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Liu Y, Xu C, Zhou H, Wang W, Liu B, Li Y, Hu X, Yu F, He J. The crystal structures of Sau3AI with and without bound DNA suggest a self-activation-based DNA cleavage mechanism. Structure 2023; 31:1463-1472.e2. [PMID: 37652002 DOI: 10.1016/j.str.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 06/12/2023] [Accepted: 08/04/2023] [Indexed: 09/02/2023]
Abstract
The type II restriction endonuclease Sau3AI cleaves the sequence 5'-GATC-3' in double-strand DNA producing two sticky ends. Sau3AI cuts both DNA strands regardless of methylation status. Here, we report the crystal structures of the active site mutant Sau3AI-E64A and the C-terminal domain Sau3AI-C with a bound GATC substrate. Interestingly, the catalytic site of the N-terminal domain (Sau3AI-N) is spatially blocked by the C-terminal domain, suggesting a potential self-inhibition of the enzyme. Interruption of Sau3AI-C binding to substrate DNA disrupts Sau3AI function, suggesting a functional linkage between the N- and C-terminal domains. We propose that Sau3AI-C behaves as an allosteric effector binding one GATC substrate, which triggers a conformational change to open the N-terminal catalytic site, resulting in the subsequent GATC recognition by Sau3AI-N and cleavage of the second GATC site. Our data indicate that Sau3AI and UbaLAI might represent a new subclass of type IIE restriction enzymes.
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Affiliation(s)
- Yahui Liu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei 430030, China
| | - Chunyan Xu
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Huan Zhou
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Weiwei Wang
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Bing Liu
- Department of Laboratory Medicine, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Yan Li
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei 430030, China; Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Xiaojian Hu
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Feng Yu
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China.
| | - Jianhua He
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, China.
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2
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Kisiala M, Kowalska M, Pastor M, Korza HJ, Czapinska H, Bochtler M. Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation. Nucleic Acids Res 2020; 48:6954-6969. [PMID: 32459314 PMCID: PMC7337904 DOI: 10.1093/nar/gkaa403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 04/30/2020] [Accepted: 05/18/2020] [Indexed: 11/13/2022] Open
Abstract
Restriction endonucleases naturally target DNA duplexes. Systematic screening has identified a small minority of these enzymes that can also cleave RNA/DNA heteroduplexes and that may therefore be useful as tools for RNA biochemistry. We have chosen AvaII (G↓GWCC, where W stands for A or T) as a representative of this group of restriction endonucleases for detailed characterization. Here, we report crystal structures of AvaII alone, in specific complex with partially cleaved dsDNA, and in scanning complex with an RNA/DNA hybrid. The specific complex reveals a novel form of semi-specific dsDNA readout by a hexa-coordinated metal cation, most likely Ca2+ or Mg2+. Substitutions of residues anchoring this non-catalytic metal ion severely impair DNA binding and cleavage. The dsDNA in the AvaII complex is in the A-like form. This creates space for 2′-OH groups to be accommodated without intra-nucleic acid steric conflicts. PD-(D/E)XK restriction endonucleases of known structure that bind their dsDNA targets in the A-like form cluster into structurally similar groups. Most such enzymes, including some not previously studied in this respect, cleave RNA/DNA heteroduplexes. We conclude that A-form dsDNA binding is a good predictor for RNA/DNA cleavage activity.
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Affiliation(s)
- Marlena Kisiala
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.,Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland.,Biological and Chemical Research Centre, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Monika Kowalska
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Michal Pastor
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.,Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Henryk J Korza
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, UK
| | - Honorata Czapinska
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.,Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Matthias Bochtler
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.,Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
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3
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Štěpán J, Kabelka I, Koča J, Kulhánek P. Behavior of BsoBI endonuclease in the presence and absence of DNA. J Mol Model 2017; 24:22. [PMID: 29264670 DOI: 10.1007/s00894-017-3557-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/01/2017] [Indexed: 11/28/2022]
Abstract
BsoBI is a type II restriction endonuclease belonging to the EcoRI family. There is only one previously published X-ray structure for this endonuclease: it shows a homodimer of BsoBI completely encircling DNA in a tunnel. In this work, molecular dynamics simulations were employed to elucidate possible ways in which DNA is loaded into this complex prior to its cleavage. We found that the dimer does not open spontaneously when DNA is removed from the complex on the timescale of our simulations (~ 0.5 μs). A biased simulation had to be used to facilitate the opening, which revealed a possible way for the two catalytic domains to separate. The α-helices connecting the catalytic and helical domains were found to act as a hinge during the separation. In addition, we found that the opening of the BsoBI dimer was influenced by the type of counterions present in the environment. A reference simulation of the BsoBI/DNA complex further showed spontaneous reorganization of the active sites due to the binding of solvent ions, which led to an active-site structure consistent with other experimental structures of type II restriction endonucleases determined in the presence of metal ions.
