8s9n: Difference between revisions
New page: '''Unreleased structure''' The entry 8s9n is ON HOLD Authors: Description: Category: Unreleased Structures |
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==DNA cytosine-N4 methyltransferase (residues 61-324) from the Bdelloid rotifer Adineta vaga - C2 crystal form== | |||
<StructureSection load='8s9n' size='340' side='right'caption='[[8s9n]], [[Resolution|resolution]] 1.89Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[8s9n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Adineta_vaga Adineta vaga]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8S9N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8S9N FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.89Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SFG:SINEFUNGIN'>SFG</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8s9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8s9n OCA], [https://pdbe.org/8s9n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8s9n RCSB], [https://www.ebi.ac.uk/pdbsum/8s9n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8s9n ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Much is known about the generation, removal, and roles of 5-methylcytosine (5mC) in eukaryote DNA, and there is a growing body of evidence regarding N6-methyladenine, but very little is known about N4-methylcytosine (4mC) in the DNA of eukaryotes. The gene for the first metazoan DNA methyltransferase generating 4mC (N4CMT) was reported and characterized recently by others, in tiny freshwater invertebrates called bdelloid rotifers. Bdelloid rotifers are ancient, apparently asexual animals, and lack canonical 5mC DNA methyltransferases. Here, we characterize the kinetic properties and structural features of the catalytic domain of the N4CMT protein from the bdelloid rotifer Adineta vaga. We find that N4CMT generates high-level methylation at preferred sites, (a/c)CG(t/c/a), and low-level methylation at disfavored sites, exemplified by ACGG. Like the mammalian de novo 5mC DNA methyltransferase 3A/3B (DNMT3A/3B), N4CMT methylates CpG dinucleotides on both DNA strands, generating hemi-methylated intermediates and eventually fully-methylated CpG sites, particularly in the context of favored symmetric sites. In addition, like DNMT3A/3B, N4CMT methylates non-CpG sites, mainly CpA/TpG, though at a lower rate. Both N4CMT and DNMT3A/3B even prefer similar CpG-flanking sequences. Structurally, the catalytic domain of N4CMT closely resembles the Caulobacter crescentus cell cycle-regulated DNA methyltransferase. The symmetric methylation of CpG, and similarity to a cell cycle-regulated DNA methyltransferase, together suggest that N4CMT might also carry out DNA synthesis-dependent methylation following DNA replication. | |||
Biochemical and structural characterization of the first-discovered metazoan DNA cytosine-N4 methyltransferase from the Bdelloid rotifer Adineta vaga.,Zhou J, Horton JR, Kaur G, Chen Q, Li X, Mendoza F, Wu T, Blumenthal RM, Zhang X, Cheng X J Biol Chem. 2023 Jul 4:105017. doi: 10.1016/j.jbc.2023.105017. PMID:37414145<ref>PMID:37414145</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 8s9n" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Adineta vaga]] | |||
[[Category: Large Structures]] | |||
[[Category: Cheng X]] | |||
[[Category: Horton JR]] | |||
[[Category: Zhou J]] | |||
Latest revision as of 13:41, 2 August 2023
DNA cytosine-N4 methyltransferase (residues 61-324) from the Bdelloid rotifer Adineta vaga - C2 crystal formDNA cytosine-N4 methyltransferase (residues 61-324) from the Bdelloid rotifer Adineta vaga - C2 crystal form
Structural highlights
Publication Abstract from PubMedMuch is known about the generation, removal, and roles of 5-methylcytosine (5mC) in eukaryote DNA, and there is a growing body of evidence regarding N6-methyladenine, but very little is known about N4-methylcytosine (4mC) in the DNA of eukaryotes. The gene for the first metazoan DNA methyltransferase generating 4mC (N4CMT) was reported and characterized recently by others, in tiny freshwater invertebrates called bdelloid rotifers. Bdelloid rotifers are ancient, apparently asexual animals, and lack canonical 5mC DNA methyltransferases. Here, we characterize the kinetic properties and structural features of the catalytic domain of the N4CMT protein from the bdelloid rotifer Adineta vaga. We find that N4CMT generates high-level methylation at preferred sites, (a/c)CG(t/c/a), and low-level methylation at disfavored sites, exemplified by ACGG. Like the mammalian de novo 5mC DNA methyltransferase 3A/3B (DNMT3A/3B), N4CMT methylates CpG dinucleotides on both DNA strands, generating hemi-methylated intermediates and eventually fully-methylated CpG sites, particularly in the context of favored symmetric sites. In addition, like DNMT3A/3B, N4CMT methylates non-CpG sites, mainly CpA/TpG, though at a lower rate. Both N4CMT and DNMT3A/3B even prefer similar CpG-flanking sequences. Structurally, the catalytic domain of N4CMT closely resembles the Caulobacter crescentus cell cycle-regulated DNA methyltransferase. The symmetric methylation of CpG, and similarity to a cell cycle-regulated DNA methyltransferase, together suggest that N4CMT might also carry out DNA synthesis-dependent methylation following DNA replication. Biochemical and structural characterization of the first-discovered metazoan DNA cytosine-N4 methyltransferase from the Bdelloid rotifer Adineta vaga.,Zhou J, Horton JR, Kaur G, Chen Q, Li X, Mendoza F, Wu T, Blumenthal RM, Zhang X, Cheng X J Biol Chem. 2023 Jul 4:105017. doi: 10.1016/j.jbc.2023.105017. PMID:37414145[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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