7eew: Difference between revisions
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[7eew]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_T7 Escherichia phage T7] and [https://en.wikipedia.org/wiki/Vibrio_vulnificus_YJ016 Vibrio vulnificus YJ016]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EEW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EEW FirstGlance]. <br> | <table><tr><td colspan='2'>[[7eew]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_T7 Escherichia phage T7] and [https://en.wikipedia.org/wiki/Vibrio_vulnificus_YJ016 Vibrio vulnificus YJ016]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EEW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EEW FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.896Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=7eew FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eew OCA], [https://pdbe.org/7eew PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eew RCSB], [https://www.ebi.ac.uk/pdbsum/7eew PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eew ProSAT]</span></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=7eew FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eew OCA], [https://pdbe.org/7eew PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eew RCSB], [https://www.ebi.ac.uk/pdbsum/7eew PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eew ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/Q7MJG0_VIBVY Q7MJG0_VIBVY] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Type I restriction-modification enzymes are oligomeric proteins composed of methylation (M), DNA sequence-recognition (S), and restriction (R) subunits. The different bipartite DNA sequences of 2-4 consecutive bases are recognized by two discerned target recognition domains (TRDs) located at the two-helix bundle of the two conserved regions (CRs). Two M-subunits and a single S-subunit form an oligomeric protein that functions as a methyltransferase (M(2)S(1) MTase). Here, we present the crystal structure of the intact MTase from Vibrio vulnificus YJ016 in complex with the DNA-mimicking Ocr protein and the S-adenosyl-L-homocysteine (SAH). This MTase includes the M-domain with a helix tail (M-tail helix) and the S(1/2)-domain of a TRD and a CR alpha-helix. The Ocr binds to the cleft of the TRD surface and SAH is located in the pocket within the M-domain. The solution- and negative-staining electron microscopy-based reconstructed (M(1)S(1/2))(2) structure reveals a symmetric (S(1/2))(2) assembly using two CR-helices and two M-tail helices as a pivot, which is plausible for recognizing two DNA regions of same sequence. The conformational flexibility of the minimal M(1)S(1/2) MTase dimer indicates a particular state resembling the structure of M(2)S(1) MTases. | |||
Structural features of a minimal intact methyltransferase of a type I restriction-modification system.,Seo PW, Hofmann A, Kim JH, Hwangbo SA, Kim JH, Kim JW, Huynh TYL, Choy HE, Kim SJ, Lee J, Lee JO, Jin KS, Park SY, Kim JS Int J Biol Macromol. 2022 May 31;208:381-389. doi: , 10.1016/j.ijbiomac.2022.03.115. Epub 2022 Mar 23. PMID:35337914<ref>PMID:35337914</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7eew" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
Latest revision as of 22:33, 29 May 2024
Crystal structure of the intact MTase from Vibrio vulnificus YJ016 in complex with the DNA-mimicking Ocr protein and the S-adenosyl-L-homocysteine (SAH)Crystal structure of the intact MTase from Vibrio vulnificus YJ016 in complex with the DNA-mimicking Ocr protein and the S-adenosyl-L-homocysteine (SAH)
Structural highlights
FunctionPublication Abstract from PubMedType I restriction-modification enzymes are oligomeric proteins composed of methylation (M), DNA sequence-recognition (S), and restriction (R) subunits. The different bipartite DNA sequences of 2-4 consecutive bases are recognized by two discerned target recognition domains (TRDs) located at the two-helix bundle of the two conserved regions (CRs). Two M-subunits and a single S-subunit form an oligomeric protein that functions as a methyltransferase (M(2)S(1) MTase). Here, we present the crystal structure of the intact MTase from Vibrio vulnificus YJ016 in complex with the DNA-mimicking Ocr protein and the S-adenosyl-L-homocysteine (SAH). This MTase includes the M-domain with a helix tail (M-tail helix) and the S(1/2)-domain of a TRD and a CR alpha-helix. The Ocr binds to the cleft of the TRD surface and SAH is located in the pocket within the M-domain. The solution- and negative-staining electron microscopy-based reconstructed (M(1)S(1/2))(2) structure reveals a symmetric (S(1/2))(2) assembly using two CR-helices and two M-tail helices as a pivot, which is plausible for recognizing two DNA regions of same sequence. The conformational flexibility of the minimal M(1)S(1/2) MTase dimer indicates a particular state resembling the structure of M(2)S(1) MTases. Structural features of a minimal intact methyltransferase of a type I restriction-modification system.,Seo PW, Hofmann A, Kim JH, Hwangbo SA, Kim JH, Kim JW, Huynh TYL, Choy HE, Kim SJ, Lee J, Lee JO, Jin KS, Park SY, Kim JS Int J Biol Macromol. 2022 May 31;208:381-389. doi: , 10.1016/j.ijbiomac.2022.03.115. Epub 2022 Mar 23. PMID:35337914[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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