1
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Pan Y, Zhao C, Fu W, Yang S, Lv S. Comparative analysis of structural dynamics and allosteric mechanisms of RecA/Rad51 family proteins: Integrated atomistic MD simulation and network-based analysis. Int J Biol Macromol 2024; 261:129843. [PMID: 38302027 DOI: 10.1016/j.ijbiomac.2024.129843] [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: 08/17/2023] [Revised: 01/26/2024] [Accepted: 01/27/2024] [Indexed: 02/03/2024]
Abstract
Homologous recombination plays a key role in double-strand break repair, stalled replication fork repair, and meiosis. The RecA/Rad51 family recombinases catalyze the DNA strand invasion reaction that occurs during homologous recombination. However, the high sequence differences between homologous groups have hindered the thoroughly studies of this ancient protein family. The dynamic mechanisms of the family, particularly at the residual level, remain poorly understood. In this work, five representative RecA/Rad51 recombinase family members from all major kingdoms of living organisms: prokaryotes, eukaryotes, archaea, and viruses, were selected to explore the molecular mechanisms behind their conserved biological significance. A variety of techniques, including all-atom molecular dynamics simulation, perturbation response scanning, and protein structure network analysis, were used to examine the flexibility and correlation of protein domains, distribution of sensors and effectors and conserved hub residues. Furthermore, the potential communication routes between the ATP-binding region and the DNA-binding region of each recombinase were identified. Our results demonstrate the conserved molecular dynamics of these recombinases in the early stage of homologous recombination, including cooperative motions between regions, conserved sensing and effecting functional residue distribution, and conserved hub residues. Meanwhile, the unique ATP-DNA communication routes of each recombinase was also revealed. These results provide new insights into the mechanism of RecA/Rad51 family proteins, and provide new theoretical guidance for the development of allosteric inhibitors and the application of RecA/Rad51 family proteins.
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Affiliation(s)
- Yue Pan
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Chong Zhao
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Wenyu Fu
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Shuo Yang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China.
| | - Shaowu Lv
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China; Bioarchaeology Laboratory, Jilin University, 2699 Qianjin Street, Changchun 130012, China.
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2
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Luo SC, Yeh MC, Lien YH, Yeh HY, Siao HL, Tu IP, Chi P, Ho MC. A RAD51-ADP double filament structure unveils the mechanism of filament dynamics in homologous recombination. Nat Commun 2023; 14:4993. [PMID: 37591853 PMCID: PMC10435448 DOI: 10.1038/s41467-023-40672-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 08/04/2023] [Indexed: 08/19/2023] Open
Abstract
ATP-dependent RAD51 recombinases play an essential role in eukaryotic homologous recombination by catalyzing a four-step process: 1) formation of a RAD51 single-filament assembly on ssDNA in the presence of ATP, 2) complementary DNA strand-exchange, 3) ATP hydrolysis transforming the RAD51 filament into an ADP-bound disassembly-competent state, and 4) RAD51 disassembly to provide access for DNA repairing enzymes. Of these steps, filament dynamics between the ATP- and ADP-bound states, and the RAD51 disassembly mechanism, are poorly understood due to the lack of near-atomic-resolution information of the ADP-bound RAD51-DNA filament structure. We report the cryo-EM structure of ADP-bound RAD51-DNA filaments at 3.1 Å resolution, revealing a unique RAD51 double-filament that wraps around ssDNA. Structural analysis, supported by ATP-chase and time-resolved cryo-EM experiments, reveals a collapsing mechanism involving two four-protomer movements along ssDNA for mechanical transition between RAD51 single- and double-filament without RAD51 dissociation. This mechanism enables elastic change of RAD51 filament length during structural transitions between ATP- and ADP-states.
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Affiliation(s)
- Shih-Chi Luo
- Institute of Biological Chemistry, Academia Sinica, 11529, Taipei, Taiwan
| | - Min-Chi Yeh
- Institute of Biological Chemistry, Academia Sinica, 11529, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, 10617, Taipei, Taiwan
| | - Yu-Hsiang Lien
- Institute of Statistical Science, Academia Sinica, 11529, Taipei, Taiwan
| | - Hsin-Yi Yeh
- Institute of Biochemical Sciences, National Taiwan University, 10617, Taipei, Taiwan
| | - Huei-Lun Siao
- Institute of Statistical Science, Academia Sinica, 11529, Taipei, Taiwan
| | - I-Ping Tu
- Institute of Statistical Science, Academia Sinica, 11529, Taipei, Taiwan
| | - Peter Chi
- Institute of Biological Chemistry, Academia Sinica, 11529, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, 10617, Taipei, Taiwan
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, 11529, Taipei, Taiwan.
- Institute of Biochemical Sciences, National Taiwan University, 10617, Taipei, Taiwan.
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3
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Appleby R, Bollschweiler D, Chirgadze DY, Joudeh L, Pellegrini L. A metal ion-dependent mechanism of RAD51 nucleoprotein filament disassembly. iScience 2023; 26:106689. [PMID: 37216117 PMCID: PMC10192527 DOI: 10.1016/j.isci.2023.106689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/21/2023] [Accepted: 04/13/2023] [Indexed: 05/24/2023] Open
Abstract
The RAD51 ATPase polymerizes on single-stranded DNA to form nucleoprotein filaments (NPFs) that are critical intermediates in the reaction of homologous recombination. ATP binding maintains the NPF in a competent conformation for strand pairing and exchange. Once strand exchange is completed, ATP hydrolysis licenses the filament for disassembly. Here we show that the ATP-binding site of the RAD51 NPF contains a second metal ion. In the presence of ATP, the metal ion promotes the local folding of RAD51 into the conformation required for DNA binding. The metal ion is absent in the ADP-bound RAD51 filament, that rearranges in a conformation incompatible with DNA binding. The presence of the second metal ion explains how RAD51 couples the nucleotide state of the filament to DNA binding. We propose that loss of the second metal ion upon ATP hydrolysis drives RAD51 dissociation from the DNA and weakens filament stability, contributing to NPF disassembly.
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Affiliation(s)
- Robert Appleby
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | | | | | - Luay Joudeh
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Luca Pellegrini
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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4
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Knadler C, Graham V W, Rolfsmeier M, Haseltine CA. Divalent metal cofactors differentially modulate RadA-mediated strand invasion and exchange in Saccharolobus solfataricus. Biosci Rep 2023; 43:BSR20221807. [PMID: 36601994 PMCID: PMC9950535 DOI: 10.1042/bsr20221807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/20/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Central to the universal process of recombination, RecA family proteins form nucleoprotein filaments to catalyze production of heteroduplex DNA between substrate ssDNAs and template dsDNAs. ATP binding assists the filament in assuming the necessary conformation for forming heteroduplex DNA, but hydrolysis is not required. ATP hydrolysis has two identified roles which are not universally conserved: promotion of filament dissociation and enhancing flexibility of the filament. In this work, we examine ATP utilization of the RecA family recombinase SsoRadA from Saccharolobus solfataricus to determine its function in recombinase-mediated heteroduplex DNA formation. Wild-type SsoRadA protein and two ATPase mutant proteins were evaluated for the effects of three divalent metal cofactors. We found that unlike other archaeal RadA proteins, SsoRadA-mediated strand exchange is not enhanced by Ca2+. Instead, the S. solfataricus recombinase can utilize Mn2+ to stimulate strand invasion and reduce ADP-binding stability. Additionally, reduction of SsoRadA ATPase activity by Walker Box mutation or cofactor alteration resulted in a loss of large, complete strand exchange products. Depletion of ADP was found to improve initial strand invasion but also led to a similar loss of large strand exchange events. Our results indicate that overall, SsoRadA is distinct in its use of divalent cofactors but its activity with Mn2+ shows similarity to human RAD51 protein with Ca2+.
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Affiliation(s)
- Corey J. Knadler
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-7520, U.S.A
| | - William J. Graham V
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-7520, U.S.A
| | - Michael L. Rolfsmeier
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-7520, U.S.A
| | - Cynthia A. Haseltine
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-7520, U.S.A
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5
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Altmannova V, Spirek M, Orlic L, Jēkabsons A, Clarence T, Henggeler A, Mlcouskova J, Chaleil RA, Matos J, Krejci L. The role of bivalent ions in the regulation of D-loop extension mediated by DMC1 during meiotic recombination. iScience 2022; 25:105439. [PMID: 36388968 PMCID: PMC9641244 DOI: 10.1016/j.isci.2022.105439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 09/06/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
During meiosis, programmed DNA double-strand breaks (DSBs) are repaired by homologous recombination. DMC1, a conserved recombinase, plays a central role in this process. DMC1 promotes DNA strand exchange between homologous chromosomes, thus creating the physical linkage between them. Its function is regulated not only by several accessory proteins but also by bivalent ions. Here, we show that whereas calcium ions in the presence of ATP cause a conformational change within DMC1, stimulating its DNA binding and D-loop formation, they inhibit the extension of the invading strand within the D-loop. Based on structural studies, we have generated mutants of two highly conserved amino acids - E162 and D317 - in human DMC1, which are deficient in calcium regulation. In vivo studies of their yeast homologues further showed that they exhibit severe defects in meiosis, thus emphasizing the importance of calcium ions in the regulation of DMC1 function and meiotic recombination.
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Affiliation(s)
- Veronika Altmannova
- Department of Biology, Masaryk University, Brno 62500, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, Brno 65691, Czech Republic
| | - Mario Spirek
- Department of Biology, Masaryk University, Brno 62500, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, Brno 65691, Czech Republic
| | - Lucija Orlic
- Max Perutz Labs, University of Vienna, Dr. Bohr-Gasse 9 1030 Vienna, Austria
| | - Atis Jēkabsons
- Department of Biology, Masaryk University, Brno 62500, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, Brno 65691, Czech Republic
| | - Tereza Clarence
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
| | - Adrian Henggeler
- Max Perutz Labs, University of Vienna, Dr. Bohr-Gasse 9 1030 Vienna, Austria
| | - Jarmila Mlcouskova
- International Clinical Research Center, St. Anne’s University Hospital, Brno 65691, Czech Republic
| | | | - Joao Matos
- Max Perutz Labs, University of Vienna, Dr. Bohr-Gasse 9 1030 Vienna, Austria
| | - Lumir Krejci
- Department of Biology, Masaryk University, Brno 62500, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, Brno 65691, Czech Republic
- National Center for Biomolecular Research, Masaryk University, Brno 62500, Czech Republic
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6
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Real-time tracking reveals catalytic roles for the two DNA binding sites of Rad51. Nat Commun 2020; 11:2950. [PMID: 32528002 PMCID: PMC7289862 DOI: 10.1038/s41467-020-16750-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 05/19/2020] [Indexed: 02/03/2023] Open
Abstract
During homologous recombination, Rad51 forms a nucleoprotein filament on single-stranded DNA to promote DNA strand exchange. This filament binds to double-stranded DNA (dsDNA), searches for homology, and promotes transfer of the complementary strand, producing a new heteroduplex. Strand exchange proceeds via two distinct three-strand intermediates, C1 and C2. C1 contains the intact donor dsDNA whereas C2 contains newly formed heteroduplex DNA. Here, we show that the conserved DNA binding motifs, loop 1 (L1) and loop 2 (L2) in site I of Rad51, play distinct roles in this process. L1 is involved in formation of the C1 complex whereas L2 mediates the C1–C2 transition, producing the heteroduplex. Another DNA binding motif, site II, serves as the DNA entry position for initial Rad51 filament formation, as well as for donor dsDNA incorporation. Our study provides a comprehensive molecular model for the catalytic process of strand exchange mediated by eukaryotic RecA-family recombinases. Rad51 drives DNA strand exchange, the central reaction in recombinational DNA repair. Two sites of Rad51 are responsible for DNA binding, but the function of these sites has proven elusive. Here, the authors employ real-time assays to reveal catalytic roles for the two DNA binding sites of Rad51.
