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Yasuno Y, Nakayama A, Saito K, Kitsuwa K, Okamura H, Komeyama M, Hemmi H, Shinada T. Total Synthesis and Structure Confirmation of trans-Anhydromevalonate-5-phosphate, a Key Biosynthetic Intermediate of the Archaeal Mevalonate Pathway. J Nat Prod 2021; 84:2749-2754. [PMID: 34597517 DOI: 10.1021/acs.jnatprod.1c00615] [Citation(s) in RCA: 2] [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: 06/13/2023]
Abstract
The mevalonate pathway is an upstream terpenoid biosynthetic route of terpenoids for providing the two five-carbon units, dimethylallyl diphosphate, and isopentenyl diphosphate. Recently, trans-anhydromevalonate-5-phosphate (tAHMP) was isolated as a new biosynthetic intermediate of the archaeal mevalonate pathway. In this study, we would like to report the first synthesis of tAHMP and its enzymatic transformation using one of the key enzymes, mevalonate-5-phosphate dehydratase from a hyperthermophilic archaeon, Aeropyrum pernix. Starting from methyl tetrolate, a Cu-catalyzed allylation provided an E-trisubstituted olefin in a stereoselective manner. The resulting E-olefin was transformed to tAHMP by cleavage of the olefin and phosphorylation. The structure of the synthetic tAHMP was unambiguously determined by NOESY analysis.
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Affiliation(s)
- Yoko Yasuno
- Graduate School of Science, Osaka City University, 3-3-138, Sugimoto, Sumiyoshi, Osaka, 558-8585, Japan
| | - Atsushi Nakayama
- Graduate School of Science, Osaka City University, 3-3-138, Sugimoto, Sumiyoshi, Osaka, 558-8585, Japan
| | - Kai Saito
- Graduate School of Science, Osaka City University, 3-3-138, Sugimoto, Sumiyoshi, Osaka, 558-8585, Japan
| | - Kohei Kitsuwa
- Graduate School of Science, Osaka City University, 3-3-138, Sugimoto, Sumiyoshi, Osaka, 558-8585, Japan
| | - Hironori Okamura
- Graduate School of Science, Osaka City University, 3-3-138, Sugimoto, Sumiyoshi, Osaka, 558-8585, Japan
| | - Mutsumi Komeyama
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Aichi, Japan
| | - Hisashi Hemmi
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Aichi, Japan
| | - Tetsuro Shinada
- Graduate School of Science, Osaka City University, 3-3-138, Sugimoto, Sumiyoshi, Osaka, 558-8585, Japan
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Skrt M, Jamnik P, Poklar Ulrih N. Antioxidative Activity of Methanolic and Water Extracts from the Hyperthermophilic Archaeon Aeropyrum pernix K1. Acta Chim Slov 2018; 65:172-182. [PMID: 29562111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023] Open
Abstract
The hyperthermophilic archaeon Aeropyrum pernix has adapted to optimal growth under high temperatures in saline environments and under oxidizing conditions. In the present study, we focused on the antioxidative activity of proteins from A. pernix K1. Following high temperature methanol and water extractions of the protein from the biomass of A. pernix K1, the total sulphydryl groups and radical scavenging activities were investigated. The total protein in the methanolic extract was 36% lower and showed 10% fewer sulphydryl groups than that from the water extract. However, the radical scavenging activity of the water extract was four-fold greater than for the methanolic extract. The proteins of both of these extracts were separated by two-dimensional electrophoresis, and selected proteins were identified using mass spectrometry. The majority of these identified proteins were intracellular proteins, such as those involved in oxidative stress responses and osmotic stress responses, and proteins with hydrolase and dehydrogenase activities. These proteins are also common to most organisms, and included putative uncharacterized proteins.
