3sse

From Proteopedia

(Difference between revisions)

Revision as of 14:17, 5 August 2016

DNA binding domain of restriction endonuclease bound to DNA

Structural highlights

3sse is a 4 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	3ssc, 3ssd
Gene:	mcrB (ECOLI)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[MCRB_ECOLI] Recognizes N4- and C5-methylcytosine (and 5-hydroxy-methylcytosines) produced by a broad range of DNA methylases and appears to act against 5-methylcytosine preceded by a purine residue. Binds to DNA containing methylated cytosines; also binds to GTP. Isoform 33 kDa is less active than isoform 51 kDa and may play a role in regulating the activity of isoform 51 kDa by competing with it in DNA and protein binding abilities.

Publication Abstract from PubMed

DNA cytosine methylation is a widespread epigenetic mark. Biological effects of DNA methylation are mediated by the proteins that preferentially bind to 5-methylcytosine (5mC) in different sequence contexts. Until now two different structural mechanisms have been established for 5mC recognition in eukaryotes; however, it is still unknown how discrimination of the 5mC modification is achieved in prokaryotes. Here we report the crystal structure of the N-terminal DNA-binding domain (McrB-N) of the methyl-specific endonuclease McrBC from Escherichia coli. The McrB-N protein shows a novel DNA-binding fold adapted for 5mC-recognition. In the McrB-N structure in complex with methylated DNA, the 5mC base is flipped out from the DNA duplex and positioned within a binding pocket. Base flipping elegantly explains why McrBC system restricts only T4-even phages impaired in glycosylation [Luria, S.E. and Human, M.L. (1952) A nonhereditary, host-induced variation of bacterial viruses. J. Bacteriol., 64, 557-569]: flipped out 5-hydroxymethylcytosine is accommodated in the binding pocket but there is no room for the glycosylated base. The mechanism for 5mC recognition employed by McrB-N is highly reminiscent of that for eukaryotic SRA domains, despite the differences in their protein folds.

The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine.,Sukackaite R, Grazulis S, Tamulaitis G, Siksnys V Nucleic Acids Res. 2012 May 8. PMID:22570415^[1]

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

References

↑ Sukackaite R, Grazulis S, Tamulaitis G, Siksnys V. The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine. Nucleic Acids Res. 2012 May 8. PMID:22570415 doi:10.1093/nar/gks332

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/3sse"

@@ Line 1: / Line 1: @@
 ==DNA binding domain of restriction endonuclease bound to DNA==
 <StructureSection load='3sse' size='340' side='right' caption='[[3sse]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3sse]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SSE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SSE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3sse]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SSE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SSE FirstGlance]. <br>
 </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ssc|3ssc]], [[3ssd|3ssd]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mcrB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mcrB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3sse FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sse OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3sse RCSB], [http://www.ebi.ac.uk/pdbsum/3sse PDBsum]</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=3sse FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sse OCA], [http://pdbe.org/3sse PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3sse RCSB], [http://www.ebi.ac.uk/pdbsum/3sse PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3sse ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 17: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3sse" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Escherichia coli]]
+[[Category: Ecoli]]
 [[Category: Grazulis, S]]
 [[Category: Siksnys, V]]

3sse

From Proteopedia

Revision as of 14:17, 5 August 2016

DNA binding domain of restriction endonuclease bound to DNA

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox