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4zcf

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Revision as of 07:48, 10 May 2023

Structural basis of asymmetric DNA methylation and ATP-triggered long-range diffusion by EcoP15I

Structural highlights

4zcf is a 5 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

T3RE_ECOLX A type III restriction enzyme that recognizes 2 inversely oriented double-stranded sequences 5'-CAGCAG-3' and cleaves DNA 25-27 base pairs downstream of one site. DNA restriction requires both the Res and Mod subunits (PubMed:11178902, PubMed:15464603). DNA topology affects its action; relaxed and negatively supercoiled DNA are digested but positively supercoiled DNA is not a good substrate (PubMed:11178902). Interacts with DNA approximately one half-turn downstream of the recognition site (PubMed:26067164). After binding to one recognition site undergoes random one-dimensional diffusion along DNA until it collides with a stationary enzyme bound to the second DNA site, which is when DNA cleavage occurs (Probable).^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

Type III R-M enzymes were identified >40 years ago and yet there is no structural information on these multisubunit enzymes. Here we report the structure of a Type III R-M system, consisting of the entire EcoP15I complex (Mod2Res1) bound to DNA. The structure suggests how ATP hydrolysis is coupled to long-range diffusion of a helicase on DNA, and how a dimeric methyltransferase functions to methylate only one of the two DNA strands. We show that the EcoP15I motor domains are specifically adapted to bind double-stranded DNA and to facilitate DNA sliding via a novel 'Pin' domain. We also uncover unexpected 'division of labour', where one Mod subunit recognizes DNA, while the other Mod subunit methylates the target adenine-a mechanism that may extend to adenine N6 RNA methylation in mammalian cells. Together the structure sheds new light on the mechanisms of both helicases and methyltransferases in DNA and RNA metabolism.

Structural basis of asymmetric DNA methylation and ATP-triggered long-range diffusion by EcoP15I.,Gupta YK, Chan SH, Xu SY, Aggarwal AK Nat Commun. 2015 Jun 12;6:7363. doi: 10.1038/ncomms8363. PMID:26067164^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Janscak P, Sandmeier U, Szczelkun MD, Bickle TA. Subunit assembly and mode of DNA cleavage of the type III restriction endonucleases EcoP1I and EcoP15I. J Mol Biol. 2001 Feb 23;306(3):417-31. PMID:11178902 doi:10.1006/jmbi.2000.4411
↑ Möncke-Buchner E, Mackeldanz P, Krüger DH, Reuter M. Overexpression and affinity chromatography purification of the Type III restriction endonuclease EcoP15I for use in transcriptome analysis. J Biotechnol. 2004 Oct 19;114(1-2):99-106. PMID:15464603 doi:10.1016/j.jbiotec.2004.06.014
↑ Gupta YK, Chan SH, Xu SY, Aggarwal AK. Structural basis of asymmetric DNA methylation and ATP-triggered long-range diffusion by EcoP15I. Nat Commun. 2015 Jun 12;6:7363. doi: 10.1038/ncomms8363. PMID:26067164 doi:http://dx.doi.org/10.1038/ncomms8363
↑ Gupta YK, Chan SH, Xu SY, Aggarwal AK. Structural basis of asymmetric DNA methylation and ATP-triggered long-range diffusion by EcoP15I. Nat Commun. 2015 Jun 12;6:7363. doi: 10.1038/ncomms8363. PMID:26067164 doi:http://dx.doi.org/10.1038/ncomms8363
↑ Gupta YK, Chan SH, Xu SY, Aggarwal AK. Structural basis of asymmetric DNA methylation and ATP-triggered long-range diffusion by EcoP15I. Nat Commun. 2015 Jun 12;6:7363. doi: 10.1038/ncomms8363. PMID:26067164 doi:http://dx.doi.org/10.1038/ncomms8363

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4zcf"

@@ Line 3: / Line 3: @@
 <StructureSection load='4zcf' size='340' side='right'caption='[[4zcf]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4zcf]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZCF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=4ZCF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4zcf]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZCF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZCF FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ecoP15Imod ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), ecoP15Ires ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=4zcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zcf OCA], [https://pdbe.org/4zcf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zcf RCSB], [https://www.ebi.ac.uk/pdbsum/4zcf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zcf ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=4zcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zcf OCA], [http://pdbe.org/4zcf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zcf RCSB], [http://www.ebi.ac.uk/pdbsum/4zcf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4zcf ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/T3RE_ECOLX T3RE_ECOLX] A type III restriction enzyme that recognizes 2 inversely oriented double-stranded sequences 5'-CAGCAG-3' and cleaves DNA 25-27 base pairs downstream of one site. DNA restriction requires both the Res and Mod subunits (PubMed:11178902, PubMed:15464603). DNA topology affects its action; relaxed and negatively supercoiled DNA are digested but positively supercoiled DNA is not a good substrate (PubMed:11178902). Interacts with DNA approximately one half-turn downstream of the recognition site (PubMed:26067164). After binding to one recognition site undergoes random one-dimensional diffusion along DNA until it collides with a stationary enzyme bound to the second DNA site, which is when DNA cleavage occurs (Probable).<ref>PMID:11178902</ref> <ref>PMID:15464603</ref> <ref>PMID:26067164</ref> <ref>PMID:26067164</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Aggarwal, A K]]
+[[Category: Aggarwal AK]]
-[[Category: Chan, S H]]
+[[Category: Chan SH]]
-[[Category: Gupta, Y K]]
+[[Category: Gupta YK]]
-[[Category: Xu, S Y]]
+[[Category: Xu SY]]
-[[Category: Asymmetric dna methylation]]
-[[Category: Atp motor]]
-[[Category: Dna methyltransferase]]
-[[Category: Hydrolase-dna complex]]
-[[Category: Hydrolase/dna]]

4zcf

From Proteopedia

Revision as of 07:48, 10 May 2023

Structural basis of asymmetric DNA methylation and ATP-triggered long-range diffusion by EcoP15I

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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