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Pederson K, Meints GA, Drobny GP. Base Dynamics in the HhaI Protein Binding Site. J Phys Chem B 2023; 127:7266-7275. [PMID: 37561575 PMCID: PMC10461302 DOI: 10.1021/acs.jpcb.3c03687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/18/2023] [Indexed: 08/12/2023]
Abstract
Protein-DNA interactions play an important role in numerous biological functions within the living cell. In many of these interactions, the DNA helix is significantly distorted upon protein-DNA complex formation. The HhaI restriction-modification system is one such system, where the methylation target is flipped out of the helix when bound to the methyltransferase. However, the base flipping mechanism is not well understood. The dynamics of the binding site of the HhaI methyltransferase and endonuclease (underlined) within the DNA oligomer [d(G1A2T3A4G5C6G7C8T9A10T11C12)]2 are studied using deuterium solid-state NMR (SSNMR). SSNMR spectra obtained from DNAs deuterated on the base of nucleotides within and flanking the [5'-GCGC-3']2 sequence indicate that all of these positions are structurally flexible. Previously, conformational flexibility within the phosphodiester backbone and furanose ring within the target sequence has been observed and hypothesized to play a role in the distortion mechanism. However, whether that distortion was occurring through an active or passive mechanism remained unclear. These NMR data demonstrate that although the [5'-GCGC-3']2 sequence is dynamic, the target cytosine is not passively flipping out of the double-helix on the millisecond-picosecond time scale. Additionally, although previous studies have shown that both the furanose ring and phosphodiester backbone experience a change in dynamics upon methylation, which may play a role in recognition and cleavage by the endonuclease, our observations here indicate that methylation has no effect on the dynamics of the base itself.
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Affiliation(s)
- Kari Pederson
- Department
of Chemistry & Biochemistry, California
State University at Dominguez Hills, Carson, California 90747, United States
| | - Gary A. Meints
- Department
of Chemistry, Missouri State University, Springfield, Missouri 65897, United States
| | - Gary P. Drobny
- Department
of Chemistry, University of Washington, Seattle, Washington 98195-1700, United
States
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2
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Dumesic PA, Stoddard CI, Catania S, Narlikar GJ, Madhani HD. ATP Hydrolysis by the SNF2 Domain of Dnmt5 Is Coupled to Both Specific Recognition and Modification of Hemimethylated DNA. Mol Cell 2020; 79:127-139.e4. [PMID: 32437639 DOI: 10.1016/j.molcel.2020.04.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 01/01/2023]
Abstract
C.neoformans Dnmt5 is an unusually specific maintenance-type CpG methyltransferase (DNMT) that mediates long-term epigenome evolution. It harbors a DNMT domain and SNF2 ATPase domain. We find that the SNF2 domain couples substrate specificity to an ATPase step essential for DNA methylation. Coupling occurs independent of nucleosomes. Hemimethylated DNA preferentially stimulates ATPase activity, and mutating Dnmt5's ATP-binding pocket disproportionately reduces ATPase stimulation by hemimethylated versus unmethylated substrates. Engineered DNA substrates that stabilize a reaction intermediate by mimicking a "flipped-out" conformation of the target cytosine bypass the SNF2 domain's requirement for hemimethylation. This result implies that ATP hydrolysis by the SNF2 domain is coupled to the DNMT domain conformational changes induced by preferred substrates. These findings establish a new role for a SNF2 ATPase: controlling an adjoined enzymatic domain's substrate recognition and catalysis. We speculate that this coupling contributes to the exquisite specificity of Dnmt5 via mechanisms related to kinetic proofreading.
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Affiliation(s)
- Phillip A Dumesic
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Caitlin I Stoddard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sandra Catania
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA.
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3
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Liu L, Shi T, Houk KN, Zhao YL. Understanding the R882H mutation effects of DNA methyltransferase DNMT3A: a combination of molecular dynamics simulations and QM/MM calculations. RSC Adv 2019; 9:31425-31434. [PMID: 35527972 PMCID: PMC9072302 DOI: 10.1039/c9ra06791d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 09/17/2019] [Indexed: 01/15/2023] Open
Abstract
The AML-related high-frequent R882H mutation of DNA (cytosine-5)-methyltransferase 3A (DNMT3A), a key enzyme forde novoepigenetic methylation in human beings, was characterized by a disturbing conformation ofS-adenosylmethionine (SAM).
