1
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Roske Y, Cappel C, Cremer N, Hoffmann P, Koudelka T, Tholey A, Heinemann U, Daumke O, Damme M. Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation. Nucleic Acids Res 2024; 52:370-384. [PMID: 37994783 PMCID: PMC10783504 DOI: 10.1093/nar/gkad1114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/31/2023] [Accepted: 11/15/2023] [Indexed: 11/24/2023] Open
Abstract
The phospholipase D (PLD) family is comprised of enzymes bearing phospholipase activity towards lipids or endo- and exonuclease activity towards nucleic acids. PLD3 is synthesized as a type II transmembrane protein and proteolytically cleaved in lysosomes, yielding a soluble active form. The deficiency of PLD3 leads to the slowed degradation of nucleic acids in lysosomes and chronic activation of nucleic acid-specific intracellular toll-like receptors. While the mechanism of PLD phospholipase activity has been extensively characterized, not much is known about how PLDs bind and hydrolyze nucleic acids. Here, we determined the high-resolution crystal structure of the luminal N-glycosylated domain of human PLD3 in its apo- and single-stranded DNA-bound forms. PLD3 has a typical phospholipase fold and forms homodimers with two independent catalytic centers via a newly identified dimerization interface. The structure of PLD3 in complex with an ssDNA-derived thymidine product in the catalytic center provides insights into the substrate binding mode of nucleic acids in the PLD family. Our structural data suggest a mechanism for substrate binding and nuclease activity in the PLD family and provide the structural basis to design immunomodulatory drugs targeting PLD3.
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Affiliation(s)
- Yvette Roske
- Structural Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Cedric Cappel
- Biochemical Institute, Kiel University, Kiel, Germany
| | - Nils Cremer
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straβe 10, 13125 Berlin, Germany
| | | | - Tomas Koudelka
- Institute of Experimental Medicine, Kiel University, 24188 Kiel, Germany
| | - Andreas Tholey
- Institute of Experimental Medicine, Kiel University, 24188 Kiel, Germany
| | - Udo Heinemann
- Structural Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Oliver Daumke
- Structural Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Markus Damme
- Biochemical Institute, Kiel University, Kiel, Germany
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2
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Mandal SC, Chakrabarti J. In-silicon studies on hydration in EcoRI-cognate DNA complex. Biophys Chem 2023; 303:107121. [PMID: 37837721 DOI: 10.1016/j.bpc.2023.107121] [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: 04/26/2023] [Revised: 09/27/2023] [Accepted: 10/01/2023] [Indexed: 10/16/2023]
Abstract
Restriction endonucleases (REs) cleave DNA at specific site in presence of Mg2+ ion. Experiments further emphasize the role of hydration in metal ion specificity and sequence specificity of DNA cleavage. However, the relation between hydration and specificity has not been understood till date. This leads us to study via all-atom molecular dynamics (MD) simulations how the hydration around the scissile phosphate group changes in presence of Mg2+ and Ca2+ and depend on the DNA sequence. We observe the least number of hydrogen bonds around the scissile phosphate group in presence of Mg2+ ion. We further find that the hydrogen bonds decrease at the scissile phosphate on mutating one base pair in the cleavage region of the DNA in Mg2+ loaded EcoRI-DNA complex. We also perform steered MD simulations and observe that the rate of decrease of fraction of hydrogen bonds is slower in the mutated complex than the unmutated complex.
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Affiliation(s)
- Sasthi Charan Mandal
- Department of Physics of Complex Systems, S.N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India
| | - Jaydeb Chakrabarti
- Department of Physics of Complex Systems, S.N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India..
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3
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Xu SY. Engineering Infrequent DNA Nicking Endonuclease by Fusion of a BamHI Cleavage-Deficient Mutant and a DNA Nicking Domain. Front Microbiol 2022; 12:787073. [PMID: 35178039 PMCID: PMC8845596 DOI: 10.3389/fmicb.2021.787073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/17/2021] [Indexed: 11/13/2022] Open
Abstract
Strand-specific DNA nicking endonucleases (NEases) typically nick 3–7 bp sites. Our goal is to engineer infrequent NEase with a >8 bp recognition sequence. A BamHI catalytic-deficient mutant D94N/E113K was constructed, purified, and shown to bind and protect the GGATCC site from BamHI restriction. The mutant was fused to a 76-amino acid (aa) DNA nicking domain of phage Gamma HNH (gHNH) NEase. The chimeric enzyme was purified, and it was shown to nick downstream of a composite site 5′ GGATCC-N(4-6)-AC↑CGR 3′ (R, A, or G) or to nick both sides of BamHI site at the composite site 5′ CCG↓GT-N5-GGATCC-N5-AC↑CGG 3′ (the down arrow ↓ indicates the strand shown is nicked; the up arrow↑indicates the bottom strand is nicked). Due to the attenuated activity of the small nicking domain, the fusion nickase is active in the presence of Mn2+ or Ni2+, and it has low activity in Mg2+ buffer. This work provided a proof-of-concept experiment in which a chimeric NEase could be engineered utilizing the binding specificity of a Type II restriction endonucleases (REases) in fusion with a nicking domain to generate infrequent nickase, which bridges the gap between natural REases and homing endonucleases. The engineered chimeric NEase provided a framework for further optimization in molecular diagnostic applications.
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4
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Sugita M, Onishi I, Irisa M, Yoshida N, Hirata F. Molecular Recognition and Self-Organization in Life Phenomena Studied by a Statistical Mechanics of Molecular Liquids, the RISM/3D-RISM Theory. Molecules 2021; 26:E271. [PMID: 33430461 PMCID: PMC7826681 DOI: 10.3390/molecules26020271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 11/18/2022] Open
Abstract
There are two molecular processes that are essential for living bodies to maintain their life: the molecular recognition, and the self-organization or self-assembly. Binding of a substrate by an enzyme is an example of the molecular recognition, while the protein folding is a good example of the self-organization process. The two processes are further governed by the other two physicochemical processes: solvation and the structural fluctuation. In the present article, the studies concerning the two molecular processes carried out by Hirata and his coworkers, based on the statistical mechanics of molecular liquids or the RISM/3D-RISM theory, are reviewed.
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Affiliation(s)
- Masatake Sugita
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, W8-76, 2-12-1, Ookayama Meguro-ku, Tokyo 152-8550, Japan;
| | - Itaru Onishi
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan; (I.O.); (M.I.)
| | - Masayuki Irisa
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan; (I.O.); (M.I.)
| | - Norio Yoshida
- Department of Chemistry, Kyushu University, Fukuoka, Fukuoka 812-8581, Japan;
| | - Fumio Hirata
- Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan
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5
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Mandal SC, Maganti L, Mondal M, Chakrabarti J. Microscopic insight to specificity of metal ion cofactor in DNA cleavage by restriction endonuclease EcoRV. Biopolymers 2020; 111:e23396. [PMID: 32858776 DOI: 10.1002/bip.23396] [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: 01/03/2020] [Revised: 07/22/2020] [Accepted: 07/27/2020] [Indexed: 11/06/2022]
Abstract
Restriction endonucleases protect bacterial cells against bacteriophage infection by cleaving the incoming foreign DNA into fragments. In presence of Mg2+ ions, EcoRV is able to cleave the DNA but not in presence of Ca2+ , although the protein binds to DNA in presence of both metal ions. We make an attempt to understand this difference using conformational thermodynamics. We calculate the changes in conformational free energy and entropy of conformational degrees of freedom, like DNA base pair steps and dihedral angles of protein residues in Mg2+ (A)-EcoRV-DNA complex compared to Ca2+ (S)-EcoRV-DNA complex using all-atom molecular dynamics (MD) trajectories of the complexes. We find that despite conformational stability and order in both complexes, the individual degrees of freedom behave differently in the presence of two different metal ions. The base pairs in cleavage region are highly disordered in Ca2+ (S)-EcoRV-DNA compared to Mg2+ (A)-EcoRV-DNA. One of the acidic residues ASP90, coordinating to the metal ion in the vicinity of the cleavage site, is conformationally destabilized and disordered, while basic residue LYS92 gets conformational stability and order in Ca2+ (S) bound complex than in Mg2+ (A) bound complex. The enhanced fluctuations hinder placement of the metal ion in the vicinity of the scissile phosphate of DNA. Similar loss of conformational stability and order in the cleavage region is observed by the replacement of the metal ion. Considering the placement of the metal ion near scissile phosphate as requirement for cleavage action, our results suggest that the changes in conformational stability and order of the base pair steps and the protein residues lead to cofactor sensitivity of the enzyme. Our method based on fluctuations of microscopic conformational variables can be applied to understand enzyme activities in other protein-DNA systems.