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7
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Pastushok L, Fu Y, Lin L, Luo Y, DeCoteau JF, Lee K, Geyer CR. A Novel Cell-Penetrating Antibody Fragment Inhibits the DNA Repair Protein RAD51. Sci Rep 2019; 9:11227. [PMID: 31375703 PMCID: PMC6677837 DOI: 10.1038/s41598-019-47600-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 07/15/2019] [Indexed: 12/19/2022] Open
Abstract
DNA damaging chemotherapies are successful in cancer therapy, however, the damage can be reversed by DNA repair mechanisms that may be up-regulated in cancer cells. We hypothesized that inhibiting RAD51, a protein involved in homologous recombination DNA repair, would block DNA repair and restore the effectiveness of DNA damaging chemotherapy. We used phage-display to generate a novel synthetic antibody fragment that bound human RAD51 with high affinity (KD = 8.1 nM) and inhibited RAD51 ssDNA binding in vitro. As RAD51 is an intracellular target, we created a corresponding intrabody fragment that caused a strong growth inhibitory phenotype on human cells in culture. We then used a novel cell-penetrating peptide "iPTD" fusion to generate a therapeutically relevant antibody fragment that effectively entered living cells and enhanced the cell-killing effect of a DNA alkylating agent. The iPTD may be similarly useful as a cell-penetrating peptide for other antibody fragments and open the door to numerous intracellular targets previously off-limits in living cells.
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Affiliation(s)
- Landon Pastushok
- Department of Pathology and Lab Medicine, University of Saskatchewan, Saskatoon, Canada.,Advanced Diagnostics Research Lab, Saskatchewan Cancer Agency, Saskatoon, Canada
| | - Yongpeng Fu
- Department of Pathology and Lab Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Leo Lin
- iProgen Biotech Inc., Burnaby, Canada
| | - Yu Luo
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Canada
| | - John F DeCoteau
- Department of Pathology and Lab Medicine, University of Saskatchewan, Saskatoon, Canada.,Advanced Diagnostics Research Lab, Saskatchewan Cancer Agency, Saskatoon, Canada
| | - Ken Lee
- iProgen Biotech Inc., Burnaby, Canada
| | - C Ronald Geyer
- Department of Pathology and Lab Medicine, University of Saskatchewan, Saskatoon, Canada. .,Advanced Diagnostics Research Lab, Saskatchewan Cancer Agency, Saskatoon, Canada.
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8
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Meiotic MCM Proteins Promote and Inhibit Crossovers During Meiotic Recombination. Genetics 2019; 212:461-468. [PMID: 31028111 PMCID: PMC6553819 DOI: 10.1534/genetics.119.302221] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 04/22/2019] [Indexed: 01/29/2023] Open
Abstract
Crossover formation as a result of meiotic recombination is vital for the proper segregation of homologous chromosomes at the end of meiosis I. In many organisms, crossovers are generated through two crossover pathways: Class I and Class II. To ensure accurate crossover formation, meiosis-specific protein complexes regulate the degree to which each pathway is used. One such complex is the mei-mini-chromosome maintenance (MCM) complex, which contains MCM and MCM-like proteins REC (ortholog of Mcm8), MEI-217, and MEI-218. The mei-MCM complex genetically promotes Class I crossovers and inhibits Class II crossovers in Drosophila, but it is unclear how individual mei-MCM proteins contribute to crossover regulation. In this study, we perform genetic analyses to understand how specific regions and motifs of mei-MCM proteins contribute to Class I and II crossover formation, and distribution. Our analyses show that the long, disordered N-terminus of MEI-218 is dispensable for crossover formation, and that mutations that disrupt REC’s Walker A and B motifs differentially affect Class I and Class II crossover formation. In rec Walker A mutants, Class I crossovers exhibit no change but Class II crossovers are increased. However, in rec Walker B mutants, Class I crossovers are severely impaired and Class II crossovers are increased. These results suggest that REC may form multiple complexes that exhibit differential REC-dependent ATP-binding and -hydrolyzing requirements. These results provide genetic insight into the mechanisms through which mei-MCM proteins promote Class I crossovers and inhibit Class II crossovers.
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9
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Vydyam P, Dutta D, Sutram N, Bhattacharyya S, Bhattacharyya MK. A small-molecule inhibitor of the DNA recombinase Rad51 from Plasmodium falciparum synergizes with the antimalarial drugs artemisinin and chloroquine. J Biol Chem 2019; 294:8171-8183. [PMID: 30936202 DOI: 10.1074/jbc.ra118.005009] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 03/27/2019] [Indexed: 11/06/2022] Open
Abstract
Malaria parasites repair DNA double-strand breaks (DSBs) primarily through homologous recombination (HR). Here, because the unrepaired DSBs lead to the death of the unicellular parasite Plasmodium falciparum, we investigated its recombinase, PfRad51, as a potential drug target. Undertaking an in silico screening approach, we identified a compound, B02, that docks to the predicted tertiary structure of PfRad51 with high affinity. B02 inhibited a drug-sensitive P. falciparum strain (3D7) and multidrug-resistant parasite (Dd2) in culture, with IC50 values of 8 and 3 μm, respectively. We found that B02 is more potent against these P. falciparum strains than against mammalian cell lines. Our findings also revealed that the antimalarial activity of B02 synergizes with those of two first-line malaria drugs, artemisinin (ART) and chloroquine (CQ), lowering the IC50 values of ART and CQ by 15- and 8-fold, respectively. Our results also provide mechanistic insights into the anti-parasitic activity of B02, indicating that it blocks the ATPase and strand-exchange activities of PfRad51 and abrogates the formation of PfRad51 foci on damaged DNA at chromosomal sites, probably by blocking homomeric interactions of PfRad51 proteins. The B02-mediated PfRad51 disruption led to the accumulation of unrepaired parasitic DNA and rendered parasites more sensitive to DNA-damaging agents, including ART. Our findings provide a rationale for targeting the Plasmodium DSB repair pathway in combination with ART. We propose that identification of a specific inhibitor of HR in Plasmodium may enable investigations of HR's role in Plasmodium biology, including generation of antigenic diversity.
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Affiliation(s)
- Pratap Vydyam
- Department of Biochemistry, University of Hyderabad, Gachibowli, Hyderabad 500046, TS, India
| | - Dibyendu Dutta
- Department of Biochemistry, University of Hyderabad, Gachibowli, Hyderabad 500046, TS, India
| | - Niranjan Sutram
- Department of Biochemistry, University of Hyderabad, Gachibowli, Hyderabad 500046, TS, India
| | - Sunanda Bhattacharyya
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, TS, India
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10
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Shalaeva DN, Cherepanov DA, Galperin MY, Golovin AV, Mulkidjanian AY. Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases in relation to the basic catalytic mechanism. eLife 2018; 7:e37373. [PMID: 30526846 PMCID: PMC6310460 DOI: 10.7554/elife.37373] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 11/26/2018] [Indexed: 01/01/2023] Open
Abstract
The ubiquitous P-loop fold nucleoside triphosphatases (NTPases) are typically activated by an arginine or lysine 'finger'. Some of the apparently ancestral NTPases are, instead, activated by potassium ions. To clarify the activation mechanism, we combined comparative structure analysis with molecular dynamics (MD) simulations of Mg-ATP and Mg-GTP complexes in water and in the presence of potassium, sodium, or ammonium ions. In all analyzed structures of diverse P-loop NTPases, the conserved P-loop motif keeps the triphosphate chain of bound NTPs (or their analogs) in an extended, catalytically prone conformation, similar to that imposed on NTPs in water by potassium or ammonium ions. MD simulations of potassium-dependent GTPase MnmE showed that linking of alpha- and gamma phosphates by the activating potassium ion led to the rotation of the gamma-phosphate group yielding an almost eclipsed, catalytically productive conformation of the triphosphate chain, which could represent the basic mechanism of hydrolysis by P-loop NTPases.
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Affiliation(s)
- Daria N Shalaeva
- School of PhysicsUniversity of OsnabrückOsnabrückGermany
- A.N. Belozersky Institute of Physico-Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
- School of Bioengineering and BioinformaticsLomonosov Moscow State UniversityMoscowRussia
| | - Dmitry A Cherepanov
- A.N. Belozersky Institute of Physico-Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
- Semenov Institute of Chemical PhysicsRussian Academy of SciencesMoscowRussia
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - Andrey V Golovin
- School of Bioengineering and BioinformaticsLomonosov Moscow State UniversityMoscowRussia
| | - Armen Y Mulkidjanian
- School of PhysicsUniversity of OsnabrückOsnabrückGermany
- A.N. Belozersky Institute of Physico-Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
- School of Bioengineering and BioinformaticsLomonosov Moscow State UniversityMoscowRussia
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11
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Metal-cation regulation of enzyme dynamics is a key factor influencing the activity of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa. Sci Rep 2018; 8:11334. [PMID: 30054521 PMCID: PMC6063907 DOI: 10.1038/s41598-018-29535-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 07/12/2018] [Indexed: 01/30/2023] Open
Abstract
S-adenosyl-l-homocysteine hydrolase from Pseudomonas aeruginosa (PaSAHase) coordinates one K+ ion and one Zn2+ ion in the substrate binding area. The cations affect the enzymatic activity and substrate binding but the molecular mechanisms of their action are unknown. Enzymatic and isothermal titration calorimetry studies demonstrated that the K+ ions stimulate the highest activity and strongest ligand binding in comparison to other alkali cations, while the Zn2+ ions inhibit the enzyme activity. PaSAHase was crystallized in the presence of adenine nucleosides and K+ or Rb+ ions. The crystal structures show that the alkali ion is coordinated in close proximity of the purine ring and a 23Na NMR study showed that the monovalent cation coordination site is formed upon ligand binding. The cation, bound in the area of a molecular hinge, orders and accurately positions the amide group of Q65 residue to allow its interaction with the ligand. Moreover, binding of potassium is required to enable unique dynamic properties of the enzyme that ensure its maximum catalytic activity. The Zn2+ ion is bound in the area of a molecular gate that regulates access to the active site. Zn2+ coordination switches the gate to a shut state and arrests the enzyme in its closed, inactive conformation.