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Affiliation(s)
- Jakub Štěpán
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Ivo Kabelka
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Jaroslav Koča
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Petr Kulhánek
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic. .,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.
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4
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Johnson PM, Gucinski GC, Garza-Sánchez F, Wong T, Hung LW, Hayes CS, Goulding CW. Functional Diversity of Cytotoxic tRNase/Immunity Protein Complexes from Burkholderia pseudomallei. J Biol Chem 2016; 291:19387-400. [PMID: 27445337 DOI: 10.1074/jbc.m116.736074] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Indexed: 12/23/2022] Open
Abstract
Contact-dependent growth inhibition (CDI) is a widespread mechanism of inter-bacterial competition. CDI(+) bacteria deploy large CdiA effector proteins, which carry variable C-terminal toxin domains (CdiA-CT). CDI(+) cells also produce CdiI immunity proteins that specifically neutralize cognate CdiA-CT toxins to prevent auto-inhibition. Here, we present the crystal structure of the CdiA-CT/CdiI(E479) toxin/immunity protein complex from Burkholderia pseudomallei isolate E479. The CdiA-CT(E479) tRNase domain contains a core α/β-fold that is characteristic of PD(D/E)XK superfamily nucleases. Unexpectedly, the closest structural homolog of CdiA-CT(E479) is another CDI toxin domain from B. pseudomallei 1026b. Although unrelated in sequence, the two B. pseudomallei nuclease domains share similar folds and active-site architectures. By contrast, the CdiI(E479) and CdiI(1026b) immunity proteins share no significant sequence or structural homology. CdiA-CT(E479) and CdiA-CT(1026b) are both tRNases; however, each nuclease cleaves tRNA at a distinct position. We used a molecular docking approach to model each toxin bound to tRNA substrate. The resulting models fit into electron density envelopes generated by small-angle x-ray scattering analysis of catalytically inactive toxin domains bound stably to tRNA. CdiA-CT(E479) is the third CDI toxin found to have structural homology to the PD(D/E)XK superfamily. We propose that CDI systems exploit the inherent sequence variability and active-site plasticity of PD(D/E)XK nucleases to generate toxin diversity. These findings raise the possibility that many other uncharacterized CDI toxins may belong to the PD(D/E)XK superfamily.
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Affiliation(s)
| | | | - Fernando Garza-Sánchez
- Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara, Santa Barbara, California 93106-9625, and
| | - Timothy Wong
- From the Departments of Molecular Biology and Biochemistry and
| | - Li-Wei Hung
- the Physics Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Christopher S Hayes
- the Biomolecular Science and Engineering Program and Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara, Santa Barbara, California 93106-9625, and
| | - Celia W Goulding
- From the Departments of Molecular Biology and Biochemistry and Pharmaceutical Sciences, University of California at Irvine, Irvine, California 92697,
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5
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Horton JR, Wang H, Mabuchi MY, Zhang X, Roberts RJ, Zheng Y, Wilson GG, Cheng X. Modification-dependent restriction endonuclease, MspJI, flips 5-methylcytosine out of the DNA helix. Nucleic Acids Res 2014; 42:12092-101. [PMID: 25262349 PMCID: PMC4231741 DOI: 10.1093/nar/gku871] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
MspJI belongs to a family of restriction enzymes that cleave DNA containing 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC). MspJI is specific for the sequence 5(h)mC-N-N-G or A and cleaves with some variability 9/13 nucleotides downstream. Earlier, we reported the crystal structure of MspJI without DNA and proposed how it might recognize this sequence and catalyze cleavage. Here we report its co-crystal structure with a 27-base pair oligonucleotide containing 5mC. This structure confirms that MspJI acts as a homotetramer and that the modified cytosine is flipped from the DNA helix into an SRA-like-binding pocket. We expected the structure to reveal two DNA molecules bound specifically to the tetramer and engaged with the enzyme's two DNA-cleavage sites. A coincidence of crystal packing precluded this organization, however. We found that each DNA molecule interacted with two adjacent tetramers, binding one specifically and the other non-specifically. The latter interaction, which prevented cleavage-site engagement, also involved base flipping and might represent the sequence-interrogation phase that precedes specific recognition. MspJI is unusual in that DNA molecules are recognized and cleaved by different subunits. Such interchange of function might explain how other complex multimeric restriction enzymes act.
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Affiliation(s)
- John R Horton
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
| | - Hua Wang
- New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | | | - Xing Zhang
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
| | | | - Yu Zheng
- New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | | | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
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6
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Pingoud A, Wilson GG, Wende W. Type II restriction endonucleases--a historical perspective and more. Nucleic Acids Res 2014; 42:7489-527. [PMID: 24878924 PMCID: PMC4081073 DOI: 10.1093/nar/gku447] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 05/02/2014] [Accepted: 05/07/2014] [Indexed: 12/17/2022] Open
Abstract
This article continues the series of Surveys and Summaries on restriction endonucleases (REases) begun this year in Nucleic Acids Research. Here we discuss 'Type II' REases, the kind used for DNA analysis and cloning. We focus on their biochemistry: what they are, what they do, and how they do it. Type II REases are produced by prokaryotes to combat bacteriophages. With extreme accuracy, each recognizes a particular sequence in double-stranded DNA and cleaves at a fixed position within or nearby. The discoveries of these enzymes in the 1970s, and of the uses to which they could be put, have since impacted every corner of the life sciences. They became the enabling tools of molecular biology, genetics and biotechnology, and made analysis at the most fundamental levels routine. Hundreds of different REases have been discovered and are available commercially. Their genes have been cloned, sequenced and overexpressed. Most have been characterized to some extent, but few have been studied in depth. Here, we describe the original discoveries in this field, and the properties of the first Type II REases investigated. We discuss the mechanisms of sequence recognition and catalysis, and the varied oligomeric modes in which Type II REases act. We describe the surprising heterogeneity revealed by comparisons of their sequences and structures.
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Affiliation(s)
- Alfred Pingoud
- Institute of Biochemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
| | - Geoffrey G Wilson
- New England Biolabs Inc., 240 County Road, Ipswich, MA 01938-2723, USA
| | - Wolfgang Wende
- Institute of Biochemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
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7
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Malhotra S, Sowdhamini R. Re-visiting protein-centric two-tier classification of existing DNA-protein complexes. BMC Bioinformatics 2012; 13:165. [PMID: 22800292 PMCID: PMC3472317 DOI: 10.1186/1471-2105-13-165] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 03/26/2012] [Indexed: 01/28/2023] Open
Abstract
Background Precise DNA-protein interactions play most important and vital role in maintaining the normal physiological functioning of the cell, as it controls many high fidelity cellular processes. Detailed study of the nature of these interactions has paved the way for understanding the mechanisms behind the biological processes in which they are involved. Earlier in 2000, a systematic classification of DNA-protein complexes based on the structural analysis of the proteins was proposed at two tiers, namely groups and families. With the advancement in the number and resolution of structures of DNA-protein complexes deposited in the Protein Data Bank, it is important to revisit the existing classification. Results On the basis of the sequence analysis of DNA binding proteins, we have built upon the protein centric, two-tier classification of DNA-protein complexes by adding new members to existing families and making new families and groups. While classifying the new complexes, we also realised the emergence of new groups and families. The new group observed was where β-propeller was seen to interact with DNA. There were 34 SCOP folds which were observed to be present in the complexes of both old and new classifications, whereas 28 folds are present exclusively in the new complexes. Some new families noticed were NarL transcription factor, Z-α DNA binding proteins, Forkhead transcription factor, AP2 protein, Methyl CpG binding protein etc. Conclusions Our results suggest that with the increasing number of availability of DNA-protein complexes in Protein Data Bank, the number of families in the classification increased by approximately three fold. The folds present exclusively in newly classified complexes is suggestive of inclusion of proteins with new function in new classification, the most populated of which are the folds responsible for DNA damage repair. The proposed re-visited classification can be used to perform genome-wide surveys in the genomes of interest for the presence of DNA-binding proteins. Further analysis of these complexes can aid in developing algorithms for identifying DNA-binding proteins and their family members from mere sequence information.
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Affiliation(s)
- Sony Malhotra
- National Centre for Biological Sciences, UAS-GKVK Campus, Bangalore 560 065, India
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8
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Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Nucleic Acids Res 2012; 40:7016-45. [PMID: 22638584 PMCID: PMC3424549 DOI: 10.1093/nar/gks382] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Proteins belonging to PD-(D/E)XK phosphodiesterases constitute a functionally diverse superfamily with representatives involved in replication, restriction, DNA repair and tRNA-intron splicing. Their malfunction in humans triggers severe diseases, such as Fanconi anemia and Xeroderma pigmentosum. To date there have been several attempts to identify and classify new PD-(D/E)KK phosphodiesterases using remote homology detection methods. Such efforts are complicated, because the superfamily exhibits extreme sequence and structural divergence. Using advanced homology detection methods supported with superfamily-wide domain architecture and horizontal gene transfer analyses, we provide a comprehensive reclassification of proteins containing a PD-(D/E)XK domain. The PD-(D/E)XK phosphodiesterases span over 21,900 proteins, which can be classified into 121 groups of various families. Eleven of them, including DUF4420, DUF3883, DUF4263, COG5482, COG1395, Tsp45I, HaeII, Eco47II, ScaI, HpaII and Replic_Relax, are newly assigned to the PD-(D/E)XK superfamily. Some groups of PD-(D/E)XK proteins are present in all domains of life, whereas others occur within small numbers of organisms. We observed multiple horizontal gene transfers even between human pathogenic bacteria or from Prokaryota to Eukaryota. Uncommon domain arrangements greatly elaborate the PD-(D/E)XK world. These include domain architectures suggesting regulatory roles in Eukaryotes, like stress sensing and cell-cycle regulation. Our results may inspire further experimental studies aimed at identification of exact biological functions, specific substrates and molecular mechanisms of reactions performed by these highly diverse proteins.
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Affiliation(s)
- Kamil Steczkiewicz
- Laboratory of Bioinformatics and Systems Biology, CENT, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
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9
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Manakova E, Grazulis S, Zaremba M, Tamulaitiene G, Golovenko D, Siksnys V. Structural mechanisms of the degenerate sequence recognition by Bse634I restriction endonuclease. Nucleic Acids Res 2012; 40:6741-51. [PMID: 22495930 PMCID: PMC3413111 DOI: 10.1093/nar/gks300] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Restriction endonuclease Bse634I recognizes and cleaves the degenerate DNA sequence 5′-R/CCGGY-3′ (R stands for A or G; Y for T or C, ‘/’ indicates a cleavage position). Here, we report the crystal structures of the Bse634I R226A mutant complexed with cognate oligoduplexes containing ACCGGT and GCCGGC sites, respectively. In the crystal, all potential H-bond donor and acceptor atoms on the base edges of the conserved CCGG core are engaged in the interactions with Bse634I amino acid residues located on the α6 helix. In contrast, direct contacts between the protein and outer base pairs are limited to van der Waals contact between the purine nucleobase and Pro203 residue in the major groove and a single H-bond between the O2 atom of the outer pyrimidine and the side chain of the Asn73 residue in the minor groove. Structural data coupled with biochemical experiments suggest that both van der Waals interactions and indirect readout contribute to the discrimination of the degenerate base pair by Bse634I. Structure comparison between related enzymes Bse634I (R/CCGGY), NgoMIV (G/CCGGC) and SgrAI (CR/CCGGYG) reveals how different specificities are achieved within a conserved structural core.
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Affiliation(s)
- Elena Manakova
- Department of Protein-DNA Interactions, Institute of Biotechnology Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
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10
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Oroguchi T, Ikeguchi M, Sato M. Towards the Structural Characterization of Intrinsically Disordered Proteins by SAXS and MD Simulation. ACTA ACUST UNITED AC 2011. [DOI: 10.1088/1742-6596/272/1/012005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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11
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Chen F, Yang Z, Yan M, Alvarado JB, Wang G, Benner SA. Recognition of an expanded genetic alphabet by type-II restriction endonucleases and their application to analyze polymerase fidelity. Nucleic Acids Res 2011; 39:3949-61. [PMID: 21245035 PMCID: PMC3089450 DOI: 10.1093/nar/gkq1274] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
To explore the possibility of using restriction enzymes in a synthetic biology based on artificially expanded genetic information systems (AEGIS), 24 type-II restriction endonucleases (REases) were challenged to digest DNA duplexes containing recognition sites where individual Cs and Gs were replaced by the AEGIS nucleotides Z and P [respectively, 6-amino-5-nitro-3-(1'-β-D-2'-deoxyribofuranosyl)-2(1H)-pyridone and 2-amino-8-(1'-β-D-2'-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one]. These AEGIS nucleotides implement complementary hydrogen bond donor-donor-acceptor and acceptor-acceptor-donor patterns. Results allowed us to classify type-II REases into five groups based on their performance, and to infer some specifics of their interactions with functional groups in the major and minor grooves of the target DNA. For three enzymes among these 24 where crystal structures are available (BcnI, EcoO109I and NotI), these interactions were modeled. Further, we applied a type-II REase to quantitate the fidelity polymerases challenged to maintain in a DNA duplex C:G, T:A and Z:P pairs through repetitive PCR cycles. This work thus adds tools that are able to manipulate this expanded genetic alphabet in vitro, provides some structural insights into the working of restriction enzymes, and offers some preliminary data needed to take the next step in synthetic biology to use an artificial genetic system inside of living bacterial cells.
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Affiliation(s)
- Fei Chen
- Foundation for Applied Molecular Evolution (FfAME), 720 SW 2nd Avenue, Suite 201, Gainesville, FL 32601, USA.
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12
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Iwamoto M, Hishiki A, Shimada T, Imasaki T, Tsuda J, Kita K, Shimizu T, Sato M, Hashimoto H. Crystallization and X-ray diffraction studies of DNA-free and DNA-bound forms of EcoO109I DNA methyltransferase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1528-30. [PMID: 21045313 DOI: 10.1107/s174430911003753x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 09/20/2010] [Indexed: 11/10/2022]
Abstract
EcoO109I DNA methyltransferase (M.EcoO109I) is a type II modification enzyme from the EcoO109I restriction-modification system identified in Escherichia coli strain H709c. M.EcoO109I recognizes double-stranded RGGNCCY (where R = A or G, Y = T or C and N is any base) and transfers a methyl group to the C5 of the inner cytosines from S-adenosylmethionine. To reveal the mechanism of substrate recognition by M.EcoO109I, DNA-free and DNA-bound forms of M.EcoO109I were successfully crystallized. Crystals of the DNA-free and DNA-bound forms belonged to space groups P4(2)2(1)2, with unit-cell parameters a = b = 120.5, c = 79.8 Å, and P2(1), with unit-cell parameters a = 55.8, b = 77.4, c = 117.4 Å, β = 93.5°, respectively.
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Affiliation(s)
- Makoto Iwamoto
- Graduate School of Nanobioscience, Yokohama City University, Japan
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13
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Firczuk M, Wojciechowski M, Czapinska H, Bochtler M. DNA intercalation without flipping in the specific ThaI-DNA complex. Nucleic Acids Res 2010; 39:744-54. [PMID: 20861000 PMCID: PMC3025569 DOI: 10.1093/nar/gkq834] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The PD-(D/E)XK type II restriction endonuclease ThaI cuts the target sequence CG/CG with blunt ends. Here, we report the 1.3 Å resolution structure of the enzyme in complex with substrate DNA and a sodium or calcium ion taking the place of a catalytic magnesium ion. The structure identifies Glu54, Asp82 and Lys93 as the active site residues. This agrees with earlier bioinformatic predictions and implies that the PD and (D/E)XK motifs in the sequence are incidental. DNA recognition is very unusual: the two Met47 residues of the ThaI dimer intercalate symmetrically into the CG steps of the target sequence. They approach the DNA from the minor groove side and penetrate the base stack entirely. The DNA accommodates the intercalating residues without nucleotide flipping by a doubling of the CG step rise to twice its usual value, which is accompanied by drastic unwinding. Displacement of the Met47 side chains from the base pair midlines toward the downstream CG steps leads to large and compensating tilts of the first and second CG steps. DNA intercalation by ThaI is unlike intercalation by HincII, HinP1I or proteins that bend or repair DNA.
