4esj: Difference between revisions

Revision as of 04:12, 7 October 2022

RESTRICTION ENDONUCLEASE DpnI IN COMPLEX WITH TARGET DNA

Structural highlights

4esj is a 6 chain structure with sequence from Streptococcus pneumoniae TIGR4 and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	6MA, AZI, GOL, UNX, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

T2D1_STRR6 Recognizes the double-stranded and methylated sequence G(Me)ATC and cleaves after A-2.

Publication Abstract from PubMed

DNA methylation-dependent restriction enzymes have many applications in genetic engineering and in the analysis of the epigenetic state of eukaryotic genomes. Nevertheless, high-resolution structures have not yet been reported, and therefore mechanisms of DNA methylation-dependent cleavage are not understood. Here, we present a biochemical analysis and high-resolution DNA co-crystal structure of the N(6)-methyladenine (m6A)-dependent restriction enzyme R.DpnI. Our data show that R.DpnI consists of an N-terminal catalytic PD-(D/E)XK domain and a C-terminal winged helix (wH) domain. Surprisingly, both domains bind DNA in a sequence- and methylation-sensitive manner. The crystal contains R.DpnI with fully methylated target DNA bound to the wH domain, but distant from the catalytic domain. Independent readout of DNA sequence and methylation by the two domains might contribute to R.DpnI specificity or could help the monomeric enzyme to cut the second strand after introducing a nick.

Crystal structure and mechanism of action of the N6-methyladenine-dependent type IIM restriction endonuclease R.DpnI.,Siwek W, Czapinska H, Bochtler M, Bujnicki J, Skowronek K Nucleic Acids Res. 2012 May 18. PMID:22610857^[1]

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

References

↑ Siwek W, Czapinska H, Bochtler M, Bujnicki J, Skowronek K. Crystal structure and mechanism of action of the N6-methyladenine-dependent type IIM restriction endonuclease R.DpnI. Nucleic Acids Res. 2012 May 18. PMID:22610857 doi:10.1093/nar/gks428

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OCA

[1] Siwek W, Czapinska H, Bochtler M, Bujnicki J, Skowronek K. Crystal structure and mechanism of action of the N6-methyladenine-dependent type IIM restriction endonuclease R.DpnI. Nucleic Acids Res. 2012 May 18. PMID:22610857 doi:10.1093/nar/gks428

[1]

@@ Line 1: / Line 1: @@
 ==RESTRICTION ENDONUCLEASE DpnI IN COMPLEX WITH TARGET DNA==
-<StructureSection load='4esj' size='340' side='right' caption='[[4esj]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
+<StructureSection load='4esj' size='340' side='right'caption='[[4esj]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4esj]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Strpn Strpn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ESJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ESJ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4esj]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_TIGR4 Streptococcus pneumoniae TIGR4] 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=4ESJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ESJ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</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=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6MA:N6-METHYL-DEOXY-ADENOSINE-5-MONOPHOSPHATE'>6MA</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=4esj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4esj OCA], [https://pdbe.org/4esj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4esj RCSB], [https://www.ebi.ac.uk/pdbsum/4esj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4esj ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dpnC, spr1665 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=170187 STRPN])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4esj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4esj OCA], [http://pdbe.org/4esj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4esj RCSB], [http://www.ebi.ac.uk/pdbsum/4esj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4esj ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/T2D1_STRR6 T2D1_STRR6]] Recognizes the double-stranded and methylated sequence G(Me)ATC and cleaves after A-2.
+[https://www.uniprot.org/uniprot/T2D1_STRR6 T2D1_STRR6] Recognizes the double-stranded and methylated sequence G(Me)ATC and cleaves after A-2.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Strpn]]
+[[Category: Large Structures]]
-[[Category: Type II site-specific deoxyribonuclease]]
+[[Category: Streptococcus pneumoniae TIGR4]]
-[[Category: Bochtler, M]]
+[[Category: Synthetic construct]]
-[[Category: Bujnicki, J M]]
+[[Category: Bochtler M]]
-[[Category: Czapinska, H]]
+[[Category: Bujnicki JM]]
-[[Category: Siwek, W]]
+[[Category: Czapinska H]]
-[[Category: Skowronek, K]]
+[[Category: Siwek W]]
-[[Category: Dna binding]]
+[[Category: Skowronek K]]
-[[Category: Dpni]]
-[[Category: Hydrolase-dna complex]]
-[[Category: Methylation dependent]]
-[[Category: N6-methyladenine]]
-[[Category: Restriction endonuclease]]
-[[Category: Restriction endonuclease-dna complex]]
-[[Category: Restriction enzyme]]
-[[Category: Type iie]]
-[[Category: Type iim]]
-[[Category: Winged helix domain]]

4esj: Difference between revisions

Revision as of 04:12, 7 October 2022

RESTRICTION ENDONUCLEASE DpnI IN COMPLEX WITH TARGET DNA

Structural highlights

Function

Publication Abstract from PubMed

References

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