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12
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Rossmann M, J Greive S, Moschetti T, Dinan M, Hyvönen M. Development of a multipurpose scaffold for the display of peptide loops. Protein Eng Des Sel 2017; 30:419-430. [PMID: 28444399 PMCID: PMC5897841 DOI: 10.1093/protein/gzx017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 02/26/2017] [Accepted: 03/28/2017] [Indexed: 12/20/2022] Open
Abstract
Protein-protein interactions (PPIs) determine a wide range of biological processes and analysis of these dynamic networks is increasingly becoming a mandatory tool for studying protein function. Using the globular ATPase domain of recombinase RadA as a scaffold, we have developed a peptide display system (RAD display), which allows for the presentation of target peptides, protein domains or full-length proteins and their rapid recombinant production in bacteria. The design of the RAD display system includes differently tagged versions of the scaffold, which allows for flexibility in the protein purification method, and chemical coupling for small molecule labeling or surface immobilization. When combined with the significant thermal stability of the RadA protein, these features create a versatile multipurpose scaffold system. Using various orthogonal biophysical techniques, we show that peptides displayed on the scaffold bind to their natural targets in a fashion similar to linear parent peptides. We use the examples of CK2β/CK2α kinase and TPX2/Aurora A kinase protein complexes to demonstrate that the peptide displayed by the RAD scaffold can be used in PPI studies with the same binding efficacy but at lower costs compared with their linear synthetic counterparts.
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Affiliation(s)
- Maxim Rossmann
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Sandra J Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Tommaso Moschetti
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Michael Dinan
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK. Correspondence:
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13
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Korolev S. Advances in structural studies of recombination mediator proteins. Biophys Chem 2016; 225:27-37. [PMID: 27974172 DOI: 10.1016/j.bpc.2016.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/01/2016] [Accepted: 12/01/2016] [Indexed: 12/25/2022]
Abstract
Recombination mediator proteins (RMPs) are critical for genome integrity in all organisms. They include phage UvsY, prokaryotic RecF, -O, -R (RecFOR) and eukaryotic Rad52, Breast Cancer susceptibility 2 (BRCA2) and Partner and localizer of BRCA2 (PALB2) proteins. BRCA2 and PALB2 are tumor suppressors implicated in cancer. RMPs regulate binding of RecA-like recombinases to sites of DNA damage to initiate the most efficient non-mutagenic repair of broken chromosome and other deleterious DNA lesions. Mechanistically, RMPs stimulate a single-stranded DNA (ssDNA) hand-off from ssDNA binding proteins (ssbs) such as gp32, SSB and RPA, to recombinases, activating DNA repair only at the time and site of the damage event. This review summarizes structural studies of RMPs and their implications for understanding mechanism and function. Comparative analysis of RMPs is complicated due to their convergent evolution. In contrast to the evolutionary conserved ssbs and recombinases, RMPs are extremely diverse in sequence and structure. Structural studies are particularly important in such cases to reveal common features of the entire family and specific features of regulatory mechanisms for each member. All RMPs are characterized by specific DNA-binding domains and include variable protein interaction motifs. The complexity of such RMPs corresponds to the ever-growing number of DNA metabolism events they participate in under normal and pathological conditions and requires additional comprehensive structure-functional studies.
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Affiliation(s)
- S Korolev
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, 1100 S Grand Blvd., St. Louis, MO 63104, USA.
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14
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Moschetti T, Sharpe T, Fischer G, Marsh ME, Ng HK, Morgan M, Scott DE, Blundell TL, R. Venkitaraman A, Skidmore J, Abell C, Hyvönen M. Engineering Archeal Surrogate Systems for the Development of Protein-Protein Interaction Inhibitors against Human RAD51. J Mol Biol 2016; 428:4589-4607. [PMID: 27725183 PMCID: PMC5117717 DOI: 10.1016/j.jmb.2016.10.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 10/02/2016] [Accepted: 10/04/2016] [Indexed: 02/02/2023]
Abstract
Protein-protein interactions (PPIs) are increasingly important targets for drug discovery. Efficient fragment-based drug discovery approaches to tackle PPIs are often stymied by difficulties in the production of stable, unliganded target proteins. Here, we report an approach that exploits protein engineering to "humanise" thermophilic archeal surrogate proteins as targets for small-molecule inhibitor discovery and to exemplify this approach in the development of inhibitors against the PPI between the recombinase RAD51 and tumour suppressor BRCA2. As human RAD51 has proved impossible to produce in a form that is compatible with the requirements of fragment-based drug discovery, we have developed a surrogate protein system using RadA from Pyrococcus furiosus. Using a monomerised RadA as our starting point, we have adopted two parallel and mutually instructive approaches to mimic the human enzyme: firstly by mutating RadA to increase sequence identity with RAD51 in the BRC repeat binding sites, and secondly by generating a chimeric archaeal human protein. Both approaches generate proteins that interact with a fourth BRC repeat with affinity and stoichiometry comparable to human RAD51. Stepwise humanisation has also allowed us to elucidate the determinants of RAD51 binding to BRC repeats and the contributions of key interacting residues to this interaction. These surrogate proteins have enabled the development of biochemical and biophysical assays in our ongoing fragment-based small-molecule inhibitor programme and they have allowed us to determine hundreds of liganded structures in support of our structure-guided design process, demonstrating the feasibility and advantages of using archeal surrogates to overcome difficulties in handling human proteins.
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Affiliation(s)
- Tommaso Moschetti
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Timothy Sharpe
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Gerhard Fischer
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - May E. Marsh
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Hong Kin Ng
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Matthew Morgan
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Duncan E. Scott
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Ashok R. Venkitaraman
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK
| | - John Skidmore
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK,Corresponding author.
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15
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Gohara DW, Di Cera E. Molecular Mechanisms of Enzyme Activation by Monovalent Cations. J Biol Chem 2016; 291:20840-20848. [PMID: 27462078 DOI: 10.1074/jbc.r116.737833] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Regulation of enzymes through metal ion complexation is widespread in biology and underscores a physiological need for stability and high catalytic activity that likely predated proteins in the RNA world. In addition to divalent metals such as Ca2+, Mg2+, and Zn2+, monovalent cations often function as efficient and selective promoters of catalysis. Advances in structural biology unravel a rich repertoire of molecular mechanisms for enzyme activation by Na+ and K+ Strategies range from short-range effects mediated by direct participation in substrate binding, to more distributed effects that propagate long-range to catalytic residues. This review addresses general considerations and examples.
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Affiliation(s)
- David W Gohara
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
| | - Enrico Di Cera
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
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16
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Leite WC, Galvão CW, Saab SC, Iulek J, Etto RM, Steffens MBR, Chitteni-Pattu S, Stanage T, Keck JL, Cox MM. Structural and Functional Studies of H. seropedicae RecA Protein - Insights into the Polymerization of RecA Protein as Nucleoprotein Filament. PLoS One 2016; 11:e0159871. [PMID: 27447485 PMCID: PMC4957752 DOI: 10.1371/journal.pone.0159871] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/08/2016] [Indexed: 11/18/2022] Open
Abstract
The bacterial RecA protein plays a role in the complex system of DNA damage repair. Here, we report the functional and structural characterization of the Herbaspirillum seropedicae RecA protein (HsRecA). HsRecA protein is more efficient at displacing SSB protein from ssDNA than Escherichia coli RecA protein. HsRecA also promotes DNA strand exchange more efficiently. The three dimensional structure of HsRecA-ADP/ATP complex has been solved to 1.7 Å resolution. HsRecA protein contains a small N-terminal domain, a central core ATPase domain and a large C-terminal domain, that are similar to homologous bacterial RecA proteins. Comparative structural analysis showed that the N-terminal polymerization motif of archaeal and eukaryotic RecA family proteins are also present in bacterial RecAs. Reconstruction of electrostatic potential from the hexameric structure of HsRecA-ADP/ATP revealed a high positive charge along the inner side, where ssDNA is bound inside the filament. The properties of this surface may explain the greater capacity of HsRecA protein to bind ssDNA, forming a contiguous nucleoprotein filament, displace SSB and promote DNA exchange relative to EcRecA. Our functional and structural analyses provide insight into the molecular mechanisms of polymerization of bacterial RecA as a helical nucleoprotein filament.
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Affiliation(s)
- Wellington C. Leite
- Department of Physics, Ponta Grossa State University (UEPG), Av. Carlos Cavalcanti, 4748, CEP. 84.030–900, Ponta Grossa, PR, Brazil
- * E-mail: (MC); (WL)
| | - Carolina W. Galvão
- Department of Structural and Molecular Biology and Genetics, Ponta Grossa State University (UEPG), CEP 84030–900, Ponta Grossa, PR, Brazil
| | - Sérgio C. Saab
- Department of Physics, Ponta Grossa State University (UEPG), Av. Carlos Cavalcanti, 4748, CEP. 84.030–900, Ponta Grossa, PR, Brazil
| | - Jorge Iulek
- Department of Chemistry, Ponta Grossa State University (UEPG), CEP 84030–900, Ponta Grossa, PR, Brazil
| | - Rafael M. Etto
- Department of Chemistry, Ponta Grossa State University (UEPG), CEP 84030–900, Ponta Grossa, PR, Brazil
| | - Maria B. R. Steffens
- Department of Biochemistry and Molecular Biology, Federal University of Parana, CEP 81531–980 Curitiba, Brazil
| | - Sindhu Chitteni-Pattu
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI, 53706–1544, United States of America
| | - Tyler Stanage
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI, 53706–1544, United States of America
| | - James L. Keck
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706, United States of America
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI, 53706–1544, United States of America
- * E-mail: (MC); (WL)
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17
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Marsh ME, Scott DE, Ehebauer MT, Abell C, Blundell TL, Hyvönen M. ATP half-sites in RadA and RAD51 recombinases bind nucleotides. FEBS Open Bio 2016; 6:372-85. [PMID: 27419043 PMCID: PMC4856416 DOI: 10.1002/2211-5463.12052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 03/03/2016] [Indexed: 12/20/2022] Open
Abstract
Homologous recombination is essential for repair of DNA double-strand breaks. Central to this process is a family of recombinases, including archeal RadA and human RAD51, which form nucleoprotein filaments on damaged single-stranded DNA ends and facilitate their ATP-dependent repair. ATP binding and hydrolysis are dependent on the formation of a nucleoprotein filament comprising RadA/RAD51 and single-stranded DNA, with ATP bound between adjacent protomers. We demonstrate that truncated, monomeric Pyrococcus furiosus RadA and monomerised human RAD51 retain the ability to bind ATP and other nucleotides with high affinity. We present crystal structures of both apo and nucleotide-bound forms of monomeric RadA. These structures reveal that while phosphate groups are tightly bound, RadA presents a shallow, poorly defined binding surface for the nitrogenous bases of nucleotides. We suggest that RadA monomers would be constitutively bound to nucleotides in the cell and that the bound nucleotide might play a structural role in filament assembly.