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14
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Pingoud V, Wende W, Friedhoff P, Reuter M, Alves J, Jeltsch A, Mones L, Fuxreiter M, Pingoud A. On the divalent metal ion dependence of DNA cleavage by restriction endonucleases of the EcoRI family. J Mol Biol 2009; 393:140-60. [PMID: 19682999 DOI: 10.1016/j.jmb.2009.08.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Revised: 08/05/2009] [Accepted: 08/06/2009] [Indexed: 11/18/2022]
Abstract
Restriction endonucleases of the PD...D/EXK family need Mg(2+) for DNA cleavage. Whereas Mg(2+) (or Mn(2+)) promotes catalysis, Ca(2+) (without Mg(2+)) only supports DNA binding. The role of Mg(2+) in DNA cleavage by restriction endonucleases has elicited many hypotheses, differing mainly in the number of Mg(2+) involved in catalysis. To address this problem, we measured the Mg(2+) and Mn(2+) concentration dependence of DNA cleavage by BamHI, BglII, Cfr10I, EcoRI, EcoRII (catalytic domain), MboI, NgoMIV, PspGI, and SsoII, which were reported in co-crystal structure analyses to bind one (BglII and EcoRI) or two (BamHI and NgoMIV) Me(2+) per active site. DNA cleavage experiments were carried out at various Mg(2+) and Mn(2+) concentrations at constant ionic strength. All enzymes show a qualitatively similar Mg(2+) and Mn(2+) concentration dependence. In general, the Mg(2+) concentration optimum (between approximately 1 and 10 mM) is higher than the Mn(2+) concentration optimum (between approximately 0.1 and 1 mM). At still higher Mg(2+) or Mn(2+) concentrations, the activities of all enzymes tested are reduced but can be reactivated by Ca(2+). Based on these results, we propose that one Mg(2+) or Mn(2+) is critical for restriction enzyme activation, and binding of a second Me(2+) plays a role in modulating the activity. Steady-state kinetics carried out with EcoRI and BamHI suggest that binding of a second Mg(2+) or Mn(2+) mainly leads to an increase in K(m), such that the inhibitory effect of excess Mg(2+) or Mn(2+) can be overcome by increasing the substrate concentration. Our conclusions are supported by molecular dynamics simulations and are consistent with the structural observations of both one and two Me(2+) binding to these enzymes.
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Affiliation(s)
- Vera Pingoud
- Institut für Biochemie, Justus-Liebig-Universität, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany.
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Oroguchi T, Hashimoto H, Shimizu T, Sato M, Ikeguchi M. Intrinsic dynamics of restriction endonuclease EcoO109I studied by molecular dynamics simulations and X-ray scattering data analysis. Biophys J 2009; 96:2808-22. [PMID: 19348764 PMCID: PMC2711268 DOI: 10.1016/j.bpj.2008.12.3914] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 11/19/2008] [Accepted: 12/08/2008] [Indexed: 11/30/2022] Open
Abstract
EcoO109I is a type II restriction endonuclease that functions as a dimer in solution. Upon DNA binding to the enzyme, the two subunits rotate counterclockwise relative to each other, as the two catalytic domains undergo structural changes to capture the cognate DNA. Using a 150-ns molecular dynamics simulation, we investigated the intrinsic dynamics of the DNA-free enzyme in solution to elucidate the relationship between enzyme dynamics and structural changes. The simulation revealed that the enzyme is considerably flexible, and thus exhibits large fluctuations in the radius of gyration. The small-angle x-ray scattering profile calculated from the simulation, including scattering from explicit hydration water, was in agreement with the experimentally observed profile. Principal component analysis revealed that the major dynamics were represented by the open-close and counterclockwise motions: the former is required for the enzyme to access DNA, whereas the latter corresponds to structural changes upon DNA binding. Furthermore, the intrinsic dynamics in the catalytic domains were consistent with motions capturing the cognate DNA. These results indicate that the structure of EcoO109I is intrinsically flexible in the direction of its functional movement, to facilitate effective structural changes for sequence-specific DNA recognition and processing.
