2y7c: Difference between revisions

Latest revision as of 21:17, 18 October 2023

Atomic model of the Ocr-bound methylase complex from the Type I restriction-modification enzyme EcoKI (M2S1). Based on fitting into EM map 1534.Atomic model of the Ocr-bound methylase complex from the Type I restriction-modification enzyme EcoKI (M2S1). Based on fitting into EM map 1534.

2y7c, resolution 18.00Å

Structural highlights

2y7c is a 5 chain structure with sequence from Escherichia coli and Escherichia phage T7. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 18Å
Experimental data:	Check
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

T1SK_ECOLI

Publication Abstract from PubMed

Type-I DNA restriction-modification (R/M) systems are important agents in limiting the transmission of mobile genetic elements responsible for spreading bacterial resistance to antibiotics. EcoKI, a Type I R/M enzyme from Escherichia coli, acts by methylation- and sequence-specific recognition, leading to either methylation of DNA or translocation and cutting at a random site, often hundreds of base pairs away. Consisting of one specificity subunit, two modification subunits, and two DNA translocase/endonuclease subunits, EcoKI is inhibited by the T7 phage antirestriction protein ocr, a DNA mimic. We present a 3D density map generated by negative-stain electron microscopy and single particle analysis of the central core of the restriction complex, the M.EcoKI M(2)S(1) methyltransferase, bound to ocr. We also present complete atomic models of M.EcoKI in complex with ocr and its cognate DNA giving a clear picture of the overall clamp-like operation of the enzyme. The model is consistent with a large body of experimental data on EcoKI published over 40 years.

The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein.,Kennaway CK, Obarska-Kosinska A, White JH, Tuszynska I, Cooper LP, Bujnicki JM, Trinick J, Dryden DT Nucleic Acids Res. 2009 Feb;37(3):762-70. Epub 2008 Dec 11. PMID:19074193^[1]

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

References

↑ Kennaway CK, Obarska-Kosinska A, White JH, Tuszynska I, Cooper LP, Bujnicki JM, Trinick J, Dryden DT. The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein. Nucleic Acids Res. 2009 Feb;37(3):762-70. Epub 2008 Dec 11. PMID:19074193 doi:10.1093/nar/gkn988

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OCA

[1] Kennaway CK, Obarska-Kosinska A, White JH, Tuszynska I, Cooper LP, Bujnicki JM, Trinick J, Dryden DT. The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein. Nucleic Acids Res. 2009 Feb;37(3):762-70. Epub 2008 Dec 11. PMID:19074193 doi:10.1093/nar/gkn988

[1]

@@ Line 1: / Line 1: @@
 ==Atomic model of the Ocr-bound methylase complex from the Type I restriction-modification enzyme EcoKI (M2S1). Based on fitting into EM map 1534.==
-<StructureSection load='2y7c' size='340' side='right'caption='[[2y7c]], [[Resolution|resolution]] 18.00&Aring;' scene=''>
+<SX load='2y7c' size='340' side='right' viewer='molstar' caption='[[2y7c]], [[Resolution|resolution]] 18.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2y7c]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt7 Bpt7] and [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y7C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Y7C FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2y7c]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Escherichia_phage_T7 Escherichia phage T7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y7C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Y7C FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1s7z|1s7z]], [[2y7h|2y7h]], [[2ar0|2ar0]], [[1yf2|1yf2]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 18&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Type_I_site-specific_deoxyribonuclease Type I site-specific deoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.3 3.1.21.3] </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=2y7c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y7c OCA], [https://pdbe.org/2y7c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2y7c RCSB], [https://www.ebi.ac.uk/pdbsum/2y7c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2y7c ProSAT]</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=2y7c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y7c OCA], [http://pdbe.org/2y7c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2y7c RCSB], [http://www.ebi.ac.uk/pdbsum/2y7c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2y7c ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/T1MK_ECOLI T1MK_ECOLI]] The M and S subunits together form a methyltransferase (MTase) that methylates two adenine residues in complementary strands of a bipartite DNA recognition sequence. In the presence of the R subunit the complex can also act as an endonuclease, binding to the same target sequence but cutting the DNA some distance from this site. Whether the DNA is cut or modified depends on the methylation state of the target sequence. When the target site is unmodified, the DNA is cut. When the target site is hemimethylated, the complex acts as a maintenance MTase modifying the DNA so that both strands become methylated. The EcoKI enzyme recognizes 5'-AACN(6)GTGC-3'.
+[https://www.uniprot.org/uniprot/T1SK_ECOLI T1SK_ECOLI]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 21: @@
 <references/>
 __TOC__
-</StructureSection>
+</SX>
-[[Category: Bpt7]]
 [[Category: Escherichia coli]]
+[[Category: Escherichia phage T7]]
 [[Category: Large Structures]]
-[[Category: Type I site-specific deoxyribonuclease]]
+[[Category: Bujnicki JM]]
-[[Category: Bujnicki, J M]]
+[[Category: Cooper LP]]
-[[Category: Cooper, L P]]
+[[Category: Dryden DTF]]
-[[Category: Dryden, D T.F]]
+[[Category: Kennaway CK]]
-[[Category: Kennaway, C K]]
+[[Category: Obarska-Kosinska A]]
-[[Category: Obarska-Kosinska, A]]
+[[Category: Trinick J]]
-[[Category: Trinick, J]]
+[[Category: Tuszynska I]]
-[[Category: Tuszynska, I]]
+[[Category: White JH]]
-[[Category: White, J H]]
-[[Category: Transferase]]

2y7c: Difference between revisions

Latest revision as of 21:17, 18 October 2023

Atomic model of the Ocr-bound methylase complex from the Type I restriction-modification enzyme EcoKI (M2S1). Based on fitting into EM map 1534.Atomic model of the Ocr-bound methylase complex from the Type I restriction-modification enzyme EcoKI (M2S1). Based on fitting into EM map 1534.

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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2y7c: Difference between revisions

Latest revision as of 21:17, 18 October 2023

Atomic model of the Ocr-bound methylase complex from the Type I restriction-modification enzyme EcoKI (M2S1). Based on fitting into EM map 1534.Atomic model of the Ocr-bound methylase complex from the Type I restriction-modification enzyme EcoKI (M2S1). Based on fitting into EM map 1534.

Structural highlights

Function

Publication Abstract from PubMed

References

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

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