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Affiliation(s)
- Lanxuan Liu
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry
- University of California
- Los Angeles
- USA
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
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4
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He S, Yang C, Peng S, Chen C, Zhao XS. Single-molecule study on conformational dynamics of M.HhaI. RSC Adv 2019; 9:14745-14749. [PMID: 35516350 PMCID: PMC9064139 DOI: 10.1039/c9ra00021f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 04/26/2019] [Indexed: 12/23/2022] Open
Abstract
We found that apo DNA methyltransferase M.HhaI under the physiological salt concentration does not possess the structure characterized by X-ray crystallography; instead, it interchanges between prefolded and unfolded states. Only after binding to the substrate, it transforms into a crystal-structure-like state. Flipping rates of its catalytic loop were directly measured. Huge conformational rearrangements in M.HhaI were observed by a single-molecule study.![]()
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Affiliation(s)
- Shanshan He
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Department of Chemical Biology
- College of Chemistry and Molecular Engineering
- Peking University
| | - Chen Yang
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Department of Chemical Biology
- College of Chemistry and Molecular Engineering
- Peking University
| | - Sijia Peng
- School of Life Sciences
- Tsinghua-Peking Joint Center for Life Sciences
- Beijing Advanced Innovation Center for Structural Biology
- Tsinghua University
- Beijing 100084
| | - Chunlai Chen
- School of Life Sciences
- Tsinghua-Peking Joint Center for Life Sciences
- Beijing Advanced Innovation Center for Structural Biology
- Tsinghua University
- Beijing 100084
| | - Xin Sheng Zhao
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Department of Chemical Biology
- College of Chemistry and Molecular Engineering
- Peking University
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5
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The sequence preference of DNA methylation variation in mammalians. PLoS One 2017; 12:e0186559. [PMID: 29045493 PMCID: PMC5646869 DOI: 10.1371/journal.pone.0186559] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 10/03/2017] [Indexed: 11/19/2022] Open
Abstract
Methylation of cytosine at the 5 position of the pyrimidine ring is the most prevalent and significant epigenetic modifications in mammalian DNA. The CpG methylation level shows a bimodal distribution but the bimodality can be overestimated due to the heterogeneity of per-base depth. Here, we developed an algorithm to eliminate the effect of per-base depth inhomogeneity on the bimodality and obtained a random CpG methylation distribution. By quantifying the deviation of the observed methylation distribution and the random one using the information formula, we find that in tetranucleotides 5’-N5CGN3-3’ (N5, N3 = A, C, G or T), GCGN3 and CCGN3 show less apparent deviation than ACGN3 and TCGN3, indicating that GCGN3 and CCGN3 are less variant in their level of methylation. The methylation variation of N5CGN3 are conserved among different cells, tissues and species, implying common features in the mechanisms of methylation and demethylation, presumably mediated by DNMTs and TETs in mammalians, respectively. Sequence dependence of DNA methylation variation also relates to gene regulatory and promotes the reexamination of the role of DNA sequence in fundamental biological processes.
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6
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Woodcock CB, Ulashchik EA, Poopeiko NE, Shmanai VV, Reich NO, Shchepinov MS. Rational Manipulation of DNA Methylation by Using Isotopically Reinforced Cytosine. Chembiochem 2016; 17:2018-2021. [PMID: 27595234 DOI: 10.1002/cbic.201600393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Indexed: 11/11/2022]
Abstract
The human DNA methyltransferase 3A (DNMT 3A) is responsible for de novo epigenetic regulation, which is essential for mammalian viability and implicated in diverse diseases. All DNA cytosine C5 methyltransferases follow a broadly conserved catalytic mechanism. We investigated whether C5 β-elimination contributes to the rate-limiting step in catalysis by DNMT3A and the bacterial M.HhaI by using deuterium substitutions of C5 and C6 hydrogens. This substitution caused a 1.59-1.83 fold change in the rate of catalysis, thus suggesting that β-elimination is partly rate-limiting for both enzymes. We used a multisite substrate to explore the consequences of slowing β-elimination during multiple cycles of catalysis. Processive catalysis was slower for both enzymes, and deuterium substitution resulted in DNMT 3A dissociating from its substrate. The decrease in DNA methylation rate by DNMT 3A provides the basis of our ongoing efforts to alter cellular DNA methylation levels without the toxicity of currently used methods.