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Abstract
The function of membrane-embedded proteins such as ion channels depends crucially on their conformation. We demonstrate how conformational changes in asymmetric membrane proteins may be inferred from measurements of their diffusion. Such proteins cause local deformations in the membrane, which induce an extra hydrodynamic drag on the protein. Using membrane tension to control the magnitude of the deformations, and hence the drag, measurements of diffusivity can be used to infer-via an elastic model of the protein-how conformation is changed by tension. Motivated by recent experimental results [Quemeneur et al., Proc. Natl. Acad. Sci. U.S.A. 111, 5083 (2014)], we focus on KvAP, a voltage-gated potassium channel from Aeropyrum pernix. The conformation of KvAP is found to change considerably due to tension, with its "walls," where the protein meets the membrane, undergoing significant angular strains. The torsional stiffness is determined to be 26.8k(B)T per radian at room temperature. This has implications for both the structure and the function of such proteins in the environment of a tension-bearing membrane.
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Affiliation(s)
- Richard G Morris
- Department of Physics and Centre for Complexity Science, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Matthew S Turner
- Department of Physics and Centre for Complexity Science, University of Warwick, Coventry CV4 7AL, United Kingdom
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Bhuiya MW, Suryadi J, Zhou Z, Brown BA. Structure of the Aeropyrum pernix L7Ae multifunctional protein and insight into its extreme thermostability. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:979-88. [PMID: 23989144 PMCID: PMC3758144 DOI: 10.1107/s1744309113021799] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 08/05/2013] [Indexed: 11/11/2022]
Abstract
Archaeal ribosomal protein L7Ae is a multifunctional RNA-binding protein that directs post-transcriptional modification of archaeal RNAs. The L7Ae protein from Aeropyrum pernix (Ap L7Ae), a member of the Crenarchaea, was found to have an extremely high melting temperature (>383 K). The crystal structure of Ap L7Ae has been determined to a resolution of 1.56 Å. The structure of Ap L7Ae was compared with the structures of two homologs: hyperthermophilic Methanocaldococcus jannaschii L7Ae and the mesophilic counterpart mammalian 15.5 kD protein. The primary stabilizing feature in the Ap L7Ae protein appears to be the large number of ion pairs and extensive ion-pair network that connects secondary-structural elements. To our knowledge, Ap L7Ae is among the most thermostable single-domain monomeric proteins presently observed.
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Affiliation(s)
| | - Jimmy Suryadi
- Department of Chemistry, Wake Forest University, Winston-Salem, NC 27109, USA
| | - Zholi Zhou
- Bristol-Myers Squibb, Syracuse, NY 13221, USA
| | - Bernard Andrew Brown
- Womble Carlyle Sandridge and Rice LLP, One West Fourth Street, Winston-Salem, NC 27101, USA
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Šnajder M, Vilfan T, Černilec M, Rupreht R, Popović M, Juntes P, Šerbec VČ, Ulrih NP. Enzymatic degradation of PrPSc by a protease secreted from Aeropyrum pernix K1. PLoS One 2012; 7:e39548. [PMID: 22761822 PMCID: PMC3386259 DOI: 10.1371/journal.pone.0039548] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 05/22/2012] [Indexed: 11/18/2022] Open
Abstract
Background An R30 fraction from the growth medium of Aeropyrum pernix was analyzed for the protease that can digest the pathological prion protein isoform (PrPSc) from different species (human, bovine, deer and mouse). Methodology/Principal Findings Degradation of the PrPSc isoform by the R30 fraction and the purified protease was evaluated using the 6H4 anti-PrP monoclonal antibody. Fragments from the N-terminal and C-terminal of PrPSc were also monitored by Western blotting using the EB8 anti-PrP monoclonal antibody, and by dot blotting using the C7/5 anti-PrP monoclonal antibody, respectively. For detection of smaller peptides from incomplete digestion of PrPSc, the EB8 monoclonal antibody was used after precipitation with sodium phosphotungstate. Characterization of the purified active protease from the R30 fraction was achieved, through purification by fast protein liquid chromatography, and identification by tandem mass spectrometry the serine metalloprotease pernisine. SDS-PAGE and zymography show the purified pernisine plus its proregion with a molecular weight of ca. 45 kDa, and the mature purified pernisine as ca. 23 kDa. The purified pernisine was active between 58°C and 99°C, and between pH 3.5 and 8.0. The temperature and pH optima of the enzymatic activity of the purified pernisine in the presence of 1 mM CaCl2 were 105°C ±0.5°C and pH 6.5±0.2, respectively. Conclusions/Significance Our study has identified and characterized pernisine as a thermostable serine metalloprotease that is secreted from A. pernix and that can digest the pathological prion protein PrPSc.
