1nw6: Difference between revisions

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-{{Seed}}
-[[Image:1nw6.png|left|200px]]
-<!--
+==Structure of the beta class N6-adenine DNA methyltransferase RsrI bound to sinefungin==
-The line below this paragraph, containing "STRUCTURE_1nw6", creates the "Structure Box" on the page.
+<StructureSection load='1nw6' size='340' side='right'caption='[[1nw6]], [[Resolution|resolution]] 1.94&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'>[[1nw6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cereibacter_sphaeroides Cereibacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NW6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NW6 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]] 1.94&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SFG:SINEFUNGIN'>SFG</scene></td></tr>
-{{STRUCTURE_1nw6|  PDB=1nw6  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nw6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nw6 OCA], [https://pdbe.org/1nw6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nw6 RCSB], [https://www.ebi.ac.uk/pdbsum/1nw6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nw6 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MTR1_CERSP MTR1_CERSP] A beta subtype methylase, recognizes the double-stranded sequence 5'-GAATTC-3', methylates A-3 on both strands, and protects the DNA from cleavage by the RsrI endonuclease.<ref>PMID:2690017</ref> <ref>PMID:12654995</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nw/1nw6_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1nw6 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structures of RsrI DNA methyltransferase (M.RsrI) bound to the substrate S-adenosyl-l-methionine (AdoMet), the product S-adenosyl-l-homocysteine (AdoHcy), the inhibitor sinefungin, as well as a mutant apo-enzyme have been determined by x-ray crystallography. Two distinct binding configurations were observed for the three ligands. The substrate AdoMet adopts a bent shape that directs the activated methyl group toward the active site near the catalytic DPPY motif. The product AdoHcy and the competitive inhibitor sinefungin bind with a straight conformation in which the amino acid moiety occupies a position near the activated methyl group in the AdoMet complex. Analysis of ligand binding in comparison with other DNA methyltransferases reveals a small, common subset of available conformations for the ligand. The structures of M.RsrI with the non-substrate ligands contained a bound chloride ion in the AdoMet carboxylate-binding pocket, explaining its inhibition by chloride salts. The L72P mutant of M.RsrI is the first DNA methyltransferase structure without bound ligand. With respect to the wild-type protein, it had a larger ligand-binding pocket and displayed movement of a loop (223-227) that is responsible for binding the ligand, which may account for the weaker affinity of the L72P mutant for AdoMet. These studies show the subtle changes in the tight specific interactions of substrate, product, and an inhibitor with M.RsrI and help explain how each displays its unique effect on the activity of the enzyme.
-===Structure of the beta class N6-adenine DNA methyltransferase RsrI bound to sinefungin===
+Structures of liganded and unliganded RsrI N6-adenine DNA methyltransferase: a distinct orientation for active cofactor binding.,Thomas CB, Scavetta RD, Gumport RI, Churchill ME J Biol Chem. 2003 Jul 11;278(28):26094-101. Epub 2003 May 4. PMID:12732637<ref>PMID:12732637</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1nw6" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12732637}}, adds the Publication Abstract to the page
+*[[DNA methyltransferase 3D structures|DNA methyltransferase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12732637 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12732637}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Cereibacter sphaeroides]]
-NW6 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NW6 OCA].
+[[Category: Large Structures]]
+[[Category: Churchill MEA]]
-==Reference==
+[[Category: Gumport RI]]
-Structures of liganded and unliganded RsrI N6-adenine DNA methyltransferase: a distinct orientation for active cofactor binding., Thomas CB, Scavetta RD, Gumport RI, Churchill ME, J Biol Chem. 2003 Jul 11;278(28):26094-101. Epub 2003 May 4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12732637 12732637]
+[[Category: Scavetta RD]]
-[[Category: Rhodobacter sphaeroides]]
+[[Category: Thomas CB]]
-[[Category: Single protein]]
-[[Category: Churchill, M E.A.]]
-[[Category: Gumport, R I.]]
-[[Category: Scavetta, R D.]]
-[[Category: Thomas, C B.]]
-[[Category: Adenine dna methyltransferase]]
-[[Category: Rossmann fold]]
-[[Category: Sinefungin]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 04:55:11 2008''