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Affiliation(s)
- May E Marsh
- Department of Biochemistry University of Cambridge UK; Present address: Paul Scherrer Institut Villingen Switzerland
| | | | - Matthias T Ehebauer
- Department of Biochemistry University of Cambridge UK; Present address: Target Discovery Institute Nuffield Department of Medicine University of Oxford UK
| | - Chris Abell
- Department of Chemistry University of Cambridge UK
| | | | - Marko Hyvönen
- Department of Biochemistry University of Cambridge UK
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18
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Dibrova DV, Galperin MY, Koonin EV, Mulkidjanian AY. Ancient Systems of Sodium/Potassium Homeostasis as Predecessors of Membrane Bioenergetics. BIOCHEMISTRY (MOSCOW) 2016; 80:495-516. [PMID: 26071768 DOI: 10.1134/s0006297915050016] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Cell cytoplasm of archaea, bacteria, and eukaryotes contains substantially more potassium than sodium, and potassium cations are specifically required for many key cellular processes, including protein synthesis. This distinct ionic composition and requirements have been attributed to the emergence of the first cells in potassium-rich habitats. Different, albeit complementary, scenarios have been proposed for the primordial potassium-rich environments based on experimental data and theoretical considerations. Specifically, building on the observation that potassium prevails over sodium in the vapor of inland geothermal systems, we have argued that the first cells could emerge in the pools and puddles at the periphery of primordial anoxic geothermal fields, where the elementary composition of the condensed vapor would resemble the internal milieu of modern cells. Marine and freshwater environments generally contain more sodium than potassium. Therefore, to invade such environments, while maintaining excess of potassium over sodium in the cytoplasm, primordial cells needed means to extrude sodium ions. The foray into new, sodium-rich habitats was the likely driving force behind the evolution of diverse redox-, light-, chemically-, or osmotically-dependent sodium export pumps and the increase of membrane tightness. Here we present a scenario that details how the interplay between several, initially independent sodium pumps might have triggered the evolution of sodium-dependent membrane bioenergetics, followed by the separate emergence of the proton-dependent bioenergetics in archaea and bacteria. We also discuss the development of systems that utilize the sodium/potassium gradient across the cell membranes.
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Affiliation(s)
- D V Dibrova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
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19
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Vašák M, Schnabl J. Sodium and Potassium Ions in Proteins and Enzyme Catalysis. Met Ions Life Sci 2016; 16:259-90. [DOI: 10.1007/978-3-319-21756-7_8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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20
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Topilina NI, Novikova O, Stanger M, Banavali NK, Belfort M. Post-translational environmental switch of RadA activity by extein-intein interactions in protein splicing. Nucleic Acids Res 2015; 43:6631-48. [PMID: 26101259 PMCID: PMC4513877 DOI: 10.1093/nar/gkv612] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 05/29/2015] [Indexed: 11/14/2022] Open
Abstract
Post-translational control based on an environmentally sensitive intervening intein sequence is described. Inteins are invasive genetic elements that self-splice at the protein level from the flanking host protein, the exteins. Here we show in Escherichia coli and in vitro that splicing of the RadA intein located in the ATPase domain of the hyperthermophilic archaeon Pyrococcus horikoshii is strongly regulated by the native exteins, which lock the intein in an inactive state. High temperature or solution conditions can unlock the intein for full activity, as can remote extein point mutations. Notably, this splicing trap occurs through interactions between distant residues in the native exteins and the intein, in three-dimensional space. The exteins might thereby serve as an environmental sensor, releasing the intein for full activity only at optimal growth conditions for the native organism, while sparing ATP consumption under conditions of cold-shock. This partnership between the intein and its exteins, which implies coevolution of the parasitic intein and its host protein may provide a novel means of post-translational control.
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Affiliation(s)
- Natalya I Topilina
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Olga Novikova
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Matthew Stanger
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Nilesh K Banavali
- Laboratory of Computational and Structural Biology, Division of Genetics, Wadsworth Center, NYS Department of Health and Department of Biomedical Sciences, University at Albany, CMS 2008, Biggs Lab, Empire State Plaza, PO Box 509, Albany, NY 12201-2002, USA
| | - Marlene Belfort
- Department of Biological Sciences and RNA Institute, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA
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21
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Han W, Shen Y, She Q. Nanobiomotors of archaeal DNA repair machineries: current research status and application potential. Cell Biosci 2014; 4:32. [PMID: 24995126 PMCID: PMC4080772 DOI: 10.1186/2045-3701-4-32] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Accepted: 06/13/2014] [Indexed: 11/10/2022] Open
Abstract
Nanobiomotors perform various important functions in the cell, and they also emerge as potential vehicle for drug delivery. These proteins employ conserved ATPase domains to convert chemical energy to mechanical work and motion. Several archaeal nucleic acid nanobiomotors, such as DNA helicases that unwind double-stranded DNA molecules during DNA damage repair, have been characterized in details. XPB, XPD and Hjm are SF2 family helicases, each of which employs two ATPase domains for ATP binding and hydrolysis to drive DNA unwinding. They also carry additional specific domains for substrate binding and regulation. Another helicase, HerA, forms a hexameric ring that may act as a DNA-pumping enzyme at the end processing of double-stranded DNA breaks. Common for all these nanobiomotors is that they contain ATPase domain that adopts RecA fold structure. This structure is characteristic for RecA/RadA family proteins and has been studied in great details. Here we review the structural analyses of these archaeal nucleic acid biomotors and the molecular mechanisms of how ATP binding and hydrolysis promote the conformation change that drives mechanical motion. The application potential of archaeal nanobiomotors in drug delivery has been discussed.
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Affiliation(s)
- Wenyuan Han
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, People's Republic of China ; Archaeal Centre, Department of Biology, University of Copenhagen, Copenhagen Biocenter, Copenhagen, Denmark
| | - Yulong Shen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, People's Republic of China
| | - Qunxin She
- Archaeal Centre, Department of Biology, University of Copenhagen, Copenhagen Biocenter, Copenhagen, Denmark
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22
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Rao DECS, Luo Y. pH-dependent activities and structural stability of loop-2-anchoring helix of RadA recombinase from Methanococcus voltae. Protein Pept Lett 2014; 21:679-87. [PMID: 24654848 PMCID: PMC4150490 DOI: 10.2174/0929866521666140320103512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 02/25/2014] [Accepted: 02/27/2014] [Indexed: 11/22/2022]
Abstract
RadA is an archaeal orthologue of human recombinase Rad51. This superfamily of recombinases, which also includes eukaryal meiosis-specific DMC1 and remotely related bacterial RecA, form filaments on single-stranded DNA in the presence of ATP and promote a strand exchange reaction between the single-stranded DNA and a homologous double-stranded DNA. Due to its feasibility of getting crystals and similarity (> 40% sequence identity) to eukaryal homologues, we have studied RadA from Methanococcus voltae (MvRadA) as a structural model for understanding the molecular mechanism of homologous strand exchange. Here we show this protein’s ATPase and strand exchange activities are minimal at pH 6.0. Interestingly, MvRadA’s pH dependence is similar to the properties of human Rad51 but dissimilar to that of the well-studied E. coli RecA. A structure subsequently determined at pH 6.0 reveals features indicative of an ATPase-inactive form with a disordered L2 loop. Comparison with a previously determined ATPase-active form at pH 7.5 implies that the stability of the ATPase-active conformation is reduced at the acidic pH. We interpret these results as further suggesting an ordered disposition of the DNA-binding L2 region, similar to what has been observed in the previously observed ATPase-active conformation, is required for promoting hydrolysis of ATP and strand exchange between single- and double-stranded DNA. His-276 in the mobile L2 region was observed to be partially responsible for the pH-dependent activities of MvRadA.
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Affiliation(s)
| | - Yu Luo
- Department of Biochemistry, University of Saskatchewan, 2D01 Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan, Canada S7N 5E5.
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23
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Girard PM, Graindorge D, Smirnova V, Rigolet P, Francesconi S, Scanlon S, Sage E. Oxidative stress in mammalian cells impinges on the cysteines redox state of human XRCC3 protein and on its cellular localization. PLoS One 2013; 8:e75751. [PMID: 24116071 PMCID: PMC3793007 DOI: 10.1371/journal.pone.0075751] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 08/19/2013] [Indexed: 11/23/2022] Open
Abstract
In vertebrates, XRCC3 is one of the five Rad51 paralogs that plays a central role in homologous recombination (HR), a key pathway for maintaining genomic stability. While investigating the potential role of human XRCC3 (hXRCC3) in the inhibition of DNA replication induced by UVA radiation, we discovered that hXRCC3 cysteine residues are oxidized following photosensitization by UVA. Our in silico prediction of the hXRCC3 structure suggests that 6 out of 8 cysteines are potentially accessible to the solvent and therefore potentially exposed to ROS attack. By non-reducing SDS-PAGE we show that many different oxidants induce hXRCC3 oxidation that is monitored in Chinese hamster ovarian (CHO) cells by increased electrophoretic mobility of the protein and in human cells by a slight decrease of its immunodetection. In both cell types, hXRCC3 oxidation was reversed in few minutes by cellular reducing systems. Depletion of intracellular glutathione prevents hXRCC3 oxidation only after UVA exposure though depending on the type of photosensitizer. In addition, we show that hXRCC3 expressed in CHO cells localizes both in the cytoplasm and in the nucleus. Mutating all hXRCC3 cysteines to serines (XR3/S protein) does not affect the subcellular localization of the protein even after exposure to camptothecin (CPT), which typically induces DNA damages that require HR to be repaired. However, cells expressing mutated XR3/S protein are sensitive to CPT, thus highlighting a defect of the mutant protein in HR. In marked contrast to CPT treatment, oxidative stress induces relocalization at the chromatin fraction of both wild-type and mutated protein, even though survival is not affected. Collectively, our results demonstrate that the DNA repair protein hXRCC3 is a target of ROS induced by environmental factors and raise the possibility that the redox environment might participate in regulating the HR pathway.