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Affiliation(s)
- Marko Šnajder
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Tanja Vilfan
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Černilec
- Blood Transfusion Center of Slovenia, Ljubljana, Slovenia
| | - Ruth Rupreht
- Blood Transfusion Center of Slovenia, Ljubljana, Slovenia
| | - Mara Popović
- Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Polona Juntes
- Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | | | - Nataša Poklar Ulrih
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CipKeBiP), Ljubljana, Slovenia
- * E-mail:
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Affiliation(s)
- Roxana E Georgescu
- Laboratory of DNA Replication, Howard Hughes Medical Institute, Rockefeller University, New York, NY 10065, USA
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Abstract
DNA replication in archaea and in eukaryotes share many similarities. We report the structure of an archaeal origin recognition complex protein, ORC1, bound to an origin recognition box, a DNA sequence that is found in multiple copies at replication origins. DNA binding is mediated principally by a C-terminal winged helix domain that inserts deeply into the major and minor grooves, widening them both. However, additional DNA contacts are made with the N-terminal AAA+ domain, which inserts into the minor groove at a characteristic G-rich sequence, inducing a 35 degrees bend in the duplex and providing directionality to the binding site. Both contact regions also induce substantial unwinding of the DNA. The structure provides insight into the initial step in assembly of a replication origin and recruitment of minichromosome maintenance (MCM) helicase to that origin.
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Affiliation(s)
- Martin Gaudier
- Cancer Research UK Clare Hall Laboratories, London Research Institute, Blanche Lane, South Mimms, Potters Bar, Herts EN6 3LD, UK
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Ulrih NP, Adamlje U, Nemec M, Sentjurc M. Temperature- and pH-Induced Structural Changes in the Membrane of the Hyperthermophilic Archaeon Aeropyrum pernix K1. J Membr Biol 2007; 219:1-8. [PMID: 17713807 DOI: 10.1007/s00232-007-9061-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [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: 04/03/2007] [Accepted: 06/20/2007] [Indexed: 11/28/2022]
Abstract
The influence of pH and temperature on the structural organization, fluidity and permeability of the hyperthermophilic archaeon membrane was investigated in situ by a combination of electron paramagnetic resonance (EPR) and fluorescence emission spectroscopy. For EPR measurements, Aeropyrum pernix cells, after growing at different pHs, were spin-labeled with the doxyl derivative of palmitic acid methylester (MeFASL(10,3)). From the EPR spectra maximal hyperfine splitting (2A (max)) and empirical correlation time (tau (emp)), which are related to mean membrane fluidity, were determined. The mean membrane fluidity increases with temperature and depends on the pH of the growth medium. Computer simulation of the EPR spectra shows that membrane of A. pernix is heterogeneous and consists of the regions characterized with three different types of motional characteristics, which define three types of membrane domains. Order parameter and proportion of the spin probes in the three types of domains define mean membrane fluidity. The fluidity changes of the membrane with pH and temperature correlate well with the ratio between the fluorescence emission intensity of the first and third bands in the vibronic spectra of pyrene, I(1)/I(3). At pH 7.0 a decrease of I(1)/I(3) from 2.0 to 1.2, due to the penetration of pyrene into the nonpolar membrane region, is achieved at temperatures above 65 degrees C, the lower temperature limit of A. pernix growth.