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Affiliation(s)
- Sasthi Charan Mandal
- Department of Chemical, Biological and Macro-Molecular Sciences, S.N. Bose National Centre for Basic Sciences, Kolkata, India
| | - Lakshmi Maganti
- Computational Science Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Manas Mondal
- Shenzhen Bay Laboratory, Institute of Systems and Physical Biology, Shenzhen, China
| | - Jaydeb Chakrabarti
- Department of Chemical, Biological and Macro-Molecular Sciences, S.N. Bose National Centre for Basic Sciences, Kolkata, India.,Thematic Unit of Excellence on Computational Materials Science, and Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Kolkata, India
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6
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Silhan J, Zhao Q, Boura E, Thomson H, Förster A, Tang CM, Freemont PS, Baldwin GS. Structural basis for recognition and repair of the 3'-phosphate by NExo, a base excision DNA repair nuclease from Neisseria meningitidis. Nucleic Acids Res 2019; 46:11980-11989. [PMID: 30329088 PMCID: PMC6294502 DOI: 10.1093/nar/gky934] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/12/2018] [Indexed: 01/29/2023] Open
Abstract
NExo is an enzyme from Neisseria meningitidis that is specialized in the removal of the 3'-phosphate and other 3'-lesions, which are potential blocks for DNA repair. NExo is a highly active DNA 3'-phosphatase, and although it is from the class II AP family it lacks AP endonuclease activity. In contrast, the NExo homologue NApe, lacks 3'-phosphatase activity but is an efficient AP endonuclease. These enzymes act together to protect the meningococcus from DNA damage arising mainly from oxidative stress and spontaneous base loss. In this work, we present crystal structures of the specialized 3'-phosphatase NExo bound to DNA in the presence and absence of a 3'-phosphate lesion. We have outlined the reaction mechanism of NExo, and using point mutations we bring mechanistic insights into the specificity of the 3'-phosphatase activity of NExo. Our data provide further insight into the molecular origins of plasticity in substrate recognition for this class of enzymes. From this we hypothesize that these specialized enzymes lead to enhanced efficiency and accuracy of DNA repair and that this is important for the biological niche occupied by this bacterium.
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Affiliation(s)
- Jan Silhan
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Czech Republic
| | - Qiyuan Zhao
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Czech Republic
| | - Hellen Thomson
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK
| | | | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Paul S Freemont
- Department of Medicine, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Geoff S Baldwin
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK
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7
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The Leishmania donovani IMPACT-like protein possesses non-specific nuclease activity. Int J Biol Macromol 2018; 119:962-973. [DOI: 10.1016/j.ijbiomac.2018.07.175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/22/2018] [Accepted: 07/27/2018] [Indexed: 12/22/2022]
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8
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Onishi I, Sunaba S, Yoshida N, Hirata F, Irisa M. Role of Mg 2+ Ions in DNA Hydrolysis by EcoRV, Studied by the 3D-Reference Interaction Site Model and Molecular Dynamics. J Phys Chem B 2018; 122:9061-9075. [PMID: 30117741 DOI: 10.1021/acs.jpcb.7b12555] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The role of Mg2+ ions during precursor formation in DNA hydrolysis by the homodimeric restriction enzyme EcoRV was elucidated based on the 3D-reference interaction site model (RISM) theory and the molecular dynamics (MD) simulation. From an analysis of the spatial distribution of Mg2+ in an active site using 3D-RISM, we identified a new position for Mg2+ in the X-ray EcoRV-DNA complex structure ( 1rvb ). We refer to the position as site IV†. Site IV† is almost at the same position as that of a Ca2+ ion in the superimposed X-ray crystallographic active-site structure of the PvuII-DNA complex ( 1f0o ). 3D-RISM was also used to locate the position of water molecules, including the water nucleophile at the active site. MD simulations were carried out with the initial structure having two Mg2+ ions at site IV† and at site I*, experimentally identified by Horton et al., to find a stable complex structure in which the DNA fragment was rearranged to orient the scissile bond direction toward the water nucleophile. The equilibrium active-site structure of the EcoRV-DNA complex obtained from the MD simulation was similar to the superimposed X-ray crystallographic structure of the BamHI-DNA complex ( 2bam ). In the active-site structure, two metal ions have almost the same position (≤1.0 Å) as that of 2bam , and the scissile phosphate is twisted to orient the scissile bond toward the water nucleophile, as is the case in 2bam . We propose the equilibrium active-site structure obtained in this study as a precursor for the hydrolysis reaction of EcoRV.
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Affiliation(s)
- Itaru Onishi
- Department of Bioscience and Bioinformatics , Kyushu Institute of Technology , Iizuka 820-8502 , Japan
| | - Shunya Sunaba
- Department of Bioscience and Bioinformatics , Kyushu Institute of Technology , Iizuka 820-8502 , Japan
| | - Norio Yoshida
- Department of Chemistry, Graduate School of Science , Kyushu University , Fukuoka 819-0395 , Japan
| | - Fumio Hirata
- Toyota Physical & Chemical Research Institute , Aichi 480-1192 , Japan.,Institute for Molecular Science , Okazaki 444-8585 , Japan
| | - Masayuki Irisa
- Department of Bioscience and Bioinformatics , Kyushu Institute of Technology , Iizuka 820-8502 , Japan
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9
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Yekwa E, Khourieh J, Canard B, Papageorgiou N, Ferron F. Activity inhibition and crystal polymorphism induced by active-site metal swapping. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2017; 73:641-649. [PMID: 28777079 DOI: 10.1107/s205979831700866x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 06/10/2017] [Indexed: 11/11/2022]
Abstract
The Arenaviridae family is one of the two RNA viral families that encode a 3'-5' exonuclease in their genome. An exonuclease domain is found in the Arenaviridae nucleoprotein and targets dsRNA specifically. This domain is directly involved in suppression of innate immunity in the host cell. Like most phosphate-processing enzymes, it requires a divalent metal ion such as Mg2+ (or Mn2+) as a cofactor to catalyse nucleotide-cleavage and nucleotide-transfer reactions. On the other hand, calcium (Ca2+) inhibits this enzymatic activity, in spite of the fact that Mg2+ and Ca2+ present comparable binding affinities and biological availabilities. Here, the molecular and structural effects of the replacement of magnesium by calcium and its inhibition mechanism for phosphodiester cleavage, an essential reaction in the viral process of innate immunity suppression, are studied. Biochemical data and high-resolution structures of the Mopeia virus exonuclease domain complexed with each ion are reported for the first time. The consequences of the ion swap for the stability of the protein, the catalytic site and the functional role of a specific metal ion in enabling the catalytic cleavage of a dsRNA substrate are outlined.
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Affiliation(s)
- Elsie Yekwa
- CNRS, AFMB UMR 7257, 13288 Marseille, France
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10
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Förster resonance energy transfer and protein-induced fluorescence enhancement as synergetic multi-scale molecular rulers. Sci Rep 2016; 6:33257. [PMID: 27641327 PMCID: PMC5027553 DOI: 10.1038/srep33257] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 08/24/2016] [Indexed: 01/24/2023] Open
Abstract
Advanced microscopy methods allow obtaining information on (dynamic) conformational changes in biomolecules via measuring a single molecular distance in the structure. It is, however, extremely challenging to capture the full depth of a three-dimensional biochemical state, binding-related structural changes or conformational cross-talk in multi-protein complexes using one-dimensional assays. In this paper we address this fundamental problem by extending the standard molecular ruler based on Förster resonance energy transfer (FRET) into a two-dimensional assay via its combination with protein-induced fluorescence enhancement (PIFE). We show that donor brightness (via PIFE) and energy transfer efficiency (via FRET) can simultaneously report on e.g., the conformational state of double stranded DNA (dsDNA) following its interaction with unlabelled proteins (BamHI, EcoRV, and T7 DNA polymerase gp5/trx). The PIFE-FRET assay uses established labelling protocols and single molecule fluorescence detection schemes (alternating-laser excitation, ALEX). Besides quantitative studies of PIFE and FRET ruler characteristics, we outline possible applications of ALEX-based PIFE-FRET for single-molecule studies with diffusing and immobilized molecules. Finally, we study transcription initiation and scrunching of E. coli RNA-polymerase with PIFE-FRET and provide direct evidence for the physical presence and vicinity of the polymerase that causes structural changes and scrunching of the transcriptional DNA bubble.