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Affiliation(s)
- Pierre-Marie Girard
- Institut Curie, Centre de Recherche, Orsay, France ; CNRS, UMR3348, Orsay, France
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24
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Molecular modeling and molecular dynamics simulations of recombinase Rad51. Biophys J 2013; 104:1556-65. [PMID: 23561532 DOI: 10.1016/j.bpj.2013.02.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 01/29/2013] [Accepted: 02/07/2013] [Indexed: 11/24/2022] Open
Abstract
The Rad51 ATPase plays central roles in DNA homologous recombination. Yeast Rad51 dimer structure in the active form of the filament was constructed using homology modeling techniques, and all-atom molecular dynamics (MD) simulations were performed using the modeled structure. We found two crucial interaction networks involving ATP: one is among the γ-phosphate of ATP, K(+) ions, H352, and D374; the other is among the adenine ring of ATP, R228, and P379. Multiple MD simulations were performed in which the number of bound K(+) ions was changed. The simulated structures suggested that K(+) ions are indispensable for the stabilization of the active dimer and resemble the arginine and lysine fingers of other P-loop containing ATPases and GTPases. MD simulations also showed that the adenine ring of ATP mediates interactions between adjacent protomers. Furthermore, in MD simulations starting from a structure just after ATP hydrolysis, the opening motion corresponding to dissociation from DNA was observed. These results support the hypothesis that ATP and K(+) ions function as glue between protomers.
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25
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The HsRAD51B-HsRAD51C stabilizes the HsRAD51 nucleoprotein filament. DNA Repair (Amst) 2013; 12:723-32. [PMID: 23810717 DOI: 10.1016/j.dnarep.2013.05.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 04/28/2013] [Accepted: 05/14/2013] [Indexed: 12/17/2022]
Abstract
There are six human RAD51 related proteins (HsRAD51 paralogs), HsRAD51B, HsRAD51C, HsRAD51D, HsXRCC2, HsXRCC3 and HsDMC1, that appear to enhance HsRAD51 mediated homologous recombinational (HR) repair of DNA double strand breaks (DSBs). Here we model the structures of HsRAD51, HsRAD51B and HsRAD51C and show similar domain orientations within a hypothetical nucleoprotein filament (NPF). We then demonstrate that HsRAD51B-HsRAD51C heterodimer forms stable complex on ssDNA and partially stabilizes the HsRAD51 NPF against the anti-recombinogenic activity of BLM. Moreover, HsRAD51B-HsRAD51C stimulates HsRAD51 mediated D-loop formation in the presence of RPA. However, HsRAD51B-HsRAD51C does not facilitate HsRAD51 nucleation on a RPA coated ssDNA. These results suggest that the HsRAD51B-HsRAD51C complex plays a role in stabilizing the HsRAD51 NPF during the presynaptic phase of HR, which appears downstream of BRCA2-mediated HsRAD51 NPF formation.
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26
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Lee M, Lipfert J, Sanchez H, Wyman C, Dekker NH. Structural and torsional properties of the RAD51-dsDNA nucleoprotein filament. Nucleic Acids Res 2013; 41:7023-30. [PMID: 23703213 PMCID: PMC3737536 DOI: 10.1093/nar/gkt425] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Human RAD51 is a key protein in the repair of DNA by homologous recombination. Its assembly onto DNA, which induces changes in DNA structure, results in the formation of a nucleoprotein filament that forms the basis of strand exchange. Here, we determine the structural and mechanical properties of RAD51-dsDNA filaments. Our measurements use two recently developed magnetic tweezers assays, freely orbiting magnetic tweezers and magnetic torque tweezers, designed to measure the twist and torque of individual molecules. By directly monitoring changes in DNA twist on RAD51 binding, we determine the unwinding angle per RAD51 monomer to be 45°, in quantitative agreement with that of its bacterial homolog, RecA. Measurements of the torque that is built up when RAD51-dsDNA filaments are twisted show that under conditions that suppress ATP hydrolysis the torsional persistence length of the RAD51-dsDNA filament exceeds that of its RecA counterpart by a factor of three. Examination of the filament’s torsional stiffness for different combinations of divalent ions and nucleotide cofactors reveals that the Ca2+ ion, apart from suppressing ATPase activity, plays a key role in increasing the torsional stiffness of the filament. These quantitative measurements of RAD51-imposed DNA distortions and accumulated mechanical stress suggest a finely tuned interplay between chemical and mechanical interactions within the RAD51 nucleoprotein filament.
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Affiliation(s)
- Mina Lee
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
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27
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Su ZY, Lee WJ, Su WS, Wang YT. Target molecular simulations of RecA family protein filaments. Int J Mol Sci 2012; 13:7138-7148. [PMID: 22837683 PMCID: PMC3397515 DOI: 10.3390/ijms13067138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 05/10/2012] [Accepted: 05/29/2012] [Indexed: 11/16/2022] Open
Abstract
Modeling of the RadA family mechanism is crucial to understanding the DNA SOS repair process. In a 2007 report, the archaeal RadA proteins function as rotary motors (linker region: I71-K88) such as shown in Figure 1. Molecular simulations approaches help to shed further light onto this phenomenon. We find 11 rotary residues (R72, T75-K81, M84, V86 and K87) and five zero rotary residues (I71, K74, E82, R83 and K88) in the simulations. Inclusion of our simulations may help to understand the RadA family mechanism.
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Affiliation(s)
- Zhi-Yuan Su
- Department of Information Management, Chia Nan University of Pharmacy & Science, No. 60, Sec. 1, Erren Rd., Rende Dist., Tainan City 71710, Taiwan; E-Mail:
| | - Wen-Jay Lee
- National Center for High-Performance Computing, Hsin-Shi, No. 28, Nan-Ke 3rd Rd., Hsin-Shi Dist., Tainan City 74147, Taiwan; E-Mails: (W.-J.L.); (W.-S.S.)
| | - Wan-Sheng Su
- National Center for High-Performance Computing, Hsin-Shi, No. 28, Nan-Ke 3rd Rd., Hsin-Shi Dist., Tainan City 74147, Taiwan; E-Mails: (W.-J.L.); (W.-S.S.)
- Department of Physics, National Chung Hsing University, No. 250, Kuo Kuang Rd., Taichung 402, Taiwan
| | - Yeng-Tseng Wang
- National Center for High-Performance Computing, Hsin-Shi, No. 28, Nan-Ke 3rd Rd., Hsin-Shi Dist., Tainan City 74147, Taiwan; E-Mails: (W.-J.L.); (W.-S.S.)
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28
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Budke B, Logan HL, Kalin JH, Zelivianskaia AS, Cameron McGuire W, Miller LL, Stark JM, Kozikowski AP, Bishop DK, Connell PP. RI-1: a chemical inhibitor of RAD51 that disrupts homologous recombination in human cells. Nucleic Acids Res 2012; 40:7347-57. [PMID: 22573178 PMCID: PMC3424541 DOI: 10.1093/nar/gks353] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Homologous recombination serves multiple roles in DNA repair that are essential for maintaining genomic stability. We here describe RI-1, a small molecule that inhibits the central recombination protein RAD51. RI-1 specifically reduces gene conversion in human cells while stimulating single strand annealing. RI-1 binds covalently to the surface of RAD51 protein at cysteine 319 that likely destabilizes an interface used by RAD51 monomers to oligomerize into filaments on DNA. Correspondingly, the molecule inhibits the formation of subnuclear RAD51 foci in cells following DNA damage, while leaving replication protein A focus formation unaffected. Finally, it potentiates the lethal effects of a DNA cross-linking drug in human cells. Given that this inhibitory activity is seen in multiple human tumor cell lines, RI-1 holds promise as an oncologic drug. Furthermore, RI-1 represents a unique tool to dissect the network of reaction pathways that contribute to DNA repair in cells.
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Affiliation(s)
- Brian Budke
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL 60637, USA
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29
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Du L, Luo Y. Structure of a hexameric form of RadA recombinase from Methanococcus voltae. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:511-6. [PMID: 22691778 PMCID: PMC3374503 DOI: 10.1107/s1744309112010226] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 03/07/2012] [Indexed: 11/27/2022]
Abstract
Archaeal RadA proteins are close homologues of eukaryal Rad51 and DMC1 proteins and are remote homologues of bacterial RecA proteins. For the repair of double-stranded breaks in DNA, these recombinases promote a pivotal strand-exchange reaction between homologous single-stranded and double-stranded DNA substrates. This DNA-repair function also plays a key role in the resistance of cancer cells to chemotherapy and radiotherapy and in the resistance of bacterial cells to antibiotics. A hexameric form of a truncated Methanococcus voltae RadA protein devoid of its small N-terminal domain has been crystallized. The RadA hexamers further assemble into two-ringed assemblies. Similar assemblies can be observed in the crystals of Pyrococcus furiosus RadA and Homo sapiens DMC1. In all of these two-ringed assemblies the DNA-interacting L1 region of each protomer points inward towards the centre, creating a highly positively charged locus. The electrostatic characteristics of the central channels can be utilized in the design of novel recombinase inhibitors.
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Affiliation(s)
- Liqin Du
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Suite A3, Saskatoon, Sasktchewan S7N 5E5, Canada
| | - Yu Luo
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Suite A3, Saskatoon, Sasktchewan S7N 5E5, Canada
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30
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Amunugama R, He Y, Willcox S, Forties RA, Shim KS, Bundschuh R, Luo Y, Griffith J, Fishel R. RAD51 protein ATP cap regulates nucleoprotein filament stability. J Biol Chem 2012; 287:8724-36. [PMID: 22275364 DOI: 10.1074/jbc.m111.239426] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
RAD51 mediates homologous recombination by forming an active DNA nucleoprotein filament (NPF). A conserved aspartate that forms a salt bridge with the ATP γ-phosphate is found at the nucleotide-binding interface between RAD51 subunits of the NPF known as the ATP cap. The salt bridge accounts for the nonphysiological cation(s) required to fully activate the RAD51 NPF. In contrast, RecA homologs and most RAD51 paralogs contain a conserved lysine at the analogous structural position. We demonstrate that substitution of human RAD51(Asp-316) with lysine (HsRAD51(D316K)) decreases NPF turnover and facilitates considerably improved recombinase functions. Structural analysis shows that archaebacterial Methanococcus voltae RadA(D302K) (MvRAD51(D302K)) and HsRAD51(D316K) form extended active NPFs without salt. These studies suggest that the HsRAD51(Asp-316) salt bridge may function as a conformational sensor that enhances turnover at the expense of recombinase activity.
