaflets of the membrane of Methanobacterium thermoautotrophicum comparing the orientation of tetraether polar lipids, which constitute a monolayer in the same membrane. Three kinds of reactions were employed for intact cells or protoplasts and unsealed membrane fragments prepared from the organism: glycosidase digestion for glycolipids, NaIO4 oxidation for glycolipids and inositol lipids, and trinitrophenylation for aminophospholipids. The results indicated that (a) most gentiobiose residues of both diether and tetraether polar lipids were exposed on the outside of the cells; (b) serine and inositol residues of both diether and tetraether polar lipids were mainly oriented to the cytoplasmic surface of the membrane; and (c) approximately 80% of archaetidylethanolamine (diether type) was distributed in the outer leaflet of the membrane bilayer, while only 25% of the ethanolamine residue of gentiobiosyl caldarchaetidylethanolamine (tetraether type) was oriented to the outer surface of the membrane. These results, except for ethanolamine lipids, are consistent with the hypothesis that the tetraether polar lipids are synthesized from the corresponding diether polar lipid precursors that have been already substituted by polar groups in the membrane by head-to-head condensation without rearrangement of lipids.
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Affiliation(s)
- H Morii
- Department of Chemistry, University of Occupational and Environmental Health, Fukuoka, Japan
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Abstract
Several plasmid DNAs have been isolated from mesophilic and thermophilic archaebacteria. Their superhelical densities were estimated at their host strain's optimal growth temperature, and in some representative strains, the presence of reverse gyrase activity (positive DNA supercoiling) was investigated. We show here that these plasmids can be grouped in two clusters with respect to their topological state. The group I plasmids have a highly negatively supercoiled DNA and belong to the mesophilic archaebacteria and all types of eubacteria. The group II plasmids have DNA which is close to the relaxed state and belong exclusively to the thermophilic archaebacteria. All archaebacteria containing a relaxed plasmid, with the exception of the moderately thermophilic methanogen Methanobacterium thermoautotrophicum Marburg, also exhibit reverse gyrase activity. These findings show that extrachromosomal DNAs with very different topological states coexist in the archaebacterial domain.
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Affiliation(s)
- F Charbonnier
- Institut de Génétique et Microbiologie, Université de Paris-Sud, Orsay, France
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Gorkovenko A, Roberts MF. Cyclic 2,3-diphosphoglycerate as a component of a new branch in gluconeogenesis in Methanobacterium thermoautotrophicum delta H. J Bacteriol 1993; 175:4087-95. [PMID: 8320225 PMCID: PMC204838 DOI: 10.1128/jb.175.13.4087-4095.1993] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
A unique compound, cyclic 2,3-diphosphoglycerate (cDPG), is the major soluble carbon and phosphorus solute in Methanobacterium thermoautotrophicum delta H under optimal conditions of cell growth. It is a component of an unusual branch in gluconeogenesis in these bacteria. [U-13C]acetate pulse-[12C]acetate chase methodology was used to observe the relationship between cDPG and other metabolites (2-phosphoglycerate and 2,3-diphosphoglycerate [2-PG and 2,3-DPG, respectively]) of this branch. It was demonstrated that cells could grow exponentially under conditions in which 2-PG and 2,3-DPG, rather than cDPG, were the major solutes. While the total concentration of these three phosphorylated molecules was maintained, rapid interconversion of 13C label among them was observed. Label flow from 2-PG to 2,3-DPG to cDPG to polymer is the usual direction in this pathway in exponentially growing cells, while the reverse reactions sometimes predominate in the stationary phase. Evidence of the presence of a polymeric compound in this pathway was provided by 13C nuclear magnetic resonance (one-dimensional and two-dimensional INADEQUATE) studies of solubilized cell debris.
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Affiliation(s)
- A Gorkovenko
- Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02167
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