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11
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Ji M, Tan L, Jen-Jacobson L, Saxena S. Insights into copper coordination in the EcoRI-DNA complex by ESR spectroscopy. Mol Phys 2014; 112:3173-3182. [PMID: 25750461 PMCID: PMC4350447 DOI: 10.1080/00268976.2014.934313] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The EcoRI restriction endonuclease requires one divalent metal ion in each of two symmetrical and identical catalytic sites to catalyse double-strand DNA cleavage. Recently, we showed that Cu2+ binds outside the catalytic sites to a pair of new sites at H114 in each sub-unit, and inhibits Mg2+ -catalysed DNA cleavage. In order to provide more detailed structural information on this new metal ion binding site, we performed W-band (~94 GHz) and X-band (~9.5 GHz) electron spin resonance spectroscopic measurements on the EcoRI-DNA-(Cu2+ )2 complex. Cu2+ binding results in two distinct components with different gzz and Azz values. X-band electron spin echo envelope modulation results indicate that both components arise from a Cu2+ coordinated to histidine. This observation is further confirmed by the hyperfine sub-level correlation results. W-band electron nuclear double resonance spectra provide evidence for equatorial coordination of water molecules to the Cu2+ ions.
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Affiliation(s)
- Ming Ji
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Likun Tan
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA, USA
| | - Linda Jen-Jacobson
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
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12
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Zhang J, Pan X, Bell CE. Crystal structure of λ exonuclease in complex with DNA and Ca(2+). Biochemistry 2014; 53:7415-25. [PMID: 25370446 DOI: 10.1021/bi501155q] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Bacteriophage λ exonuclease (λexo) is a ring-shaped homotrimer that resects double-stranded DNA ends in the 5'-3' direction to generate a long 3'-overhang that is a substrate for recombination. λexo is a member of the type II restriction endonuclease-like superfamily of proteins that use a Mg(2+)-dependent mechanism for nucleotide cleavage. A previous structure of λexo in complex with DNA and Mg(2+) was determined using a nuclease defective K131A variant to trap a stable complex. This structure revealed the detailed coordination of the two active site Mg(2+) ions but did not show the interactions involving the side chain of the conserved active site Lys-131 residue. Here, we have determined the crystal structure of wild-type (WT) λexo in complex with the same DNA substrate, but in the presence of Ca(2+) instead of Mg(2+). Surprisingly, there is only one Ca(2+) bound in the active site, near the position of Mg(A) in the structure with Mg(2+). The scissile phosphate is displaced by 2.2 Å relative to its position in the structure with Mg(2+), and the network of interactions involving the attacking water molecule is broken. Thus, the structure does not represent a catalytic configuration. However, the crystal structure does show clear electron density for the side chain of Lys-131, which is held in place by interactions with Gln-157 and Glu-129. By combining the K131A-Mg(2+) and WT-Ca(2+) structures, we constructed a composite model to show the likely interactions of Lys-131 during catalysis. The implications with regard to the catalytic mechanism are discussed.
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Affiliation(s)
- Jinjin Zhang
- Ohio State Biochemistry Program, ‡Department of Molecular and Cellular Biochemistry, and §Department of Chemistry and Biochemistry, The Ohio State University , 1645 Neil Avenue, Columbus, Ohio 43210, United States
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13
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Rosta E, Yang W, Hummer G. Calcium inhibition of ribonuclease H1 two-metal ion catalysis. J Am Chem Soc 2014; 136:3137-44. [PMID: 24499076 PMCID: PMC3985467 DOI: 10.1021/ja411408x] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Indexed: 01/05/2023]
Abstract
Most phosphate-processing enzymes require Mg(2+) as a cofactor to catalyze nucleotide cleavage and transfer reactions. Ca(2+) ions inhibit many of these enzymatic activities, despite Ca(2+) and Mg(2+) having comparable binding affinities and overall biological abundances. Here we study the molecular details of the calcium inhibition mechanism for phosphodiester cleavage, an essential reaction in the metabolism of nucleic acids and nucleotides, by comparing Ca(2+)- and Mg(2+) catalyzed reactions. We study the functional roles of the specific metal ion sites A and B in enabling the catalytic cleavage of an RNA/DNA hybrid substrate by B. halodurans ribonuclease (RNase) H1 using hybrid quantum-mechanics/molecular mechanics (QM/MM) free energy calculations. We find that Ca(2+) substitution of either of the two active-site Mg(2+) ions substantially increases the height of the reaction barrier and thereby abolishes the catalytic activity. Remarkably, Ca(2+) at the A site is inactive also in Mg(2+)-optimized active-site structures along the reaction path, whereas Mg(2+) substitution recovers activity in Ca(2+)-optimized structures. Geometric changes resulting from Ca(2+) substitution at metal ion site A may thus be a secondary factor in the loss of catalytic activity. By contrast, at metal ion site B geometry plays a more important role, with only a partial recovery of activity after Mg(2+) substitution in Ca(2+)-optimized structures. Ca(2+)-substitution also leads to a change in mechanism, with deprotonation of the water nucleophile requiring a closer approach to the scissile phosphate, which in turn increases the barrier. As a result, Ca(2+) is less efficient in activating the water. As a likely cause for the different reactivities of Mg(2+) and Ca(2+) ions in site A, we identify differences in charge transfer to the ions and the associated decrease in the pKa of the oxygen nucleophile attacking the phosphate group.
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Affiliation(s)
- Edina Rosta
- Laboratory
of Chemical Physics, National Institute of
Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
- Department
of Chemistry, King’s College London, London SE1 1DB, United Kingdom
| | - Wei Yang
- Laboratory
of Molecular Biology, National Institute
of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Gerhard Hummer
- Laboratory
of Chemical Physics, National Institute of
Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, 60438 Frankfurt am Main, Germany
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14
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Ferrandino R, Sidorova N, Rau D. Using single-turnover kinetics with osmotic stress to characterize the EcoRV cleavage reaction. Biochemistry 2014; 53:235-46. [PMID: 24328115 DOI: 10.1021/bi401089y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Type II restriction endonucleases require metal ions to specifically cleave DNA at canonical sites. Despite the wealth of structural and biochemical information, the number of Mg(2+) ions used for cleavage by EcoRV, in particular, at physiological divalent ion concentrations has not been established. In this work, we employ a single-turnover technique that uses osmotic stress to probe reaction kinetics between an initial specific EcoRV-DNA complex formed in the absence of Mg(2+) and the final cleavage step. With osmotic stress, complex dissociation before cleavage is minimized and the reaction rates are slowed to a convenient time scale of minutes to hours. We find that cleavage occurs by a two-step mechanism that can be characterized by two rate constants. The dependence of these rate constants on Mg(2+) concentration and osmotic pressure gives the number of Mg(2+) ions and water molecules coupled to each kinetic step of the EcoRV cleavage reaction. Each kinetic step is coupled to the binding 1.5-2.5 Mg(2+) ions, the uptake of ∼30 water molecules, and the cleavage of a DNA single strand. We suggest that each kinetic step reflects an independent, rate-limiting conformational change of each monomer of the dimeric enzyme that allows Mg(2+) ion binding. This modified single-turnover protocol has general applicability for metalloenzymes.
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Affiliation(s)
- Rocco Ferrandino
- The Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland 20892, United States
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15
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Cao W. Endonuclease V: an unusual enzyme for repair of DNA deamination. Cell Mol Life Sci 2013; 70:3145-56. [PMID: 23263163 PMCID: PMC11114013 DOI: 10.1007/s00018-012-1222-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2012] [Revised: 11/25/2012] [Accepted: 11/26/2012] [Indexed: 10/27/2022]
Abstract
Endonuclease V (endo V) was first discovered as the fifth endonuclease in Escherichia coli in 1977 and later rediscovered as a deoxyinosine 3' endonuclease. Decades of biochemical and genetic investigations have accumulated rich information on its role as a DNA repair enzyme for the removal of deaminated bases. Structural and biochemical analyses have offered invaluable insights on its recognition capacity, catalytic mechanism, and multitude of enzymatic activities. The roles of endo V in genome maintenance have been validated in both prokaryotic and eukaryotic organisms. The ubiquitous nature of endo V in the three domains of life: Bacteria, Archaea, and Eukaryotes, indicates its existence in the early evolutionary stage of cellular life. The application of endo V in mutation detection and DNA manipulation underscores its value beyond cellular DNA repair. This review is intended to provide a comprehensive account of the historic aspects, biochemical, structural biological, genetic and biotechnological studies of this unusual DNA repair enzyme.
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Affiliation(s)
- Weiguo Cao
- Department of Genetics and Biochemistry, South Carolina Experiment Station, Clemson University, Room 049 Life Science Building, 190 Collings Street, Clemson, SC, 29634, USA.