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Affiliation(s)
- Ravindra Amunugama
- Biophysics Graduate Program, Department of Molecular Virology, Immunology, and Medical Genetics, Ohio State University, Columbus, Ohio 43210, USA
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31
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Amunugama R, Fishel R. Homologous Recombination in Eukaryotes. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2012; 110:155-206. [DOI: 10.1016/b978-0-12-387665-2.00007-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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32
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Adikesavan AK, Katsonis P, Marciano DC, Lua R, Herman C, Lichtarge O. Separation of recombination and SOS response in Escherichia coli RecA suggests LexA interaction sites. PLoS Genet 2011; 7:e1002244. [PMID: 21912525 PMCID: PMC3164682 DOI: 10.1371/journal.pgen.1002244] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 06/29/2011] [Indexed: 12/29/2022] Open
Abstract
RecA plays a key role in homologous recombination, the induction of the DNA damage response through LexA cleavage and the activity of error-prone polymerase in Escherichia coli. RecA interacts with multiple partners to achieve this pleiotropic role, but the structural location and sequence determinants involved in these multiple interactions remain mostly unknown. Here, in a first application to prokaryotes, Evolutionary Trace (ET) analysis identifies clusters of evolutionarily important surface amino acids involved in RecA functions. Some of these clusters match the known ATP binding, DNA binding, and RecA-RecA homo-dimerization sites, but others are novel. Mutation analysis at these sites disrupted either recombination or LexA cleavage. This highlights distinct functional sites specific for recombination and DNA damage response induction. Finally, our analysis reveals a composite site for LexA binding and cleavage, which is formed only on the active RecA filament. These new sites can provide new drug targets to modulate one or more RecA functions, with the potential to address the problem of evolution of antibiotic resistance at its root. In eubacteria, genome integrity is in large part orchestrated by RecA, which directly participates in recombination, induction of DNA damage response through LexA repressor cleavage and error-prone DNA synthesis. Yet, most of the interaction sites necessary for these vital processes are largely unknown. By comparing divergences among RecA sequences and computing putative functional regions, we discovered four functional sites of RecA. Targeted point-mutations were then tested for both recombination and DNA damage induction and reveal distinct RecA functions at each one of these sites. In particular, one new set of mutants is deficient in promoting LexA cleavage and yet maintains the ability to induce the DNA damage response. These results reveal specific amino acid determinants of the RecA–LexA interaction and suggest that LexA binds RecAi and RecAi+6 at a composite site on the RecA filament, which could explain the role of the active filament during LexA cleavage.
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Affiliation(s)
- Anbu K Adikesavan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
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33
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Amunugama R, Fishel R. Subunit interface residues F129 and H294 of human RAD51 are essential for recombinase function. PLoS One 2011; 6:e23071. [PMID: 21857994 PMCID: PMC3155514 DOI: 10.1371/journal.pone.0023071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Accepted: 07/05/2011] [Indexed: 11/30/2022] Open
Abstract
RAD51 mediated homologous recombinational repair (HRR) of DNA double-strand breaks (DSBs) is essential to maintain genomic integrity. RAD51 forms a nucleoprotein filament (NPF) that catalyzes the fundamental homologous pairing and strand exchange reaction (recombinase) required for HRR. Based on structural and functional homology with archaeal and yeast RAD51, we have identified the human RAD51 (HsRAD51) subunit interface residues HsRad51(F129) in the Walker A box and HsRad51(H294) in the L2 ssDNA binding region as potentially important participants in salt-induced conformational transitions essential for recombinase activity. We demonstrate that the HsRad51(F129V) and HsRad51(H294V) substitution mutations reduce DNA dependent ATPase activity and are largely defective in the formation of a functional NPF, which ultimately eliminates recombinase catalytic functions. Our data are consistent with the conclusion that the HsRAD51(F129) and HsRAD51(H294) residues are important participants in the cation-induced allosteric activation of HsRAD51.
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Affiliation(s)
- Ravindra Amunugama
- Biophysics Graduate Program, The Ohio State University Medical Center and Comprehensive Cancer Center, Columbus, Ohio, United States of America
- Department of Molecular Virology, Immunology, and Medical Genetics, Human Cancer Genetics, The Ohio State University Medical Center and Comprehensive Cancer Center, Columbus, Ohio, United States of America
| | - Richard Fishel
- Department of Molecular Virology, Immunology, and Medical Genetics, Human Cancer Genetics, The Ohio State University Medical Center and Comprehensive Cancer Center, Columbus, Ohio, United States of America
- Physics Department, The Ohio State University Columbus, Columbus, Ohio, United States of America
- * E-mail:
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34
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Rolfsmeier ML, Haseltine CA. The Single-Stranded DNA Binding Protein of Sulfolobus solfataricus Acts in the Presynaptic Step of Homologous Recombination. J Mol Biol 2010; 397:31-45. [DOI: 10.1016/j.jmb.2010.01.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Revised: 12/13/2009] [Accepted: 01/05/2010] [Indexed: 12/31/2022]
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35
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Okorokov AL, Chaban YL, Bugreev DV, Hodgkinson J, Mazin AV, Orlova EV. Structure of the hDmc1-ssDNA filament reveals the principles of its architecture. PLoS One 2010; 5:e8586. [PMID: 20062530 PMCID: PMC2797393 DOI: 10.1371/journal.pone.0008586] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Accepted: 12/08/2009] [Indexed: 01/05/2023] Open
Abstract
In eukaryotes, meiotic recombination is a major source of genetic diversity, but its defects in humans lead to abnormalities such as Down's, Klinefelter's and other syndromes. Human Dmc1 (hDmc1), a RecA/Rad51 homologue, is a recombinase that plays a crucial role in faithful chromosome segregation during meiosis. The initial step of homologous recombination occurs when hDmc1 forms a filament on single-stranded (ss) DNA. However the structure of this presynaptic complex filament for hDmc1 remains unknown. To compare hDmc1-ssDNA complexes to those known for the RecA/Rad51 family we have obtained electron microscopy (EM) structures of hDmc1-ssDNA nucleoprotein filaments using single particle approach. The EM maps were analysed by docking crystal structures of Dmc1, Rad51, RadA, RecA and DNA. To fully characterise hDmc1-DNA complexes we have analysed their organisation in the presence of Ca2+, Mg2+, ATP, AMP-PNP, ssDNA and dsDNA. The 3D EM structures of the hDmc1-ssDNA filaments allowed us to elucidate the principles of their internal architecture. Similar to the RecA/Rad51 family, hDmc1 forms helical filaments on ssDNA in two states: extended (active) and compressed (inactive). However, in contrast to the RecA/Rad51 family, and the recently reported structure of hDmc1-double stranded (ds) DNA nucleoprotein filaments, the extended (active) state of the hDmc1 filament formed on ssDNA has nine protomers per helical turn, instead of the conventional six, resulting in one protomer covering two nucleotides instead of three. The control reconstruction of the hDmc1-dsDNA filament revealed 6.4 protein subunits per helical turn indicating that the filament organisation varies depending on the DNA templates. Our structural analysis has also revealed that the N-terminal domain of hDmc1 accomplishes its important role in complex formation through domain swapping between adjacent protomers, thus providing a mechanistic basis for coordinated action of hDmc1 protomers during meiotic recombination.
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Affiliation(s)
- Andrei L. Okorokov
- Wolfson Institute for Biomedical Research, University College London, Gower Street, London, United Kingdom
- * E-mail: (ALO); (EVO)
| | - Yuriy L. Chaban
- School of Crystallography, Birkbeck College, Malet Street, London, United Kingdom
| | - Dmitry V. Bugreev
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Novosibirsk, Russia
| | - Julie Hodgkinson
- School of Crystallography, Birkbeck College, Malet Street, London, United Kingdom
| | - Alexander V. Mazin
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Elena V. Orlova
- School of Crystallography, Birkbeck College, Malet Street, London, United Kingdom
- * E-mail: (ALO); (EVO)
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36
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Kagawa W, Kurumizaka H. From meiosis to postmeiotic events: uncovering the molecular roles of the meiosis-specific recombinase Dmc1. FEBS J 2009; 277:590-8. [PMID: 20015079 DOI: 10.1111/j.1742-4658.2009.07503.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In meiosis, the accurate segregation of maternal and paternal chromosomes is accomplished by homologous recombination. A central player in meiotic recombination is the Dmc1 recombinase, a member of the RecA/Rad51 recombinase superfamily, which is widely conserved from viruses to humans. Dmc1 is a meiosis-specific protein that functions with the ubiquitously expressed homolog, the Rad51 recombinase, which is essential for both mitotic and meiotic recombination. Since its discovery, it has been speculated that Dmc1 is important for unique aspects of meiotic recombination. Understanding the distinctive properties of Dmc1, namely, the features that distinguish it from Rad51, will further clarify the mechanisms of meiotic recombination. Recent structural, biochemical, and genetic findings are now revealing the molecular mechanisms of Dmc1-mediated homologous recombination and its regulation by various recombination mediators.
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Affiliation(s)
- Wataru Kagawa
- Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan.
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37
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Li Y, He Y, Luo Y. Crystal structure of an archaeal Rad51 homologue in complex with a metatungstate inhibitor. Biochemistry 2009; 48:6805-10. [PMID: 19555119 DOI: 10.1021/bi900832t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Archaeal RadAs are close homologues of eukaryal Rad51s ( approximately 40% sequence identities). These recombinases promote a hallmark strand exchange process between homologous single-stranded and double-stranded DNA substrates. This DNA-repairing function also plays a key role in cancer cells' resistance to chemo- and radiotherapy. Inhibition of the strand exchange process may render cancer cells more susceptible to therapeutic treatment. We found that metatungstate is a potent inhibitor of RadA from Methanococcus voltae. The tungsten cluster binds RadA in the axial DNA-binding groove. This polyanionic species appears to inhibit RadA by locking the protein in its inactive conformation.