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Affiliation(s)
| | | | | | | | - Mitsunori Ikeguchi
- International Graduate School of Arts and Sciences, Yokohama City University, Yokohama 230-0045, Japan
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16
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Orlowski J, Bujnicki JM. Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses. Nucleic Acids Res 2008; 36:3552-69. [PMID: 18456708 PMCID: PMC2441816 DOI: 10.1093/nar/gkn175] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
For a very long time, Type II restriction enzymes (REases) have been a paradigm of ORFans: proteins with no detectable similarity to each other and to any other protein in the database, despite common cellular and biochemical function. Crystallographic analyses published until January 2008 provided high-resolution structures for only 28 of 1637 Type II REase sequences available in the Restriction Enzyme database (REBASE). Among these structures, all but two possess catalytic domains with the common PD-(D/E)XK nuclease fold. Two structures are unrelated to the others: R.BfiI exhibits the phospholipase D (PLD) fold, while R.PabI has a new fold termed 'half-pipe'. Thus far, bioinformatic studies supported by site-directed mutagenesis have extended the number of tentatively assigned REase folds to five (now including also GIY-YIG and HNH folds identified earlier in homing endonucleases) and provided structural predictions for dozens of REase sequences without experimentally solved structures. Here, we present a comprehensive study of all Type II REase sequences available in REBASE together with their homologs detectable in the nonredundant and environmental samples databases at the NCBI. We present the summary and critical evaluation of structural assignments and predictions reported earlier, new classification of all REase sequences into families, domain architecture analysis and new predictions of three-dimensional folds. Among 289 experimentally characterized (not putative) Type II REases, whose apparently full-length sequences are available in REBASE, we assign 199 (69%) to contain the PD-(D/E)XK domain. The HNH domain is the second most common, with 24 (8%) members. When putative REases are taken into account, the fraction of PD-(D/E)XK and HNH folds changes to 48% and 30%, respectively. Fifty-six characterized (and 521 predicted) REases remain unassigned to any of the five REase folds identified so far, and may exhibit new architectures. These enzymes are proposed as the most interesting targets for structure determination by high-resolution experimental methods. Our analysis provides the first comprehensive map of sequence-structure relationships among Type II REases and will help to focus the efforts of structural and functional genomics of this large and biotechnologically important class of enzymes.
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Affiliation(s)
- Jerzy Orlowski
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
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17
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Petoukhov MV, Svergun DI. Joint use of small-angle X-ray and neutron scattering to study biological macromolecules in solution. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2006; 35:567-76. [PMID: 16636827 DOI: 10.1007/s00249-006-0063-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2006] [Revised: 03/16/2006] [Accepted: 03/22/2006] [Indexed: 01/24/2023]
Abstract
Novel techniques for simultaneous analysis of X-ray and neutron scattering patterns from macromolecular complexes in solution are presented. They include ab initio shape and internal structure determination of multicomponent particles and more detailed rigid body modeling of complexes using high resolution structures of subunits. The methods fit simultaneously X-ray and neutron scattering curves including contrast variation data sets from selectively deuterated complexes. Biochemically sound interconnected models without steric clashes between the components displaying a pre-defined symmetry are generated. For rigid body modeling, distance restraints between specified residues/nucleotides or their ranges are taken into account. The efficiency of the methods is demonstrated in model examples, and potential sources of ambiguity are discussed.
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Affiliation(s)
- Maxim V Petoukhov
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Notkestrasse 85, 22603, Hamburg, Germany
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18
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Bochtler M, Szczepanowski RH, Tamulaitis G, Grazulis S, Czapinska H, Manakova E, Siksnys V. Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease. EMBO J 2006; 25:2219-29. [PMID: 16628220 PMCID: PMC1462983 DOI: 10.1038/sj.emboj.7601096] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2006] [Accepted: 03/24/2006] [Indexed: 01/08/2023] Open
Abstract
Restricion endonuclease Ecl18kI is specific for the sequence /CCNGG and cleaves it before the outer C to generate 5 nt 5'-overhangs. It has been suggested that Ecl18kI is evolutionarily related to NgoMIV, a 6-bp cutter that cleaves the sequence G/CCGGC and leaves 4 nt 5'-overhangs. Here, we report the crystal structure of the Ecl18kI-DNA complex at 1.7 A resolution and compare it with the known structure of the NgoMIV-DNA complex. We find that Ecl18kI flips both central nucleotides within the CCNGG sequence and buries the extruded bases in pockets within the protein. Nucleotide flipping disrupts Watson-Crick base pairing, induces a kink in the DNA and shifts the DNA register by 1 bp, making the distances between scissile phosphates in the Ecl18kI and NgoMIV cocrystal structures nearly identical. Therefore, the two enzymes can use a conserved DNA recognition module, yet recognize different sequences, and form superimposable dimers, yet generate different cleavage patterns. Hence, Ecl18kI is the first example of a restriction endonuclease that flips nucleotides to achieve specificity for its recognition site.
