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1yf2

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Revision as of 06:59, 25 April 2018

Three-dimensional structure of DNA sequence specificity (S) subunit of a type I restriction-modification enzyme and its functional implications

Structural highlights

1yf2 is a 2 chain structure with sequence from Metja. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

[T1S1_METJA] 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. Subunit S dictates DNA sequences specificity (By similarity).

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Type I restriction-modification enzymes are differentiated from type II and type III enzymes by their recognition of two specific dsDNA sequences separated by a given spacer and cleaving DNA randomly away from the recognition sites. They are oligomeric proteins formed by three subunits: a specificity subunit, a methylation subunit, and a restriction subunit. We solved the crystal structure of a specificity subunit from Methanococcus jannaschii at 2.4-A resolution. Two highly conserved regions (CRs) in the middle and at the C terminus form a coiled-coil of long antiparallel alpha-helices. Two target recognition domains form globular structures with almost identical topologies and two separate DNA binding clefts with a modeled DNA helix axis positioned across the CR helices. The structure suggests that the coiled-coil CRs act as a molecular ruler for the separation between two recognized DNA sequences. Furthermore, the relative orientation of the two DNA binding clefts suggests kinking of bound dsDNA and exposing of target adenines from the recognized DNA sequences.

Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications.,Kim JS, DeGiovanni A, Jancarik J, Adams PD, Yokota H, Kim R, Kim SH Proc Natl Acad Sci U S A. 2005 Mar 1;102(9):3248-53. Epub 2005 Feb 22. PMID:15728358^[1]

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

References

↑ Kim JS, DeGiovanni A, Jancarik J, Adams PD, Yokota H, Kim R, Kim SH. Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications. Proc Natl Acad Sci U S A. 2005 Mar 1;102(9):3248-53. Epub 2005 Feb 22. PMID:15728358

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1yf2"

@@ Line 1: / Line 1: @@
 ==Three-dimensional structure of DNA sequence specificity (S) subunit of a type I restriction-modification enzyme and its functional implications==
 <StructureSection load='1yf2' size='340' side='right' caption='[[1yf2]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
 <table><tr><td colspan='2'>[[1yf2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Metja Metja]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YF2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YF2 FirstGlance]. <br>
-</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=1yf2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yf2 OCA], [http://pdbe.org/1yf2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yf2 RCSB], [http://www.ebi.ac.uk/pdbsum/1yf2 PDBsum], [http://www.topsan.org/Proteins/BSGC/1yf2 TOPSAN]</span></td></tr>
+</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=1yf2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yf2 OCA], [http://pdbe.org/1yf2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yf2 RCSB], [http://www.ebi.ac.uk/pdbsum/1yf2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yf2 ProSAT], [http://www.topsan.org/Proteins/BSGC/1yf2 TOPSAN]</span></td></tr>
 </table>
 == Function ==
@@ Line 11: / Line 12: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yf/1yf2_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yf/1yf2_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

1yf2

From Proteopedia

Revision as of 06:59, 25 April 2018

Three-dimensional structure of DNA sequence specificity (S) subunit of a type I restriction-modification enzyme and its functional implications

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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