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Affiliation(s)
- Yang Li
- Department of Biochemistry, University of Saskatchewan, A3 Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan, Canada S7N 5E5
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38
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Li Y, He Y, Luo Y. Conservation of a conformational switch in RadA recombinase from Methanococcus maripaludis. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:602-10. [PMID: 19465774 PMCID: PMC2685736 DOI: 10.1107/s0907444909011871] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Accepted: 03/30/2009] [Indexed: 12/26/2022]
Abstract
Archaeal RadAs are close homologues of eukaryal Rad51s ( approximately 40% sequence identity). These recombinases promote ATP hydrolysis and a hallmark strand-exchange reaction between homologous single-stranded and double-stranded DNA substrates. Pairing of the 3'-overhangs located at the damaged DNA with a homologous double-stranded DNA enables the re-synthesis of the damaged region using the homologous DNA as the template. In recent studies, conformational changes in the DNA-interacting regions of Methanococcus voltae RadA have been correlated with the presence of activity-stimulating potassium or calcium ions in the ATPase centre. The series of crystal structures of M. maripaludis RadA presented here further suggest the conservation of an allosteric switch in the ATPase centre which controls the conformational status of DNA-interacting loops. Structural comparison with the distant Escherichia coli RecA homologue supports the notion that the conserved Lys248 and Lys250 residues in RecA play a role similar to that of cations in RadA. The conservation of a cationic bridge between the DNA-interacting L2 region and the terminal phosphate of ATP, together with the apparent stability of the nucleoprotein filament, suggests a gap-displacement model which may explain the advantage of ATP hydrolysis for DNA-strand exchange.
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Affiliation(s)
- Yang Li
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
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39
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Shimizu H, Popova M, Fleury F, Kobayashi M, Hayashi N, Sakane I, Kurumizaka H, Venkitaraman AR, Takahashi M, Yamamoto KI. c-ABL tyrosine kinase stabilizes RAD51 chromatin association. Biochem Biophys Res Commun 2009; 382:286-91. [DOI: 10.1016/j.bbrc.2009.03.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Accepted: 03/04/2009] [Indexed: 10/21/2022]
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40
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Chang YW, Ko TP, Lee CD, Chang YC, Lin KA, Chang CS, Wang AHJ, Wang TF. Three new structures of left-handed RADA helical filaments: structural flexibility of N-terminal domain is critical for recombinase activity. PLoS One 2009; 4:e4890. [PMID: 19295907 PMCID: PMC2654063 DOI: 10.1371/journal.pone.0004890] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2009] [Accepted: 02/19/2009] [Indexed: 12/02/2022] Open
Abstract
RecA family proteins, including bacterial RecA, archaeal RadA, and eukaryotic Dmc1 and Rad51, mediate homologous recombination, a reaction essential for maintaining genome integrity. In the presence of ATP, these proteins bind a single-strand DNA to form a right-handed nucleoprotein filament, which catalyzes pairing and strand exchange with a homologous double-stranded DNA (dsDNA), by as-yet unknown mechanisms. We recently reported a structure of RadA left-handed helical filament, and here present three new structures of RadA left-handed helical filaments. Comparative structural analysis between different RadA/Rad51 helical filaments reveals that the N-terminal domain (NTD) of RadA/Rad51, implicated in dsDNA binding, is highly flexible. We identify a hinge region between NTD and polymerization motif as responsible for rigid body movement of NTD. Mutant analysis further confirms that structural flexibility of NTD is essential for RadA's recombinase activity. These results support our previous hypothesis that ATP-dependent axial rotation of RadA nucleoprotein helical filament promotes homologous recombination.
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Affiliation(s)
- Yu-Wei Chang
- Institute of Biochemical Science, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chien-Der Lee
- Institute of Biochemical Science, National Taiwan University, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | | | - Kuei-Ann Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | | | - Andrew H.-J. Wang
- Institute of Biochemical Science, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- * E-mail: (AHJW); (TFW)
| | - Ting-Fang Wang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- * E-mail: (AHJW); (TFW)
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41
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Haseltine CA, Kowalczykowski SC. An archaeal Rad54 protein remodels DNA and stimulates DNA strand exchange by RadA. Nucleic Acids Res 2009; 37:2757-70. [PMID: 19282450 PMCID: PMC2677860 DOI: 10.1093/nar/gkp068] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Rad54 protein is a key member of the RAD52 epistasis group required for homologous recombination in eukaryotes. Rad54 is a duplex DNA translocase that remodels both DNA and protein–DNA complexes, and functions at multiple steps in the recombination process. Here we use biochemical criteria to demonstrate the existence of this important protein in a prokaryotic organism. The Sulfolobus solfataricus Rad54 (SsoRad54) protein is a double-strand DNA-dependent ATPase that can alter the topology of duplex DNA. Like its eukaryotic homolog, it interacts directly with the S. solfataricus Rad51 homologue, SsoRadA, to stimulate DNA strand exchange. Confirmation of this protein as an authentic Rad54 homolog establishes an essential phylogenetic bridge for identifying Rad54 homologs in the archaeal and bacterial domains.
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Affiliation(s)
- Cynthia A Haseltine
- Department of Microbiology, University of California, Davis, CA 95616-8665, USA
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42
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Green S, Squire CJ, Nieuwenhuizen NJ, Baker EN, Laing W. Defining the potassium binding region in an apple terpene synthase. J Biol Chem 2009; 284:8661-9. [PMID: 19181671 DOI: 10.1074/jbc.m807140200] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Terpene synthases are a family of enzymes largely responsible for synthesizing the vast array of terpenoid compounds known to exist in nature. Formation of terpenoids from their respective 10-, 15-, or 20-carbon atom prenyl diphosphate precursors is initiated by divalent (M(2+)) metal ion-assisted electrophilic attack. In addition to M(2+), monovalent cations (M(+)) have also been shown to be essential for the activity of certain terpene synthases most likely by facilitating substrate binding or catalysis. An apple alpha-farnesene synthase (MdAFS1), which has a dependence upon potassium (K(+)), was used to identify active site regions that may be important for M(+) binding. Protein homology modeling revealed a surface-exposed loop (H-alphal loop) in MdAFS1 that fulfilled the necessary requirements for a K(+) binding region. Site-directed mutagenesis analysis of specific residues within this loop then revealed their crucial importance to this K(+) response and strongly implicated specific residues in direct K(+) binding. The role of the H-alphal loop in terpene synthase K(+) coordination was confirmed in a Conifer pinene synthase also using site-directed mutagenesis. These findings provide the first direct evidence for a specific M(+) binding region in two functionally and phylogenetically divergent terpene synthases. They also provide a basis for understanding K(+) activation in other terpene synthases and establish a new role for the H-alphal loop region in terpene synthase catalysis.
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Affiliation(s)
- Sol Green
- The New Zealand Institute for Plant and Food Research, Mt. Albert, Private Bag 92169, Auckland, New Zeland.
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43
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Grigorescu AA, Vissers JHA, Ristic D, Pigli YZ, Lynch TW, Wyman C, Rice PA. Inter-subunit interactions that coordinate Rad51's activities. Nucleic Acids Res 2008; 37:557-67. [PMID: 19066203 PMCID: PMC2632893 DOI: 10.1093/nar/gkn973] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Rad51 is the central catalyst of homologous recombination in eukaryotes and is thus critical for maintaining genomic integrity. Recent crystal structures of filaments formed by Rad51 and the closely related archeal RadA and eubacterial RecA proteins place the ATPase site at the protomeric interface. To test the relevance of this feature, we mutated conserved residues at this interface and examined their effects on key activities of Rad51: ssDNA-stimulated ATP hydrolysis, DNA binding, polymerization on DNA substrates and catalysis of strand-exchange reactions. Our results show that the interface seen in the crystal structures is very important for nucleoprotein filament formation. H352 and R357 of yeast Rad51 are essential for assembling the catalytically competent form of the enzyme on DNA substrates and coordinating its activities. However, contrary to some previous suggestions, neither of these residues is critical for ATP hydrolysis.
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Affiliation(s)
- Arabela A Grigorescu
- Department of Biochemistry, Molecular Biology and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
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44
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Hikiba J, Takizawa Y, Ikawa S, Shibata T, Kurumizaka H. Biochemical analysis of the human DMC1-I37N polymorphism. FEBS J 2008; 276:457-65. [PMID: 19076215 DOI: 10.1111/j.1742-4658.2008.06786.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The DMC1 protein, a meiosis-specific DNA recombinase, promotes homologous pairing and strand exchange. The I37N single nucleotide polymorphism of the human DMC1 protein was reported as a result of human genome sequencing projects. In this study, we purified the human DMC1-I37N variant, as a recombinant protein. The DMC1 protein is known to require DNA for efficient ATP hydrolysis. By contrast, the DMC1-I37N variant efficiently hydrolyzed ATP in the absence of DNA. Like the conventional DMC1 protein, the DMC1-I37N variant promoted strand exchange, but it required a high Ca2+ concentration (4-8 mm), a condition that inactivates the strand-exchange activity of the conventional DMC1 protein. These biochemical differences between the DMC1 and DMC1-I37N proteins suggest that the DMC1-I37N polymorphism may be a source of improper meiotic recombination, causing meiotic defects in humans.
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Affiliation(s)
- Juri Hikiba
- Laboratory of Structural Biology, Waseda University, Tokyo, Japan
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Zhang XP, Galkin VE, Yu X, Egelman EH, Heyer WD. Loop 2 in Saccharomyces cerevisiae Rad51 protein regulates filament formation and ATPase activity. Nucleic Acids Res 2008; 37:158-71. [PMID: 19033358 PMCID: PMC2615628 DOI: 10.1093/nar/gkn914] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Previous studies showed that the K342E substitution in the Saccharomyces cerevisiae Rad51 protein increases the interaction with Rad54 protein in the two-hybrid system, leads to increased sensitivity to the alkylating agent MMS and hyper-recombination in an oligonucleotide-mediated gene targeting assay. K342 localizes in loop 2, a region of Rad51 whose function is not well understood. Here, we show that Rad51-K342E displays DNA-independent and DNA-dependent ATPase activities, owing to its ability to form filaments in the absence of a DNA lattice. These filaments exhibit a compressed pitch of 81 Å, whereas filaments of wild-type Rad51 and Rad51-K342E on DNA form extended filaments with a 97 Å pitch. Rad51-K342E shows near normal binding to ssDNA, but displays a defect in dsDNA binding, resulting in less stable protein-dsDNA complexes. The mutant protein is capable of catalyzing the DNA strand exchange reaction and is insensitive to inhibition by the early addition of dsDNA. Wild-type Rad51 protein is inhibited under such conditions, because of its ability to bind dsDNA. No significant changes in the interaction between Rad51-K342E and Rad54 could be identified. These findings suggest that loop 2 contributes to the primary DNA-binding site in Rad51, controlling filament formation and ATPase activity.