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16
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van Loenhout MTJ, De Vlaminck I, Flebus B, den Blanken JF, Zweifel LP, Hooning KM, Kerssemakers JWJ, Dekker C. Scanning a DNA molecule for bound proteins using hybrid magnetic and optical tweezers. PLoS One 2013; 8:e65329. [PMID: 23755219 PMCID: PMC3670887 DOI: 10.1371/journal.pone.0065329] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 04/24/2013] [Indexed: 11/25/2022] Open
Abstract
The functional state of the genome is determined by its interactions with proteins that bind, modify, and move along the DNA. To determine the positions and binding strength of proteins localized on DNA we have developed a combined magnetic and optical tweezers apparatus that allows for both sensitive and label-free detection. A DNA loop, that acts as a scanning probe, is created by looping an optically trapped DNA tether around a DNA molecule that is held with magnetic tweezers. Upon scanning the loop along the λ-DNA molecule, EcoRI proteins were detected with ∼17 nm spatial resolution. An offset of 33±5 nm for the detected protein positions was found between back and forwards scans, corresponding to the size of the DNA loop and in agreement with theoretical estimates. At higher applied stretching forces, the scanning loop was able to remove bound proteins from the DNA, showing that the method is in principle also capable of measuring the binding strength of proteins to DNA with a force resolution of 0.1 pN/. The use of magnetic tweezers in this assay allows the facile preparation of many single-molecule tethers, which can be scanned one after the other, while it also allows for direct control of the supercoiling state of the DNA molecule, making it uniquely suitable to address the effects of torque on protein-DNA interactions.
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Affiliation(s)
- Marijn T. J. van Loenhout
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Iwijn De Vlaminck
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Benedetta Flebus
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Johan F. den Blanken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Ludovit P. Zweifel
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Koen M. Hooning
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Jacob W. J. Kerssemakers
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- * E-mail:
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17
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Ruthstein S, Ji M, Mehta P, Jen-Jacobson L, Saxena S. Sensitive Cu2+-Cu2+ distance measurements in a protein-DNA complex by double-quantum coherence ESR. J Phys Chem B 2013; 117:6227-30. [PMID: 23631829 DOI: 10.1021/jp4037149] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Double quantum coherence (DQC) ESR spectroscopy is applied to measure the Cu(2+)-Cu(2+) distance in the EcoRI-DNA complex. A simple method is proposed to reduce the contribution of nuclear hyperfine and quadrupole interactions to such data. The effects of such interactions between the electron spin of Cu(2+) and neighboring nuclei on the DQC data make it difficult to measure the nanometer range interspin distance. The DQC data is in good agreement with results obtained by double electron electron resonance (DEER) spectroscopy. At the same time, the signal-to-noise ratio per shot in DQC is high. Taken together, these results provide impetus for further development of paramagnetic metal ion-based DQC techniques.
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Affiliation(s)
- Sharon Ruthstein
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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18
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Marcia M, Somarowthu S, Pyle AM. Now on display: a gallery of group II intron structures at different stages of catalysis. Mob DNA 2013; 4:14. [PMID: 23634971 PMCID: PMC3669008 DOI: 10.1186/1759-8753-4-14] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 04/08/2013] [Indexed: 11/10/2022] Open
Abstract
Group II introns are mobile genetic elements that self-splice and retrotranspose into DNA and RNA. They are considered evolutionary ancestors of the spliceosome, the ribonucleoprotein complex essential for pre-mRNA processing in higher eukaryotes. Over a 20-year period, group II introns have been characterized first genetically, then biochemically, and finally by means of X-ray crystallography. To date, 17 crystal structures of a group II intron are available, representing five different stages of the splicing cycle. This review provides a framework for classifying and understanding these new structures in the context of the splicing cycle. Structural and functional implications for the spliceosome are also discussed.
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Affiliation(s)
- Marco Marcia
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA.
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19
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Kim S, Broströmer E, Xing D, Jin J, Chong S, Ge H, Wang S, Gu C, Yang L, Gao YQ, Su XD, Sun Y, Xie XS. Probing allostery through DNA. Science 2013; 339:816-9. [PMID: 23413354 DOI: 10.1126/science.1229223] [Citation(s) in RCA: 200] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Allostery is well documented for proteins but less recognized for DNA-protein interactions. Here, we report that specific binding of a protein on DNA is substantially stabilized or destabilized by another protein bound nearby. The ternary complex's free energy oscillates as a function of the separation between the two proteins with a periodicity of ~10 base pairs, the helical pitch of B-form DNA, and a decay length of ~15 base pairs. The binding affinity of a protein near a DNA hairpin is similarly dependent on their separation, which-together with molecular dynamics simulations-suggests that deformation of the double-helical structure is the origin of DNA allostery. The physiological relevance of this phenomenon is illustrated by its effect on gene expression in live bacteria and on a transcription factor's affinity near nucleosomes.
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Affiliation(s)
- Sangjin Kim
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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20
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Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis. Proc Natl Acad Sci U S A 2012; 109:16852-7. [PMID: 23035246 DOI: 10.1073/pnas.1206563109] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Base excision repair (BER) is a highly conserved DNA repair pathway throughout all kingdoms from bacteria to humans. Whereas several enzymes are required to complete the multistep repair process of damaged bases, apurinic-apyrimidic (AP) endonucleases play an essential role in enabling the repair process by recognizing intermediary abasic sites cleaving the phosphodiester backbone 5' to the abasic site. Despite extensive study, there is no structure of a bacterial AP endonuclease bound to substrate DNA. Furthermore, the structural mechanism for AP-site cleavage is incomplete. Here we report a detailed structural and biochemical study of the AP endonuclease from Neisseria meningitidis that has allowed us to capture structural intermediates providing more complete snapshots of the catalytic mechanism. Our data reveal subtle differences in AP-site recognition and kinetics between the human and bacterial enzymes that may reflect different evolutionary pressures.
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21
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Belkebir A, Azeddoug H. Metal ion dependence of DNA cleavage by SepMI and EhoI restriction endonucleases. Microbiol Res 2012; 168:99-105. [PMID: 23017231 DOI: 10.1016/j.micres.2012.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 07/04/2012] [Accepted: 08/12/2012] [Indexed: 10/27/2022]
Abstract
Most of type II restriction endonucleases show an absolute requirement for divalent metal ions as cofactors for DNA cleavage. While Mg(2+) is the natural cofactor other metal ions can substitute it and mediate the catalysis, however Ca(2+) (alone) only supports DNA binding. To investigate the role of Mg(2+) in DNA cleavage by restriction endonucleases, we have studied the Mg(2+) and Mn(2+) concentration dependence of DNA cleavage by SepMI and EhoI. Digestion reactions were carried out at different Mg(2+) and Mn(2+) concentrations at constant ionic strength. These enzymes showed different behavior regarding the ions requirement, SepMI reached near maximal level of activity between 10 and 20mM while no activity was detected in the presence of Mn(2+) and in the presence of Ca(2+) cleavage activity was significantly decreased. However, EhoI was more highly active in the presence of Mn(2+) than in the presence of Mg(2+) and can be activated by Ca(2+). Our results propose the two-metal ion mechanism for EhoI and the one-metal ion mechanism for SepMI restriction endonuclease. The analysis of the kinetic parameters under steady state conditions showed that SepMI had a K(m) value for pTrcHisB DNA of 6.15 nM and a V(max) of 1.79×10(-2)nM min(-1), while EhoI had a K(m) for pUC19 plasmid of 8.66 nM and a V(max) of 2×10(-2)nM min(-1).
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Affiliation(s)
- Abdelkarim Belkebir
- Laboratoire de Biochimie et de Biologie Moléculaire, Faculté des Sciences, Université Hassan II-Ain Chock - Casablanca, km 8, route d'El Jadida BP. 5366, Casablanca, Morocco.
