1yf2

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:57, 14 February 2024) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1yf2.gif|left|200px]]
 
-
<!--
+
==Three-dimensional structure of DNA sequence specificity (S) subunit of a type I restriction-modification enzyme and its functional implications==
-
The line below this paragraph, containing "STRUCTURE_1yf2", creates the "Structure Box" on the page.
+
<StructureSection load='1yf2' size='340' side='right'caption='[[1yf2]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[1yf2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii_DSM_2661 Methanocaldococcus jannaschii DSM 2661]. 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 [https://proteopedia.org/fgij/fg.htm?mol=1YF2 FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</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=1yf2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yf2 OCA], [https://pdbe.org/1yf2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yf2 RCSB], [https://www.ebi.ac.uk/pdbsum/1yf2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yf2 ProSAT], [https://www.topsan.org/Proteins/BSGC/1yf2 TOPSAN]</span></td></tr>
-
{{STRUCTURE_1yf2| PDB=1yf2 | SCENE= }}
+
</table>
-
 
+
== Function ==
-
'''Three-dimensional structure of DNA sequence specificity (S) subunit of a type I restriction-modification enzyme and its functional implications'''
+
[https://www.uniprot.org/uniprot/T1S1_METJA 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 ==
-
 
+
[[Image:Consurf_key_small.gif|200px|right]]
-
==Overview==
+
Check<jmol>
-
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.
+
<jmolCheckbox>
-
 
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yf/1yf2_consurf.spt"</scriptWhenChecked>
-
==About this Structure==
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
1YF2 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii_dsm_2661 Methanocaldococcus jannaschii dsm 2661]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YF2 OCA].
+
<text>to colour the structure by Evolutionary Conservation</text>
-
 
+
</jmolCheckbox>
-
==Reference==
+
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1yf2 ConSurf].
-
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:[http://www.ncbi.nlm.nih.gov/pubmed/15728358 15728358]
+
<div style="clear:both"></div>
-
[[Category: Methanocaldococcus jannaschii dsm 2661]]
+
__TOC__
-
[[Category: Single protein]]
+
</StructureSection>
-
[[Category: Adams, P D.]]
+
[[Category: Large Structures]]
-
[[Category: BSGC, Berkeley Structural Genomics Center.]]
+
[[Category: Methanocaldococcus jannaschii DSM 2661]]
-
[[Category: Degiovanni, A.]]
+
[[Category: Adams PD]]
-
[[Category: Jancarik, J.]]
+
[[Category: Degiovanni A]]
-
[[Category: Kim, J S.]]
+
[[Category: Jancarik J]]
-
[[Category: Kim, R.]]
+
[[Category: Kim JS]]
-
[[Category: Kim, S H.]]
+
[[Category: Kim R]]
-
[[Category: Yokota, H A.]]
+
[[Category: Kim SH]]
-
[[Category: Berkeley structural genomics center]]
+
[[Category: Yokota HA]]
-
[[Category: Bsgc]]
+
-
[[Category: Protein structure initiative]]
+
-
[[Category: Psi]]
+
-
[[Category: S-subunit]]
+
-
[[Category: Structural genomic]]
+
-
[[Category: Type i restriction modification enzyme]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 16:14:38 2008''
+

Current revision

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

PDB ID 1yf2

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

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