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Affiliation(s)
- Natasa Poklar Ulrih
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 1001, 1000 Ljubljana, Slovenia.
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Tanaka H, Umehara T, Inaka K, Takahashi S, Shibata R, Bessho Y, Sato M, Sugiyama S, Fusatomi E, Terada T, Shirouzu M, Sano S, Motohara M, Kobayashi T, Tanaka T, Tanaka A, Yokoyama S. Crystallization of the archaeal transcription termination factor NusA: a significant decrease in twinning under microgravity conditions. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:69-73. [PMID: 17277442 PMCID: PMC2330117 DOI: 10.1107/s1744309106054625] [Citation(s) in RCA: 6] [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] [Received: 08/14/2006] [Accepted: 12/15/2006] [Indexed: 11/11/2022]
Abstract
The transcription termination factor NusA from Aeropyrum pernix was crystallized using a counter-diffusion technique in both terrestrial and microgravity environments. Crystallization under microgravity conditions significantly reduced the twinning content (1.0%) compared with terrestrially grown crystals (18.3%) and improved the maximum resolution from 3.0 to 2.29 A, with similar unit-cell parameters. Based on a comparison of the crystal parameters, the effect of microgravity on protein crystallization is discussed.
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Affiliation(s)
- Hiroaki Tanaka
- Confocal Science Inc., Wakamatsu Building 7F, 3-3-6 Nihonbashi Hon-cho, Chuo-ku, Tokyo 103-0023, Japan
| | - Takashi Umehara
- RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Koji Inaka
- Maruwa Foods Inc., 170 Tsutsui-cho, Yamatokoriyama, Nara 639-1123, Japan
| | - Sachiko Takahashi
- Confocal Science Inc., Wakamatsu Building 7F, 3-3-6 Nihonbashi Hon-cho, Chuo-ku, Tokyo 103-0023, Japan
| | - Rie Shibata
- RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Yoshitaka Bessho
- RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Masaru Sato
- Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan
| | - Shigeru Sugiyama
- MolLogics Inc., 1-7 Hikari-dai, Seika-cho, Soraku-gun, Kyoto 619-0203, Japan
| | - Emiko Fusatomi
- RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Takaho Terada
- RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Mikako Shirouzu
- RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Satoshi Sano
- Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan
| | - Moritoshi Motohara
- Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan
| | - Tomoyuki Kobayashi
- Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan
| | - Tetsuo Tanaka
- Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan
| | - Akiko Tanaka
- RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Correspondence e-mail:
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Yamazaki S, Yamazaki J, Nishijima K, Otsuka R, Mise M, Ishikawa H, Sasaki K, Tago SI, Isono K. Proteome Analysis of an Aerobic Hyperthermophilic Crenarchaeon, Aeropyrum pernix K1. Mol Cell Proteomics 2006; 5:811-23. [PMID: 16455681 DOI: 10.1074/mcp.m500312-mcp200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [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
We analyzed the proteome of a crenararchaeon, Aeropyrum pernix K1, by using the following four methods: (i) two-dimensional PAGE followed by MALDI-TOF MS, (ii) one-dimensional SDS-PAGE in combination with two-dimensional LC-MS/MS, (iii) multidimensional LC-MS/MS, and (iv) two-dimensional PAGE followed by amino-terminal amino acid sequencing. These methods were found to be complementary to each other, and biases in the data obtained in one method could largely be compensated by the data obtained in the other methods. Consequently a total of 704 proteins were successfully identified, 134 of which were unique to A. pernix K1, and 19 were not described previously in the genomic annotation. We found that the original annotation of the genomic data of this archaeon was not adequate in particular with respect to proteins of 10-20 kDa in size, many of which were described as hypothetical. Furthermore the amino-terminal amino acid sequence analysis indicated that surprisingly the translation of 52% of their genes starts with TTG in contrast to ATG (28%) and GTG (20%). Thus, A. pernix K1 is the first example of an organism in which TTG is the most predominant translational initiation codon.