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Affiliation(s)
- Clayton B Woodcock
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Egor A Ulashchik
- Institute of Physical Organic Chemistry, National Academy of Science of Belarus, Surganova str. 13, 220072, Minsk, Belarus
| | - Nikolai E Poopeiko
- Institute of Physical Organic Chemistry, National Academy of Science of Belarus, Surganova str. 13, 220072, Minsk, Belarus
| | - Vadim V Shmanai
- Institute of Physical Organic Chemistry, National Academy of Science of Belarus, Surganova str. 13, 220072, Minsk, Belarus
| | - Norbert O Reich
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.
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Matje DM, Krivacic CT, Dahlquist FW, Reich NO. Distal structural elements coordinate a conserved base flipping network. Biochemistry 2013; 52:1669-76. [PMID: 23409802 DOI: 10.1021/bi301284f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
One of the most dramatic illustrations of enzymatic promotion of a high-energy intermediate is observed in DNA modification and repair enzymes where an individual base is rotated (flipped) 180° around the deoxyribose-phosphate backbone and into the active site. While the end states have been extensively characterized, experimental techniques have yet to yield a full description of the base flipping process and the role played by the enzyme. The C5 cytosine methyltransferase M.HhaI coordinates an ensemble of reciprocal DNA and enzyme rearrangements to efficiently flip the target cytosine from the DNA helix. We sought to understand the role of individual amino acids during base flipping. Our results demonstrate that M.HhaI initiates base flipping before closure of the catalytic loop and utilizes the conserved serine 85 in the catalytic loop to accelerate flipping and maintain distortion of the DNA backbone. Serine 87, which forms specific contacts within the DNA helix after base flipping, is not involved in the flipping process or in maintaining the catalytically competent complex. At the base of the catalytic loop, glycine 98 acts as a hinge to allow conformational dynamism of the loop and mutation to alanine inhibits stabilization of the closed loop. Our results illustrate how an enzyme utilizes numerous, distal residues in concert to transform substrate recognition into catalysis.
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Affiliation(s)
- Douglas M Matje
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106-9510, United States
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8
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Didovyk A, Verdine GL. Structural origins of DNA target selection and nucleobase extrusion by a DNA cytosine methyltransferase. J Biol Chem 2012; 287:40099-105. [PMID: 23012373 DOI: 10.1074/jbc.m112.413054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND How DNA 5-cytosine methyltransferases (DCMTases) select their substrate nucleobase for extrusion from DNA duplex is poorly understood. RESULTS The crystal structure of a pre-extrusion M.HaeIII DCMTase-substrate DNA complex is reported here. CONCLUSION M.HaeIII selects its substrate cytosine for extrusion by selectively interfering with its stacking and hydrogen bonding interactions within the DNA duplex. SIGNIFICANCE This is the first structural elucidation of the target cytosine selection by a DCMTase. Epigenetic methylation of cytosine residues in DNA is an essential element of genome maintenance and function in organisms ranging from bacteria to humans. DNA 5-cytosine methyltransferase enzymes (DCMTases) catalyze cytosine methylation via reaction intermediates in which the DNA is drastically remodeled, with the target cytosine residue extruded from the DNA helix and plunged into the active site pocket of the enzyme. We have determined a crystal structure of M.HaeIII DCMTase in complex with its DNA substrate at a previously unobserved state, prior to extrusion of the target cytosine and frameshifting of the DNA recognition sequence. The structure reveals that M.HaeIII selects the target cytosine and destabilizes its base-pairing through a precise, focused, and coordinated assault on the duplex DNA, which isolates the target cytosine from its nearest neighbors and thereby facilitates its extrusion from DNA.
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Affiliation(s)
- Andriy Didovyk
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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9
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Holz-Schietinger C, Reich NO. RNA modulation of the human DNA methyltransferase 3A. Nucleic Acids Res 2012; 40:8550-7. [PMID: 22730298 PMCID: PMC3458530 DOI: 10.1093/nar/gks537] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2012] [Revised: 04/30/2012] [Accepted: 05/11/2012] [Indexed: 12/19/2022] Open
Abstract
DNA methyltransferase 3A (DNMT3A) is one of two human de novo DNA methyltransferases essential for transcription regulation during cellular development and differentiation. There is increasing evidence that RNA plays a role in directing DNA methylation to specific genomic locations within mammalian cells. Here, we describe two modes of RNA regulation of DNMT3A in vitro. We show a single-stranded RNA molecule that is antisense to the E-cadherin promoter binds tightly to the catalytic domain in a structurally dependent fashion causing potent inhibition of DNMT3A activity. Two other RNA molecules bind DNMT3A at an allosteric site outside the catalytic domain, causing no change in catalysis. Our observation of the potent and specific in vitro modulation of DNMT3A activity by RNA supports in vivo data that RNA interacts with DNMT3A to regulate transcription.