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22
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Gao R, Huang SYN, Marchand C, Pommier Y. Biochemical characterization of human tyrosyl-DNA phosphodiesterase 2 (TDP2/TTRAP): a Mg(2+)/Mn(2+)-dependent phosphodiesterase specific for the repair of topoisomerase cleavage complexes. J Biol Chem 2012; 287:30842-52. [PMID: 22822062 DOI: 10.1074/jbc.m112.393983] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
TDP2 is a multifunctional enzyme previously known for its role in signal transduction as TRAF and TNF receptor-associated protein (TTRAP) and ETS1-associated protein 2 (EAPII). The gene has recently been renamed TDP2 because it plays a critical role for the repair of topoisomerase II cleavage complexes (Top2cc) and encodes an enzyme that hydrolyzes 5'-tyrosine-DNA adducts that mimic abortive Top2cc. Here we further elucidate the DNA-processing activities of human recombinant TDP2 and its biochemical characteristics. The preferred substrate for TDP2 is single-stranded DNA or duplex DNA with a four-base pair overhang, which is consistent with the known structure of Top2cc or Top3cc. The k(cat)/K(m) of TDP1 and TDP2 was determined. It was found to be 4 × 10(5) s(-1)M(-1) for TDP2 using single-stranded 5'-tyrosyl-DNA. The processing of substrates as short as five nucleotides long suggests that TDP2 can directly bind DNA ends. 5'-Phosphodiesterase activity requires a phosphotyrosyl linkage and tolerates an extended group attached to the tyrosine. TDP2 requires Mg(2+) or Mn(2+) for efficient catalysis but is weakly active with Ca(2+) or Zn(2+). Titration with Ca(2+) demonstrates a two-metal binding site in TDP2. Sequence alignment suggests that TDP2 contains four conserved catalytic motifs shared by Mg(2+)-dependent endonucleases, such as APE1. Substitutions at each of the four catalytic motifs identified key residues Asn-120, Glu-152, Asp-262, and His-351, whose mutation to alanine significantly reduced or completely abolished enzymatic activity. Our study characterizes the substrate specificity and kinetic parameters of TDP2. In addition, a two-metal catalytic mechanism is proposed.
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Affiliation(s)
- Rui Gao
- Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
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23
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ESR spectroscopy identifies inhibitory Cu2+ sites in a DNA-modifying enzyme to reveal determinants of catalytic specificity. Proc Natl Acad Sci U S A 2012; 109:E993-1000. [PMID: 22493217 DOI: 10.1073/pnas.1200733109] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The relationship between DNA sequence recognition and catalytic specificity in a DNA-modifying enzyme was explored using paramagnetic Cu(2+) ions as probes for ESR spectroscopic and biochemical studies. Electron spin echo envelope modulation spectroscopy establishes that Cu(2+) coordinates to histidine residues in the EcoRI endonuclease homodimer bound to its specific DNA recognition site. The coordinated His residues were identified by a unique use of Cu(2+)-ion based long-range distance constraints. Double electron-electron resonance data yield Cu(2+)-Cu(2+) and Cu(2+)-nitroxide distances that are uniquely consistent with one Cu(2+) bound to His114 in each subunit. Isothermal titration calorimetry confirms that two Cu(2+) ions bind per complex. Unexpectedly, Mg(2+)-catalyzed DNA cleavage by EcoRI is profoundly inhibited by Cu(2+) binding at these hitherto unknown sites, 13 Å away from the Mg(2+) positions in the catalytic centers. Molecular dynamics simulations suggest a model for inhibition of catalysis, whereby the Cu(2+) ions alter critical protein-DNA interactions and water molecule positions in the catalytic sites. In the absence of Cu(2+), the Mg(2+)-dependence of EcoRI catalysis shows positive cooperativity, which would enhance EcoRI inactivation of foreign DNA by irreparable double-strand cuts, in preference to readily repaired single-strand nicks. Nonlinear Poisson-Boltzmann calculations suggest that this cooperativity arises because the binding of Mg(2+) in one catalytic site makes the surface electrostatic potential in the distal catalytic site more negative, thus enhancing binding of the second Mg(2+). Taken together, our results shed light on the structural and electrostatic factors that affect site-specific catalysis by this class of endonucleases.
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24
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Binding and cleavage of DNA with the restriction enzyme EcoR1 using time-resolved second harmonic generation. Proc Natl Acad Sci U S A 2011; 108:19979-84. [PMID: 22114185 DOI: 10.1073/pnas.1115498108] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The binding of EcoR1 to a 90-bp DNA duplex attached to colloidal microparticles and the subsequent cleavage by the enzyme was observed in real time and label-free with time-resolved second harmonic (SH) spectroscopy. This method provides a unique way to investigate biomolecular interactions based on its sensitivity to changes in structure and electrical charge on formation of a complex and subsequent dynamics. The binding of EcoR1 to the recognition sequence in DNA appears as a rapid increase in the SH signal, which is attributed to the enzyme-induced change in the DNA conformation, going from a rod-like to a bent shape. In the presence of the cofactor Mg(2+), the subsequent decay in the SH signal was monitored in real time as the following processes occurred: cleavage of DNA, dissociation of the enzyme from the DNA, and diffusion of the 74-bp fragment into the bulk solution leaving the 16-bp fragment attached to the microparticle. The observed decay was dependent on the concentration of Mg(2+), which functions as a cofactor and as an electrolyte. With SH spectroscopy the rehybridization dynamics between the rehybridized microparticle bound and free cleaved DNA fragments was observed in real time and label-free following the cleavage of DNA. Collectively, the experiments reported here establish SH spectroscopy as a powerful method to investigate equilibrium and time-dependent biological processes in a noninvasive and label-free way.
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25
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Hien LT, Zatsepin TS, Schierling B, Volkov EM, Wende W, Pingoud A, Kubareva EA, Oretskaya TS. Restriction endonuclease SsoII with photoregulated activity--a "molecular gate" approach. Bioconjug Chem 2011; 22:1366-73. [PMID: 21688832 DOI: 10.1021/bc200063m] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel method for regulating the activity of homodimeric proteins--"molecular gate" approach--was proposed and its usefulness illustrated for the type II restriction endonuclease SsoII (R.SsoII) as a model. The "molecular gate" approach is based on the modification of R.SsoII with azobenzene derivatives, which allows regulating DNA binding and cleavage via illumination with light. R.SsoII variants with single cysteine residues introduced at selected positions were obtained and modified with maleimidoazobenzene derivatives. A twofold change in the enzymatic activity after illumination with light of wavelengths of 365 and 470 nm, respectively, was demonstrated when one or two molecules of azobenzene derivatives were attached to the R.SsoII at the entrance of or within the DNA-binding site.
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Affiliation(s)
- Le Thi Hien
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory, Moscow 119991, Russia
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26
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Li ZH, Li P, Dzyuba B, Randak T. Influence of environmental related concentrations of heavy metals on motility parameters and antioxidant responses in sturgeon sperm. Chem Biol Interact 2010; 188:473-7. [DOI: 10.1016/j.cbi.2010.09.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Revised: 08/24/2010] [Accepted: 09/02/2010] [Indexed: 10/19/2022]
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27
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Bheemanaik S, Sistla S, Krishnamurthy V, Arathi S, Desirazu NR. Kinetics of Methylation by EcoP1I DNA Methyltransferase. Enzyme Res 2010; 2010:302731. [PMID: 21048863 PMCID: PMC2962900 DOI: 10.4061/2010/302731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2010] [Accepted: 06/21/2010] [Indexed: 11/20/2022] Open
Abstract
EcoP1I DNA MTase (M.EcoP1I), an N6-adenine MTase from bacteriophage P1, is a part of the EcoP1I restriction-modification (R-M) system which belongs to the Type III R-M system. It recognizes the sequence 5′-AGACC-3′ and methylates the internal adenine. M.EcoP1I requires Mg2+ for the transfer of methyl groups to DNA. M.EcoP1I is shown to exist as dimer in solution, and even at high salt concentrations (0.5 M) the dimeric M.EcoP1I does not dissociate into monomers suggesting a strong interaction between the monomer subunits. Preincubation and isotope partitioning studies with M.EcoP1I indicate a kinetic mechanism where the duplex DNA binds first followed by AdoMet. Interestingly, M.EcoP1I methylates DNA substrates in the presence of Mn2+ and Ca2+ other than Mg2+ with varying affinities. Amino acid analysis and methylation assays in the presence of metal ions suggest that M.EcoP1I has indeed two metal ion-binding sites [358ID(x)n … ExK401 and 600DxDxD604 motif]. EcoP1I DNA MTase catalyzes the transfer of methyl groups using a distributive mode of methylation on DNA containing more than one recognition site. A chemical modification of EcoP1I DNA MTase using N-ethylmaleimide resulted in an irreversible inactivation of enzyme activity suggesting the possible role of cysteine residues in catalysis.
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28
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Prasannan CB, Xie F, Dupureur CM. Characterizing metalloendonuclease mixed metal complexes by global kinetic analysis. J Biol Inorg Chem 2010; 15:533-45. [PMID: 20084532 DOI: 10.1007/s00775-010-0621-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 12/21/2009] [Indexed: 11/25/2022]
Affiliation(s)
- Charulata B Prasannan
- Department of Chemistry and Biochemistry, Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, USA
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29
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Dupureur CM. One is enough: insights into the two-metal ion nuclease mechanism from global analysis and computational studies. Metallomics 2010; 2:609-20. [PMID: 21072352 DOI: 10.1039/c0mt00013b] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Cynthia M Dupureur
- Department of Chemistry & Biochemistry and The Center for Nanoscience, University of Missouri-St. Louis, One University Blvd., St. Louis, MO 63121, USA.