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Affiliation(s)
- Matthias Bochtler
- International Institute of Molecular and Cell Biology, Warsaw, Poland
- Max-Planck-Institute for Molecular Cell Biology and Genetics, Dresden, Germany
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland. Tel.: +48 22 5970732; Fax: +48 22 5970715; E-mail:
| | - Roman H Szczepanowski
- International Institute of Molecular and Cell Biology, Warsaw, Poland
- Max-Planck-Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | | | | | - Honorata Czapinska
- International Institute of Molecular and Cell Biology, Warsaw, Poland
- Max-Planck-Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius, Lithuania
- Institute of Biotechnology, Graiciuno 8, Vilnius LT-02241, Lithuania. Tel.: +370 5 2602108; Fax: +370 5 2602116; E-mail:
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Lee JY, Chang J, Joseph N, Ghirlando R, Rao DN, Yang W. MutH Complexed with Hemi- and Unmethylated DNAs: Coupling Base Recognition and DNA Cleavage. Mol Cell 2005; 20:155-66. [PMID: 16209953 DOI: 10.1016/j.molcel.2005.08.019] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2005] [Revised: 06/29/2005] [Accepted: 08/17/2005] [Indexed: 11/24/2022]
Abstract
MutH initiates mismatch repair by nicking the transiently unmethylated daughter strand 5' to a GATC sequence. Here, we report crystal structures of MutH complexed with hemimethylated and unmethylated GATC substrates. Both structures contain two Ca2+ ions jointly coordinated by a conserved aspartate and the scissile phosphate, as observed in the restriction endonucleases BamHI and BglI. In the hemimethylated complexes, the active site is more compact and DNA cleavage is more efficient. The Lys residue in the conserved DEK motif coordinates the nucleophilic water in conjunction with the phosphate 3' to the scissile bond; the same Lys is also hydrogen bonded with a carbonyl oxygen in the DNA binding module. We propose that this Lys, which is conserved in many restriction endonucleases and is replaced by Glu or Gln in BamHI and BglII, is a sensor for DNA binding and the linchpin that couples base recognition and DNA cleavage.
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Affiliation(s)
- Jae Young Lee
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Pingoud V, Geyer H, Geyer R, Kubareva E, Bujnicki JM, Pingoud A. Identification of base-specific contacts in protein-DNA complexes by photocrosslinking and mass spectrometry: a case study using the restriction endonuclease SsoII. MOLECULAR BIOSYSTEMS 2005; 1:135-41. [PMID: 16880975 DOI: 10.1039/b503091a] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Specific protein-nucleic acid interactions are of paramount importance for the propagation, maintenance and expression of genetic information. Restriction endonucleases serve as model systems to study the mechanisms of DNA recognition by proteins. SsoII is a Type II restriction endonuclease that recognizes the double stranded sequence downward arrow CCNGG and cleaves it in the presence of Mg(2+)-ions, as indicated. SsoII shows sequence similarity over a stretch of approximately 70 amino acid residues with several other restriction endonucleases that recognize a similar sequence as SsoII (Cfr10I, EcoRII, NgoMIV, PspGI). In NgoMIV this stretch is involved in DNA recognition and cleavage, as shown by the crystal structure analysis of an enzyme-product complex. To find out whether the presumptive DNA recognition region in SsoII is indeed in contact with DNA we have photocrosslinked SsoII with an oligodeoxyribonucleotide in which the first guanine of the recognition sequence was replaced by 5-iodouracil. Following digestion by trypsin, the peptide-oligodeoxyribonucleotide conjugate was purified by Fe(3+)-IMAC and then incubated with hydrogen fluoride, which hydrolyzes the oligodeoxyribonucleotide to yield the peptide-deoxyuridine conjugate. The site of photocrosslinking was identified by MALDI-TOF-MS and MALDI-TOF-MS/MS to be Trp189, adjacent to Arg188, which aligns with Arg194 in NgoMIV, involved in recognition of the second guanine in the NgoMIV recognition sequence G downward arrow CCGGC. This result confirms previously published conclusions drawn on the basis of a mutational analysis of SsoII. The methodology that was employed here can be used in principle to identify the DNA binding site of any protein.
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Affiliation(s)
- Vera Pingoud
- Institut für Biochemie (FB 08), Justus-Liebig-Universität, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany.
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