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Affiliation(s)
- Xiao-Ping Zhang
- Department of Microbiology, University of California, Davis, CA 95616-8665, USA
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Sarai N, Kagawa W, Fujikawa N, Saito K, Hikiba J, Tanaka K, Miyagawa K, Kurumizaka H, Yokoyama S. Biochemical analysis of the N-terminal domain of human RAD54B. Nucleic Acids Res 2008; 36:5441-50. [PMID: 18718930 PMCID: PMC2553597 DOI: 10.1093/nar/gkn516] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Revised: 07/16/2008] [Accepted: 07/29/2008] [Indexed: 01/28/2023] Open
Abstract
The human RAD54B protein is a paralog of the RAD54 protein, which plays important roles in homologous recombination. RAD54B contains an N-terminal region outside the SWI2/SNF2 domain that shares less conservation with the corresponding region in RAD54. The biochemical roles of this region of RAD54B are not known, although the corresponding region in RAD54 is known to physically interact with RAD51. In the present study, we have biochemically characterized an N-terminal fragment of RAD54B, consisting of amino acid residues 26-225 (RAD54B(26-225)). This fragment formed a stable dimer in solution and bound to branched DNA structures. RAD54B(26-225) also interacted with DMC1 in both the presence and absence of DNA. Ten DMC1 segments spanning the entire region of the DMC1 sequence were prepared, and two segments, containing amino acid residues 153-214 and 296-340, were found to directly bind to the N-terminal domain of RAD54B. A structural alignment of DMC1 with the Methanococcus voltae RadA protein, a homolog of DMC1 in the helical filament form, indicated that these RAD54B-binding sites are located near the ATP-binding site at the monomer-monomer interface in the DMC1 helical filament. Thus, RAD54B binding may affect the quaternary structure of DMC1. These observations suggest that the N-terminal domain of RAD54B plays multiple roles of in homologous recombination.
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Affiliation(s)
- Naoyuki Sarai
- Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai 980-8575 and Laboratory of Molecular Radiology, Center of Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Wataru Kagawa
- Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai 980-8575 and Laboratory of Molecular Radiology, Center of Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Norie Fujikawa
- Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai 980-8575 and Laboratory of Molecular Radiology, Center of Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kengo Saito
- Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai 980-8575 and Laboratory of Molecular Radiology, Center of Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Juri Hikiba
- Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai 980-8575 and Laboratory of Molecular Radiology, Center of Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kozo Tanaka
- Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai 980-8575 and Laboratory of Molecular Radiology, Center of Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kiyoshi Miyagawa
- Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai 980-8575 and Laboratory of Molecular Radiology, Center of Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hitoshi Kurumizaka
- Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai 980-8575 and Laboratory of Molecular Radiology, Center of Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shigeyuki Yokoyama
- Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku, Sendai 980-8575 and Laboratory of Molecular Radiology, Center of Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Hikiba J, Hirota K, Kagawa W, Ikawa S, Kinebuchi T, Sakane I, Takizawa Y, Yokoyama S, Mandon-Pépin B, Nicolas A, Shibata T, Ohta K, Kurumizaka H. Structural and functional analyses of the DMC1-M200V polymorphism found in the human population. Nucleic Acids Res 2008; 36:4181-90. [PMID: 18566005 PMCID: PMC2475644 DOI: 10.1093/nar/gkn362] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The M200V polymorphism of the human DMC1 protein, which is an essential, meiosis-specific DNA recombinase, was found in an infertile patient, raising the question of whether this homozygous human DMC1-M200V polymorphism may cause infertility by affecting the function of the human DMC1 protein. In the present study, we determined the crystal structure of the human DMC1-M200V variant in the octameric-ring form. Biochemical analyses revealed that the human DMC1-M200V variant had reduced stability, and was moderately defective in catalyzing in vitro recombination reactions. The corresponding M194V mutation introduced in the Schizosaccharomyces pombe dmc1 gene caused a significant decrease in the meiotic homologous recombination frequency. Together, these structural, biochemical and genetic results provide extensive evidence that the human DMC1-M200V mutation impairs its function, supporting the previous interpretation that this single-nucleotide polymorphism is a source of human infertility.
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Affiliation(s)
- Juri Hikiba
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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López-Casamichana M, Orozco E, Marchat LA, López-Camarillo C. Transcriptional profile of the homologous recombination machinery and characterization of the EhRAD51 recombinase in response to DNA damage in Entamoeba histolytica. BMC Mol Biol 2008; 9:35. [PMID: 18402694 PMCID: PMC2324109 DOI: 10.1186/1471-2199-9-35] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2007] [Accepted: 04/10/2008] [Indexed: 01/19/2023] Open
Abstract
Background In eukaryotic and prokaryotic cells, homologous recombination is an accurate mechanism to generate genetic diversity, and it is also used to repair DNA double strand-breaks. RAD52 epistasis group genes involved in recombinational DNA repair, including mre11, rad50, nsb1/xrs2, rad51, rad51c/rad57, rad51b/rad55, rad51d, xrcc2, xrcc3, rad52, rad54, rad54b/rdh54 and rad59 genes, have been studied in human and yeast cells. Notably, the RAD51 recombinase catalyses strand transfer between a broken DNA and its undamaged homologous strand, to allow damaged region repair. In protozoan parasites, homologous recombination generating antigenic variation and genomic rearrangements is responsible for virulence variation and drug resistance. However, in Entamoeba histolytica the protozoan parasite responsible for human amoebiasis, DNA repair and homologous recombination mechanisms are still unknown. Results In this paper, we initiated the study of the mechanism for DNA repair by homologous recombination in the primitive eukaryote E. histolytica using UV-C (150 J/m2) irradiated trophozoites. DNA double strand-breaks were evidenced in irradiated cells by TUNEL and comet assays and evaluation of the EhH2AX histone phosphorylation status. In E. histolytica genome, we identified genes homologous to yeast and human RAD52 epistasis group genes involved in DNA double strand-breaks repair by homologous recombination. Interestingly, the E. histolytica RAD52 epistasis group related genes were differentially expressed before and after UV-C treatment. Next, we focused on the characterization of the putative recombinase EhRAD51, which conserves the typical architecture of RECA/RAD51 proteins. Specific antibodies immunodetected EhRAD51 protein in both nuclear and cytoplasmic compartments. Moreover, after DNA damage, EhRAD51 was located as typical nuclear foci-like structures in E. histolytica trophozoites. Purified recombinant EhRAD51 exhibited DNA binding and pairing activities and exchanging reactions between homologous strands in vitro. Conclusion E. histolytica genome contains most of the RAD52 epistasis group related genes, which were differentially expressed when DNA double strand-breaks were induced by UV-C irradiation. In response to DNA damage, EhRAD51 protein is overexpressed and relocalized in nuclear foci-like structures. Functional assays confirmed that EhRAD51 is a bonafide recombinase. These data provided the first insights about the potential roles of the E. histolytica RAD52 epistasis group genes and EhRAD51 protein function in DNA damage response of this ancient eukaryotic parasite.
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Affiliation(s)
- Mavil López-Casamichana
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, México DF, México.
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Davies OR, Pellegrini L. Interaction with the BRCA2 C terminus protects RAD51-DNA filaments from disassembly by BRC repeats. Nat Struct Mol Biol 2008; 14:475-83. [PMID: 17515903 PMCID: PMC2096194 DOI: 10.1038/nsmb1251] [Citation(s) in RCA: 141] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2007] [Accepted: 04/11/2007] [Indexed: 11/09/2022]
Abstract
BRCA2 has an essential function in DNA repair by homologous recombination, interacting with RAD51 via short motifs in the middle and at the C terminus of BRCA2. Here, we report that a conserved 36-residue sequence of human BRCA2 encoded by exon 27 (BRCA2Exon27) interacts with RAD51 through the specific recognition of oligomerized RAD51 ATPase domains. BRCA2Exon27 binding stabilizes the RAD51 nucleoprotein filament against disassembly by BRC repeat 4. The protection is specific for RAD51 filaments formed on single-stranded DNA and is lost when BRCA2Exon27 is phosphorylated on Ser3291. We propose that productive recombination results from the functional balance between the different RAD51-binding modes [corrected] of the BRC repeat and exon 27 regions of BRCA2. Our results further suggest a mechanism in which CDK phosphorylation of BRCA2Exon27 at the G2-M transition alters the balance in favor of RAD51 filament disassembly, thus terminating recombination.
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Affiliation(s)
| | - Luca Pellegrini
- Corresponding author. L Pellegrini, University of Cambridge, Department of Biochemistry, Tennis Court Road, Cambridge CB2 1GA, UK. E-mail:
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50
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Chen LT, Ko TP, Chang YW, Lin KA, Wang AHJ, Wang TF. Structural and functional analyses of five conserved positively charged residues in the L1 and N-terminal DNA binding motifs of archaeal RADA protein. PLoS One 2007; 2:e858. [PMID: 17848989 PMCID: PMC1964548 DOI: 10.1371/journal.pone.0000858] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Accepted: 08/16/2007] [Indexed: 12/29/2022] Open
Abstract
RecA family proteins engage in an ATP-dependent DNA strand exchange reaction that includes a ssDNA nucleoprotein helical filament and a homologous dsDNA sequence. In spite of more than 20 years of efforts, the molecular mechanism of homology pairing and strand exchange is still not fully understood. Here we report a crystal structure of Sulfolobus solfataricus RadA overwound right-handed filament with three monomers per helical pitch. This structure reveals conformational details of the first ssDNA binding disordered loop (denoted L1 motif) and the dsDNA binding N-terminal domain (NTD). L1 and NTD together form an outwardly open palm structure on the outer surface of the helical filament. Inside this palm structure, five conserved basic amino acid residues (K27, K60, R117, R223 and R229) surround a 25 A pocket that is wide enough to accommodate anionic ssDNA, dsDNA or both. Biochemical analyses demonstrate that these five positively charged residues are essential for DNA binding and for RadA-catalyzed D-loop formation. We suggest that the overwound right-handed RadA filament represents a functional conformation in the homology search and pairing reaction. A new structural model is proposed for the homologous interactions between a RadA-ssDNA nucleoprotein filament and its dsDNA target.
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Affiliation(s)
- Li-Tzu Chen
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yu-Wei Chang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Kuei-An Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Andrew H.-J. Wang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Department of Life Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- National Core Facility of High-Throughput Protein Crystallography, Academia Sinica, Taipei, Taiwan
- * To whom correspondence should be addressed. E-mail: (AW); (TW)
| | - Ting-Fang Wang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- * To whom correspondence should be addressed. E-mail: (AW); (TW)
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