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30
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Imhof P, Fischer S, Smith JC. Catalytic Mechanism of DNA Backbone Cleavage by the Restriction Enzyme EcoRV: A Quantum Mechanical/Molecular Mechanical Analysis. Biochemistry 2009; 48:9061-75. [DOI: 10.1021/bi900585m] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Petra Imhof
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
| | - Stefan Fischer
- Computational Biochemistry, IWR, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
| | - Jeremy C. Smith
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
- Oak Ridge National Laboratory, P.O. Box 2008 MS 6309, Oak Ridge, Tennessee 37831-6309
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31
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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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32
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Sissi C, Palumbo M. Effects of magnesium and related divalent metal ions in topoisomerase structure and function. Nucleic Acids Res 2009; 37:702-11. [PMID: 19188255 PMCID: PMC2647314 DOI: 10.1093/nar/gkp024] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The catalytic steps through which DNA topoisomerases produce their biological effects and the interference of drug molecules with the enzyme–DNA cleavage complex have been thoroughly investigated both from the biophysical and the biochemical point of view. This provides the basic structural insight on how this family of essential enzymes works in living systems and how their functions can be impaired by natural and synthetic compounds. Besides other factors, the physiological environment is known to affect substantially the biological properties of topoisomerases, a key role being played by metal ion cofactors, especially divalent ions (Mg2+), that are crucial to bestow and modulate catalytic activity by exploiting distinctive chemical features such as ionic size, hardness and characteristics of the coordination sphere including coordination number and geometry. Indeed, metal ions mediate fundamental aspects of the topoisomerase-driven transphosphorylation process by affecting the kinetics of the forward and the reverse steps and by modifying the enzyme conformation and flexibility. Of particular interest in type IA and type II enzymes are ionic interactions involving the Toprim fold, a protein domain conserved through evolution that contains a number of acidic residues essential for catalysis. A general two-metal ion mechanism is widely accepted to account for the biophysical and biochemical data thus far available.
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Affiliation(s)
- Claudia Sissi
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
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33
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Syson K, Tomlinson C, Chapados BR, Sayers JR, Tainer JA, Williams NH, Grasby JA. Three metal ions participate in the reaction catalyzed by T5 flap endonuclease. J Biol Chem 2008; 283:28741-6. [PMID: 18697748 DOI: 10.1074/jbc.m801264200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein nucleases and RNA enzymes depend on divalent metal ions to catalyze the rapid hydrolysis of phosphate diester linkages of nucleic acids during DNA replication, DNA repair, RNA processing, and RNA degradation. These enzymes are widely proposed to catalyze phosphate diester hydrolysis using a "two-metal-ion mechanism." Yet, analyses of flap endonuclease (FEN) family members, which occur in all domains of life and act in DNA replication and repair, exemplify controversies regarding the classical two-metal-ion mechanism for phosphate diester hydrolysis. Whereas substrate-free structures of FENs identify two active site metal ions, their typical separation of > 4 A appears incompatible with this mechanism. To clarify the roles played by FEN metal ions, we report here a detailed evaluation of the magnesium ion response of T5FEN. Kinetic investigations reveal that overall the T5FEN-catalyzed reaction requires at least three magnesium ions, implying that an additional metal ion is bound. The presence of at least two ions bound with differing affinity is required to catalyze phosphate diester hydrolysis. Analysis of the inhibition of reactions by calcium ions is consistent with a requirement for two viable cofactors (Mg2+ or Mn2+). The apparent substrate association constant is maximized by binding two magnesium ions. This may reflect a metal-dependent unpairing of duplex substrate required to position the scissile phosphate in contact with metal ion(s). The combined results suggest that T5FEN primarily uses a two-metal-ion mechanism for chemical catalysis, but that its overall metallobiochemistry is more complex and requires three ions.
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Affiliation(s)
- Karl Syson
- Department of Chemistry, Centre for Chemical Biology, Krebs Institute, University of Sheffield, Sheffield S3 7HF, United Kingdom
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A spectroscopic method to determine the activity of the restriction endonuclease EcoRV that involves a single reaction. Anal Biochem 2008; 497:103-5. [PMID: 18489897 DOI: 10.1016/j.ab.2008.04.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2008] [Revised: 04/20/2008] [Accepted: 04/24/2008] [Indexed: 11/23/2022]
Abstract
A one-step protocol is presented to determine the activity of EcoRV as a model of restriction enzymes. The protocol involved a molecular beacon as DNA substrate, with the target sequence recognized by EcoRV in the stem. EcoRV cleaved the stem forming two fragments, one of which contained the fluorophore and quencher, initially bound by 3 bp. This shorter fragment rapidly dissociated at 37 °C, causing an increase of fluorescence intensity that was used to gauge the reaction kinetics. The reaction can be described using the Michaelis-Menten mechanism, and the kinetic parameters obtained were compared with literature values involving other protocols.
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On-gel fluorescent visualization and the site identification of S-nitrosylated proteins. Anal Biochem 2008; 377:150-5. [PMID: 18395505 DOI: 10.1016/j.ab.2008.03.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2007] [Revised: 03/11/2008] [Accepted: 03/13/2008] [Indexed: 11/23/2022]
Abstract
Mounting evidence indicates that S-nitrosylation of critical cysteine residues in a protein represents a common feature of protein function regulation and cell signaling. However, the progress in studying the exact role of S-nitrosylation has been hampered by a lack of rapid and accurate methods for the detection of these S-nitrosylated proteins and the exact modification sites. In this article, we report a fluorescence-based method in which the S-nitrosylated cysteines are converted into 7-amino-4-methylcoumarin-3-acetic acid (AMCA) fluorophore-labeled cysteines-termed the AMCA switch method. The labeled proteins are then analyzed by nonreducing SDS-PAGE, and the S-nitrosylated proteins can be readily detected as brilliant blue bands after the activation of ultraviolet light. Furthermore, the sites of modification can be determined by liquid chromatography-tandem mass spectrometry (LC-MS/MS) after in-gel tryptic digestion of the fluorescent band, and the recognizable AMCA tag in the MS spectra ensures the accurate site identification of the nitrosocysteines. Therefore, our method offers some apparent advantages by direct visualization of on-gel image of S-nitrosylated proteins, shorter experiment time by skipping the anti-biotin immunoblotting step, and elimination of the potential interference of endogenous biotinylated proteins. Based on this method, we detected the S-nitrosylation and the modified site in bovine serum albumin and gankyrin after in vitro S-nitrosylation. Overall, our results indicate that the AMCA switch method is a fast and accurate method to identify the S-nitrosylated protein and the modification sites.
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Oezguen N, Schein CH, Peddi SR, Power TD, Izumi T, Braun W. A "moving metal mechanism" for substrate cleavage by the DNA repair endonuclease APE-1. Proteins 2007; 68:313-23. [PMID: 17427952 DOI: 10.1002/prot.21397] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Apurinic/apyrimidinic endonuclease (APE-1) is essential for base excision repair (BER) of damaged DNA. Here molecular dynamics (MD) simulations of APE1 complexed with cleaved and uncleaved damaged DNA were used to determine the role and position of the metal ion(s) in the active site before and after DNA cleavage. The simulations started from an energy minimized wild-type structure of the metal-free APE1/damaged-DNA complex (1DE8). A grid search with one Mg2+ ion located two low energy clusters of Mg2+ consistent with the experimentally determined metal ion positions. At the start of the longer MD simulations, Mg2+ ions were placed at different positions as seen in the crystal structures and the movement of the ion was followed over the course of the trajectory. Our analysis suggests a "moving metal mechanism" in which one Mg2+ ion moves from the B- (more buried) to the A-site during substrate cleavage. The anticipated inversion of the phosphate oxygens occurs during the in-line cleavage reaction. Experimental results, which show competition between Ca2+ and Mg2+ for catalyzing the reaction, and high concentrations of Mg2+ are inhibitory, indicate that both sites cannot be simultaneously occupied for maximal activity.