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Affiliation(s)
- Syuji Yamazaki
- Department of Biotechnology, Genome Analysis Division, National Institute of Technology and Evaluation, Shibuya, Tokyo 151-0066, Japan.
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Wang QY, Yang GY, Liu YL, Wang YP, Feng Y. [Directed evolution of Thermophilic esterase from the archaeon Aeropyrum pemix K1]. Wei Sheng Wu Xue Bao 2006; 46:259-62. [PMID: 16736588] [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] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Thermophilic esterase (APE1547) from Aeropyrum pernix K1 was subjected to error-prone PCR (epPCR) to enhance activity. For the screening of mutants, an efficient and reliable assay suitable for high throughput screening was developed based on the enzyme thermostability. Two successive rounds of random mutagenesis by epPCR resulted in a four amino acid substitution variant M020 with significantly increased activity (six-fold under the screening condition. Further assay for the purified enzymes showed that the mutant possess 1.5-fold higher specific activity and nearly 4-fold higher expressed level than the wild-type. The mutant has an optimal activity at pH 8.5, corresponding to an alkaline shift of 0.5 pH unit compared to the wild type. The structure analysis suggests that R526S may contribute to the enhanced activity and the shift of pKi.
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Affiliation(s)
- Qiu-Yan Wang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun 130023, China.
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Mueller P, Egorova K, Vorgias CE, Boutou E, Trauthwein H, Verseck S, Antranikian G. Cloning, overexpression, and characterization of a thermoactive nitrilase from the hyperthermophilic archaeon Pyrococcus abyssi. Protein Expr Purif 2006; 47:672-81. [PMID: 16495079 DOI: 10.1016/j.pep.2006.01.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2005] [Revised: 01/09/2006] [Accepted: 01/09/2006] [Indexed: 11/17/2022]
Abstract
Four open reading frames encoding putative nitrilases were identified in the genomes of the hyperthermophilic archaea Pyrococcus abyssi, Pyrococcus horikoshii, Pyrococcus furiosus, and Aeropyrum pernix (growth temperature 90-100 degrees C). The nitrilase encoding genes were cloned and overexpressed in Escherichia coli. Enzymatic activity could only be detected in the case of Py. abyssi. This recombinant nitrilase was purified by heat treatment of E. coli crude extract followed by anion-exchange chromatography with a yield of 88% and a specific activity of 0.14 U/mg. The recombinant enzyme, which represents the first archaeal nitrilase, is a dimer (29.8 kDa/subunit) with an isoelectric point of pI 5.3. The nitrilase is active at a broad temperature (60-90 degrees C) and neutral pH range (pH 6.0-8.0). The recombinant enzyme is highly thermostable with a half-life of 25 h at 70 degrees C, 9 h at 80 degrees C, and 6 h at 90 degrees C. Thermostability measurements by employing circular dichroism spectroscopy and differential scanning microcalorimetry, at neutral pH, have shown that the enzyme unfolds up to 90 degrees C reversibly and has a T(m) of 112.7 degrees C. An inhibition of the enzymatic activity was observed in the presence of acetone and metal ions such as Ag(2+) and Hg(2+). The nitrilase hydrolyzes preferentially aliphatic substrates and the best substrate is malononitrile with a K(m) value of 3.47 mM.