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Affiliation(s)
- Celeste Holz-Schietinger
- Interdepartmental Program in Biomolecular Science and Engineering and Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA
| | - Norbert O. Reich
- Interdepartmental Program in Biomolecular Science and Engineering and Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA
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10
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Matje DM, Reich NO. Molecular drivers of base flipping during sequence-specific DNA methylation. Chembiochem 2012; 13:1574-7. [PMID: 22730226 DOI: 10.1002/cbic.201200104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2012] [Indexed: 11/07/2022]
Abstract
One step at a time: Substrates containing nucleotide analogues lacking sequence-specific contacts to the C5 methyltransferase M.HhaI were used to probe the role of individual interactions in effecting conformational transitions during base flipping. A segregation of duties, that is, specific recognition and chemomechanical force for base flipping and active site assembly, within the enzyme is confirmed.
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Affiliation(s)
- Douglas M Matje
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA 93106-9510, USA
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11
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Holz-Schietinger C, Matje DM, Reich NO. Mutations in DNA methyltransferase (DNMT3A) observed in acute myeloid leukemia patients disrupt processive methylation. J Biol Chem 2012; 287:30941-51. [PMID: 22722925 DOI: 10.1074/jbc.m112.366625] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA methylation is a key regulator of gene expression and changes in DNA methylation occur early in tumorigenesis. Mutations in the de novo DNA methyltransferase gene, DNMT3A, frequently occur in adult acute myeloid leukemia patients with poor prognoses. Most of the mutations occur within the dimer or tetramer interface, including Arg-882. We have identified that the most prevalent mutation, R882H, and three additional mutants along the tetramer interface disrupt tetramerization. The processive methylation of multiple CpG sites is disrupted when tetramerization is eliminated. Our results provide a possible mechanism that accounts for how DNMT3A mutations may contribute to oncogenesis and its progression.
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Affiliation(s)
- Celeste Holz-Schietinger
- Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara, California 93106-9510, USA
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12
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Holz-Schietinger C, Matje DM, Harrison MF, Reich NO. Oligomerization of DNMT3A controls the mechanism of de novo DNA methylation. J Biol Chem 2011; 286:41479-41488. [PMID: 21979949 PMCID: PMC3308859 DOI: 10.1074/jbc.m111.284687] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 09/26/2011] [Indexed: 01/01/2023] Open
Abstract
DNMT3A is one of two human de novo DNA methyltransferases essential for regulating gene expression through cellular development and differentiation. Here we describe the consequences of single amino acid mutations, including those implicated in the development of acute myeloid leukemia (AML) and myelodysplastic syndromes, at the DNMT3A·DNMT3A homotetramer and DNMT3A·DNMT3L heterotetramer interfaces. A model for the DNMT3A homotetramer was developed via computational interface scanning and tested using light scattering and electrophoretic mobility shift assays. Distinct oligomeric states were functionally characterized using fluorescence anisotropy and steady-state kinetics. Replacement of residues that result in DNMT3A dimers, including those identified in AML patients, show minor changes in methylation activity but lose the capacity for processive catalysis on multisite DNA substrates, unlike the highly processive wild-type enzyme. Our results are consistent with the bimodal distribution of DNA methylation in vivo and the loss of clustered methylation in AML patients. Tetramerization with the known interacting partner DNMT3L rescues processive catalysis, demonstrating that protein binding at the DNMT3A tetramer interface can modulate methylation patterning. Our results provide a structural mechanism for the regulation of DNMT3A activity and epigenetic imprinting.
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Affiliation(s)
- Celeste Holz-Schietinger
- Interdepartmental Program in Biomolecular Science & Engineering, University of California, Santa Barbara, California 93106-9510
| | - Douglas M Matje
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106-9510
| | - Madeleine Flexer Harrison
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106-9510
| | - Norbert O Reich
- Interdepartmental Program in Biomolecular Science & Engineering, University of California, Santa Barbara, California 93106-9510; Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106-9510.
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