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Affiliation(s)
- Numan Oezguen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555-0857, USA
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37
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Homodimeric Structure and Double-stranded RNA Cleavage Activity of the C-terminal RNase III Domain of Human Dicer. J Mol Biol 2007; 374:106-20. [DOI: 10.1016/j.jmb.2007.08.069] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2007] [Revised: 08/26/2007] [Accepted: 08/31/2007] [Indexed: 11/18/2022]
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Reinhard BM, Sheikholeslami S, Mastroianni A, Alivisatos AP, Liphardt J. Use of plasmon coupling to reveal the dynamics of DNA bending and cleavage by single EcoRV restriction enzymes. Proc Natl Acad Sci U S A 2007; 104:2667-72. [PMID: 17307879 PMCID: PMC1815239 DOI: 10.1073/pnas.0607826104] [Citation(s) in RCA: 249] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pairs of Au nanoparticles have recently been proposed as "plasmon rulers" based on the dependence of their light scattering on the interparticle distance. Preliminary work has suggested that plasmon rulers can be used to measure and monitor dynamic distance changes over the 1- to 100-nm length scale in biology. Here, we substantiate that plasmon rulers can be used to measure dynamical biophysical processes by applying the ruler to a system that has been investigated extensively by using ensemble kinetic measurements: the cleavage of DNA by the restriction enzyme EcoRV. Temporal resolutions of up to 240 Hz were obtained, and the end-to-end extension of up to 1,000 individual dsDNA enzyme substrates could be simultaneously monitored for hours. The kinetic parameters extracted from our single-molecule cleavage trajectories agree well with values obtained in bulk through other methods and confirm well known features of the cleavage process, such as DNA bending before cleavage. Previously unreported dynamical information is revealed as well, for instance, the degree of softening of the DNA just before cleavage. The unlimited lifetime, high temporal resolution, and high signal/noise ratio make the plasmon ruler a unique tool for studying macromolecular assemblies and conformational changes at the single-molecule level.
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Affiliation(s)
- Björn M. Reinhard
- Departments of *Physics and
- Chemistry, University of California, Berkeley, CA 94720; and
- Divisions of Physical Biosciences and
| | - Sassan Sheikholeslami
- Chemistry, University of California, Berkeley, CA 94720; and
- Materials Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Alexander Mastroianni
- Chemistry, University of California, Berkeley, CA 94720; and
- Materials Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - A. Paul Alivisatos
- Chemistry, University of California, Berkeley, CA 94720; and
- Materials Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Jan Liphardt
- Departments of *Physics and
- Divisions of Physical Biosciences and
- To whom correspondence should be addressed. E-mail:
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Abstract
DNA and a large proportion of RNA are antiparallel duplexes composed of an unvarying phosphosugar backbone surrounding uniformly stacked and highly similar base pairs. How do the myriad of enzymes (including ribozymes) that perform catalysis on nucleic acids achieve exquisite structure or sequence specificity? In all DNA and RNA polymerases and many nucleases and transposases, two Mg2+ ions are jointly coordinated by the nucleic acid substrate and catalytic residues of the enzyme. Based on the exquisite sensitivity of Mg2+ ions to the ligand geometry and electrostatic environment, we propose that two-metal-ion catalysis greatly enhances substrate recognition and catalytic specificity.
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Affiliation(s)
- Wei Yang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
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40
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Macrae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD, Doudna JA. Structural basis for double-stranded RNA processing by Dicer. Science 2006; 311:195-8. [PMID: 16410517 DOI: 10.1126/science.1121638] [Citation(s) in RCA: 654] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The specialized ribonuclease Dicer initiates RNA interference by cleaving double-stranded RNA (dsRNA) substrates into small fragments about 25 nucleotides in length. In the crystal structure of an intact Dicer enzyme, the PAZ domain, a module that binds the end of dsRNA, is separated from the two catalytic ribonuclease III (RNase III) domains by a flat, positively charged surface. The 65 angstrom distance between the PAZ and RNase III domains matches the length spanned by 25 base pairs of RNA. Thus, Dicer itself is a molecular ruler that recognizes dsRNA and cleaves a specified distance from the helical end.
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Affiliation(s)
- Ian J Macrae
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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41
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van den Broek B, Vanzi F, Normanno D, Pavone FS, Wuite GJ. Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI. Nucleic Acids Res 2006; 34:167-74. [PMID: 16407332 PMCID: PMC1326248 DOI: 10.1093/nar/gkj432] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Many restriction enzymes require binding of two copies of a recognition sequence for DNA cleavage, thereby introducing a loop in the DNA. We investigated looping dynamics of Type IIE restriction enzymes NaeI and NarI by tracking the Brownian motion of single tethered DNA molecules. DNA containing two endonuclease recognition sites spaced a few 100 bp apart connect small polystyrene beads to a glass surface. The position of a bead is tracked through video microscopy. Protein-mediated looping and unlooping is then observed as a sudden specific change in Brownian motion of the bead. With this method we are able to directly follow DNA looping kinetics of single protein–DNA complexes to obtain loop stability and loop formation times. We show that, in the absence of divalent cations, NaeI induces DNA loops of specific size. In contrast, under these conditions NarI mainly creates non-specific loops, resulting in effective DNA compaction for higher enzyme concentrations. Addition of Ca2+ increases the NaeI-DNA loop lifetime by two orders of magnitude and stimulates specific binding by NarI. Finally, for both enzymes we observe exponentially distributed loop formation times, indicating that looping is dominated by (re)binding the second recognition site.
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Affiliation(s)
| | - Francesco Vanzi
- European Laboratory for Non-linear Spectroscopy (LENS), Via Nello Carrara 150019 Sesto Fiorentino (Firenze), Italy
| | - Davide Normanno
- European Laboratory for Non-linear Spectroscopy (LENS), Via Nello Carrara 150019 Sesto Fiorentino (Firenze), Italy
| | - Francesco S. Pavone
- European Laboratory for Non-linear Spectroscopy (LENS), Via Nello Carrara 150019 Sesto Fiorentino (Firenze), Italy
| | - Gijs J.L. Wuite
- To whom correspondence should be addressed. Tel: +31205987987; Fax: +31205987991;
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42
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Roberts KD, Lambert JN, Ede NJ, Bray AM. Efficient methodology for the cyclization of linear peptide libraries via intramolecularS-alkylation using Multipin™ solid phase peptide synthesis. J Pept Sci 2006; 12:525-32. [PMID: 16710870 DOI: 10.1002/psc.761] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Methodology is described here for the efficient parallel synthesis and cyclization of linear peptide libraries using intramolecular S-alkylation chemistry in combination with Multipin solid phase peptide synthesis (Multipin SPPS). The effective use of this methodology was demonstrated with the synthesis of a 72-member combinatorial library of cyclic thioether peptide derivatives of the conserved four-residue structural motif DD/EXK found in the active sites of the five crystallographically defined orthodox type II restriction endonucleases, EcoRV, EcoRI, PvuII, BamHI and BglI.
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Affiliation(s)
- Kade D Roberts
- School of Chemistry, The University of Melbourne, Grattan Street, Parkville, Victoria 3010, Australia.
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Xu QS, Roberts RJ, Guo HC. Two crystal forms of the restriction enzyme MspI-DNA complex show the same novel structure. Protein Sci 2005; 14:2590-600. [PMID: 16195548 PMCID: PMC2253285 DOI: 10.1110/ps.051565105] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The crystal structure of the Type IIP restriction endonuclease MspI bound to DNA containing its cognate recognition sequence has been determined in both monoclinic and orthorhombic space groups. Significantly, these two independent crystal forms present an identical structure of a novel monomer-DNA complex, suggesting a functional role for this novel enzyme-DNA complex. In both crystals, MspI interacts with the CCGG DNA recognition sequence as a monomer, using an asymmetric mode of recognition by two different structural motifs in a single polypeptide. In the crystallographic asymmetric unit, the two DNA molecules in the two MspI-DNA complexes appear to stack with each other forming an end-to-end pseudo-continuous 19-mer duplex. They are primarily B-form and no major bends or kinks are observed. For DNA recognition, most of the specific contacts between the enzyme and the DNA are preserved in the orthorhombic structure compared with the monoclinic structure. A cation is observed near the catalytic center in the monoclinic structure at a position homologous to the 74/45 metal site of EcoRV, and the orthorhombic structure also shows signs of this same cation. However, the coordination ligands of the metal are somewhat different from those of the 74/45 metal site of EcoRV. Combined with structural information from other solved structures of Type II restriction enzymes, the possible relationship between the structures of the enzymes and their cleavage behaviors is discussed.
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Affiliation(s)
- Qian Steven Xu
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA 02118, USA.