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Affiliation(s)
- Patrick Mueller
- Hamburg University of Technology, Institute of Technical Microbiology, Germany
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Singleton MR, Morales R, Grainge I, Cook N, Isupov MN, Wigley DB. Conformational changes induced by nucleotide binding in Cdc6/ORC from Aeropyrum pernix. J Mol Biol 2004; 343:547-57. [PMID: 15465044 DOI: 10.1016/j.jmb.2004.08.044] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [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: 03/22/2004] [Revised: 08/12/2004] [Accepted: 08/12/2004] [Indexed: 11/19/2022]
Abstract
Archaea contain one or more proteins with homology to eukaryotic ORC/Cdc6 proteins. Sequence analysis suggests the existence of at least two subfamilies of these proteins, for which we propose the nomenclature ORC1 and ORC2. We have determined crystal structures of the ORC2 protein from the archaeon Aeropyrum pernix in complexes with ADP or a non-hydrolysable ATP analogue, ADPNP. Between two crystal forms, there are three crystallographically independent views of the ADP complex and two of the ADPNP complex. The protein molecules in the three complexes with ADP adopt very different conformations, while the two complexes with ADPNP are the same. These structures indicate that there is considerable conformational flexibility in ORC2 but that ATP binding stabilises a single conformation. We show that the ORC2 protein can bind DNA, and that this activity is associated with the C-terminal domain of the protein. We present a model for the interaction of the winged helix (WH) domain of ORC2 with DNA that differs from that proposed previously for Pyrobaculum aerophilum ORC/Cdc6.
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Affiliation(s)
- Martin R Singleton
- Cancer Research UK Clare Hall Laboratories, The London Research Institute, Blanche Lane, South Mimms, Potters Bar, Herts EN6 3LD, UK
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Jiang QX, Wang DN, MacKinnon R. Electron microscopic analysis of KvAP voltage-dependent K+ channels in an open conformation. Nature 2004; 430:806-10. [PMID: 15306816 DOI: 10.1038/nature02735] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.7] [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: 03/17/2004] [Accepted: 06/03/2004] [Indexed: 11/09/2022]
Abstract
Voltage-dependent ion channels serve as field-effect transistors by opening a gate in response to membrane voltage changes. The gate's response to voltage is mediated by voltage sensors, which are arginine-containing structures that must move with respect to the membrane electric field. We have analysed by electron microscopy a voltage-dependent K(+) channel from Aeropyrum pernix (KvAP). Fab fragments were attached to 'voltage sensor paddles' and identified in the electron microscopy map at 10.5 A resolution. The extracellular surface location of the Fab fragments in the map is consistent with the membrane-depolarized, open conformation of the channel in electrophysiological experiments. Comparison of the map with a crystal structure demonstrates that the voltage sensor paddles are 'up' (that is, near the channel's extracellular surface) and situated at the protein-lipid interface. This finding supports the hypothesis that in response to changes in voltage the sensors move at the protein-lipid interface rather than in a gating pore surrounded by protein.
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Affiliation(s)
- Qiu-Xing Jiang
- Howard Hughes Medical Institute and Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, 1230 York Avenue, New York, New York 10021,USA
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Abstract
MOTIVATION Separation of protein sequence regions according to their local information complexity and subsequent masking of low complexity regions has greatly enhanced the reliability of function prediction by sequence similarity. Comparisons with alternative methods that focus on compositional sequence bias rather than information complexity measures have shown that removal of compositional bias yields at least as sensitive and much more specific results. Besides the application of sequence masking algorithms to sequence similarity searches, the study of the masked regions themselves is of great interest. Traditionally, however, these have been neglected despite evidence of their functional relevance. RESULTS Here we demonstrate that compositional bias seems to be a more effective measure for the detection of biologically meaningful signals. Typical results on proteins are compared to results for sequences that have been randomized in various ways, conserving composition and local correlations for individual proteins or the entire set. It is remarkable that low-complexity regions have the same form of distribution in proteins as in randomized sequences, and that the signal from randomized sequences with conserved local correlations and amino acid composition almost matches the signal from proteins. This is not the case for sequence bias, which hence seems to be a genuinely biological phenomenon in contrast to patches of low complexity.
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Affiliation(s)
- David P Kreil
- Department of Genetics/Inference Group (Cavendish Laboratory), University of Cambridge, Cambridge, UK.
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