7vs4: Difference between revisions
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==Crystal structure of PacII_M1M2S-DNA(m6A)-SAH complex== | |||
<StructureSection load='7vs4' size='340' side='right'caption='[[7vs4]], [[Resolution|resolution]] 2.55Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[7vs4]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_alcaligenes Pseudomonas alcaligenes] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VS4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VS4 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]] 2.55Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6MA:N6-METHYL-DEOXY-ADENOSINE-5-MONOPHOSPHATE'>6MA</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</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=7vs4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vs4 OCA], [https://pdbe.org/7vs4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vs4 RCSB], [https://www.ebi.ac.uk/pdbsum/7vs4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vs4 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A142ISP4_PSEAC A0A142ISP4_PSEAC] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Type I restriction-modification systems help establish the prokaryotic DNA methylation landscape and provide protection against invasive DNA. In addition to classical m6A modifications, non-canonical type I enzymes catalyze both m6A and m4C using alternative DNA-modification subunits M1 and M2. Here, we report the crystal structures of the non-canonical PacII_M1M2S methyltransferase bound to target DNA and reaction product S-adenosylhomocysteine in a closed clamp-like conformation. Target DNA binds tightly within the central tunnel of the M1M2S complex and forms extensive contacts with all three protein subunits. Unexpectedly, while the target cytosine properly inserts into M2's pocket, the target adenine (either unmethylated or methylated) is anchored outside M1's pocket. A unique asymmetric catalysis is established where PacII_M1M2S has precisely coordinated the relative conformations of different subunits and evolved specific amino acids within M2/M1. This work provides insights into mechanisms of m6A/m4C catalysis and guidance for designing tools based on type I restriction-modification enzymes. | |||
Molecular insights into DNA recognition and methylation by non-canonical type I restriction-modification systems.,Zhu J, Gao Y, Wang Y, Zhan Q, Feng H, Luo X, Li P, Liu S, Hou H, Gao P Nat Commun. 2022 Oct 27;13(1):6391. doi: 10.1038/s41467-022-34085-z. PMID:36302770<ref>PMID:36302770</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 7vs4" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
==See Also== | |||
*[[DNA methyltransferase 3D structures|DNA methyltransferase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Pseudomonas alcaligenes]] | |||
[[Category: Synthetic construct]] | |||
[[Category: Gao P]] | |||
[[Category: Zhu J]] | |||
Latest revision as of 20:31, 29 November 2023
Crystal structure of PacII_M1M2S-DNA(m6A)-SAH complexCrystal structure of PacII_M1M2S-DNA(m6A)-SAH complex
Structural highlights
FunctionPublication Abstract from PubMedType I restriction-modification systems help establish the prokaryotic DNA methylation landscape and provide protection against invasive DNA. In addition to classical m6A modifications, non-canonical type I enzymes catalyze both m6A and m4C using alternative DNA-modification subunits M1 and M2. Here, we report the crystal structures of the non-canonical PacII_M1M2S methyltransferase bound to target DNA and reaction product S-adenosylhomocysteine in a closed clamp-like conformation. Target DNA binds tightly within the central tunnel of the M1M2S complex and forms extensive contacts with all three protein subunits. Unexpectedly, while the target cytosine properly inserts into M2's pocket, the target adenine (either unmethylated or methylated) is anchored outside M1's pocket. A unique asymmetric catalysis is established where PacII_M1M2S has precisely coordinated the relative conformations of different subunits and evolved specific amino acids within M2/M1. This work provides insights into mechanisms of m6A/m4C catalysis and guidance for designing tools based on type I restriction-modification enzymes. Molecular insights into DNA recognition and methylation by non-canonical type I restriction-modification systems.,Zhu J, Gao Y, Wang Y, Zhan Q, Feng H, Luo X, Li P, Liu S, Hou H, Gao P Nat Commun. 2022 Oct 27;13(1):6391. doi: 10.1038/s41467-022-34085-z. PMID:36302770[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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