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44
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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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45
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Bellamy SRW, Milsom SE, Scott DJ, Daniels LE, Wilson GG, Halford SE. Cleavage of individual DNA strands by the different subunits of the heterodimeric restriction endonuclease BbvCI. J Mol Biol 2005; 348:641-53. [PMID: 15826661 DOI: 10.1016/j.jmb.2005.02.035] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2005] [Revised: 02/11/2005] [Accepted: 02/18/2005] [Indexed: 11/26/2022]
Abstract
BbvCI cleaves an asymmetric DNA sequence, 5'-CC downward arrow TCAGC-3'/5'-GC downward arrow TGAGG-3', as indicated. While many Type II restriction enzymes consist of identical subunits, BbvCI has two different subunits: R(1), which acts at GC downward arrow TGAGG; and R(2), which acts at CC downward arrow TCAGC. Some mutants of BbvCI with defects in one subunit, either R(1)(-)R(2)(+) or R(1)(+)R(2)(-), cleave only one strand, that attacked by the native subunit. In analytical ultracentrifugation at various concentrations of protein, wild-type and mutant BbvCI enzymes aggregated extensively, but are R(1)R(2) heterodimers at the concentrations used in DNA cleavage reactions. On a plasmid with one recognition site, wild-type BbvCI cleaved both strands before dissociating from the DNA, while the R(1)(-)R(2)(+) and R(1)(+)R(2)(-) mutants acted almost exclusively on their specified strands, albeit at relatively slow rates. During the wild-type reaction, the DNA is cleaved initially in one strand, mainly that targeted by the R(1) subunit. The other strand is then cleaved slowly by R(2) before the enzyme dissociates from the DNA. Hence, the nicked form accumulates as a transient intermediate. This behaviour differs from that of many other restriction enzymes, which cut both strands at equal rates. However, the activities of the R(1)(+) and R(2)(+) subunits in the wild-type enzyme can differ from their activities in the R(1)(+)R(2)(-) and R(1)(-)R(2)(+) mutants. Each active site in BbvCI therefore influences the other.
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Affiliation(s)
- Stuart R W Bellamy
- Department of Biochemistry, School of Medical Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK.
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46
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Sapienza PJ, Dela Torre CA, McCoy WH, Jana SV, Jen-Jacobson L. Thermodynamic and kinetic basis for the relaxed DNA sequence specificity of "promiscuous" mutant EcoRI endonucleases. J Mol Biol 2005; 348:307-24. [PMID: 15811370 DOI: 10.1016/j.jmb.2005.02.051] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2004] [Revised: 02/15/2005] [Accepted: 02/17/2005] [Indexed: 11/18/2022]
Abstract
Promiscuous mutant EcoRI endonucleases produce lethal to sublethal effects because they cleave Escherichia coli DNA despite the presence of the EcoRI methylase. Three promiscuous mutant forms, Ala138Thr, Glu192Lys and His114Tyr, have been characterized with respect to their binding affinities and first-order cleavage rate constants towards the three classes of DNA sites: specific, miscognate (EcoRI*) and non-specific. We have made the unanticipated and counterintuitive observations that the mutant restriction endonucleases that exhibit relaxed specificity in vivo nevertheless bind more tightly than the wild-type enzyme to the specific recognition sequence in vitro, and show even greater preference for binding to the cognate GAATTC site over miscognate sites. Binding preference for EcoRI* over non-specific DNA is also improved. The first-order cleavage rate constants of the mutant enzymes are normal for the cognate site GAATTC, but are greater than those of the wild-type enzyme at EcoRI* sites. Thus, the mutant enzymes use two mechanisms to partially bypass the multiple fail-safe mechanisms that protect against cleavage of genomic DNA in cells carrying the wild-type EcoRI restriction-modification system: (a) binding to EcoRI* sites is more probable than for wild-type enzyme because non-specific DNA is less effective as a competitive inhibitor; (b) the combination of increased affinity and elevated cleavage rate constants at EcoRI* sites makes double-strand cleavage of these sites a more probable outcome than it is for the wild-type enzyme. Semi-quantitative estimates of rates of EcoRI* site cleavage in vivo, predicted using the binding and cleavage constants measured in vitro, are in accord with the observed lethal phenotypes associated with the three mutations.
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Affiliation(s)
- Paul J Sapienza
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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47
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Lamm G, Pack GR. Induced coalescence of cations through low-temperature Poisson-Boltzmann calculations. Biophys J 2005; 87:764-7. [PMID: 15298885 PMCID: PMC1304486 DOI: 10.1529/biophysj.104.040220] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The computational determination of preferred binding regions of divalent counterions to nucleic acids is either inaccurate (standard Poisson-Boltzmann approaches) or extremely time-consuming (Monte Carlo or molecular dynamics simulations). A novel "selective low-temperature" Poisson-Boltzmann method is introduced that, although approximate in nature, qualitatively accounts for ion correlation and charge-transfer effects and allows for the rapid determination of such regions through an "induced coalescence" of divalent ions. The method is illustrated here for the binding of Mg(2+) to a double-helical sequence of B-form DNA (CGCGAATTCGCG) but the technique is readily applicable to locating divalent cations in other systems such as DNA-endonuclease complexes and ribozymes.
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Affiliation(s)
- Gene Lamm
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA
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48
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Tsunaka Y, Takano K, Matsumura H, Yamagata Y, Kanaya S. Identification of Single Mn2+ Binding Sites Required for Activation of the Mutant Proteins of E.coli RNase HI at Glu48 and/or Asp134 by X-ray Crystallography. J Mol Biol 2005; 345:1171-83. [PMID: 15644213 DOI: 10.1016/j.jmb.2004.11.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2004] [Revised: 11/03/2004] [Accepted: 11/04/2004] [Indexed: 10/26/2022]
Abstract
Escherichia coli RNase HI has two Mn(2+)-binding sites. Site 1 is formed by Asp10, Glu48, and Asp70, and site 2 is formed by Asp10 and Asp134. Site 1 and site 2 have been proposed to be an activation site and an attenuation site, respectively. However, Glu48 and Asp134 are dispensable for Mn(2+)-dependent activity. In order to identify the Mn(2+)-binding sites of the mutant proteins at Glu48 and/or Asp134, the crystal structures of the mutant proteins E48A-RNase HI*, D134A-RNase HI*, and E48A/D134N-RNase HI* in complex with Mn(2+) were determined. In E48A-RNase HI*, Glu48 and Lys87 are replaced by Ala. In D134A-RNase HI*, Asp134 and Lys87 are replaced by Ala. In E48A/D134N-RNase HI*, Glu48 and Lys87 are replaced by Ala and Asp134 is replaced by Asn. All crystals had two or four protein molecules per asymmetric unit and at least two of which had detectable manganese ions. These structures indicated that only one manganese ion binds to the various positions around the center of the active-site pocket. These positions are different from one another, but none of them is similar to site 1. The temperature factors of these manganese ions were considerably larger than those of the surrounding residues. These results suggest that the first manganese ion required for activation of the wild-type protein fluctuates among various positions around the center of the active-site pockets. We propose that this fluctuation is responsible for efficient hydrolysis of the substrates by the protein (metal fluctuation model). The binding position of the first manganese ion is probably forced to shift to site 1 or site 2 upon binding of the second manganese ion.
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Affiliation(s)
- Yasuo Tsunaka
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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Anindya R, Savithri HS. Potyviral NIa proteinase, a proteinase with novel deoxyribonuclease activity. J Biol Chem 2004; 279:32159-69. [PMID: 15163663 DOI: 10.1074/jbc.m404135200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The NIa proteinase from pepper vein banding virus (PVBV) is a sequence-specific proteinase required for processing of viral polyprotein in the cytoplasm. It accumulates in the nucleus of the infected plant cell and forms inclusion bodies. The function of this protein in the nucleus is not clear. The purified recombinant NIa proteinase was active, and the mutation of the catalytic residues His-46, Asp-81, and Cys-151 resulted in complete loss of activity. Most interesting, the PVBV NIa proteinase exhibited previously unidentified activity, namely nonspecific double-stranded DNA degradation. This DNase activity of the NIa proteinase showed an absolute requirement for Mg(2+). Site-specific mutational analysis showed that of the three catalytic residues, Asp-81 was the crucial residue for DNase activity. Mutation of His-46 and Cys-151 had no effect on the DNase activity, whereas mutant D81N was partially active, and D81G was completely inactive. Based on kinetic analysis and molecular modeling, a metal ion-dependent catalysis similar to that observed in other nonspecific DNases is proposed. Similar results were obtained with glutathione S-transferase-fused PVBV NIa proteinase and tobacco etch virus NIa proteinase, confirming that the DNase function is an intrinsic property of potyviral NIa proteinase. The NIa protein present in the infected plant nuclear extract also showed the proteinase and the DNase activities, suggesting that the PVBV NIa protein that accumulates in the nucleus late in the infection cycle might serve to degrade the host DNA. Thus the dual function of the NIa proteinase could play an important role in the life cycle of the virus.
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Affiliation(s)
- Roy Anindya
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
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