3jy1

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:06, 6 September 2023) (edit) (undo)
 
(7 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3jy1.jpg|left|200px]]
 
-
<!--
+
==Bacillus cereus Alkylpurine DNA Glycosylase AlkD Bound to DNA Containing an Abasic Site (across from C)==
-
The line below this paragraph, containing "STRUCTURE_3jy1", creates the "Structure Box" on the page.
+
<StructureSection load='3jy1' size='340' side='right'caption='[[3jy1]], [[Resolution|resolution]] 1.75&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'>[[3jy1]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_cereus_ATCC_10987 Bacillus cereus ATCC 10987]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JY1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JY1 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]] 1.754&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
-
{{STRUCTURE_3jy1| PDB=3jy1 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3jy1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jy1 OCA], [https://pdbe.org/3jy1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jy1 RCSB], [https://www.ebi.ac.uk/pdbsum/3jy1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jy1 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/Q816E8_BACCR Q816E8_BACCR]
 +
== 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/jy/3jy1_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=3jy1 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
DNA glycosylases that remove alkylated and deaminated purine nucleobases are essential DNA repair enzymes that protect the genome, and at the same time confound cancer alkylation therapy, by excising cytotoxic N3-methyladenine bases formed by DNA-targeting anticancer compounds. The basis for glycosylase specificity towards N3- and N7-alkylpurines is believed to result from intrinsic instability of the modified bases and not from direct enzyme functional group chemistry. Here we present crystal structures of the recently discovered Bacillus cereus AlkD glycosylase in complex with DNAs containing alkylated, mismatched and abasic nucleotides. Unlike other glycosylases, AlkD captures the extrahelical lesion in a solvent-exposed orientation, providing an illustration for how hydrolysis of N3- and N7-alkylated bases may be facilitated by increased lifetime out of the DNA helix. The structures and supporting biochemical analysis of base flipping and catalysis reveal how the HEAT repeats of AlkD distort the DNA backbone to detect non-Watson-Crick base pairs without duplex intercalation.
-
===Bacillus cereus Alkylpurine DNA Glycosylase AlkD Bound to DNA Containing an Abasic Site (across from C)===
+
An unprecedented nucleic acid capture mechanism for excision of DNA damage.,Rubinson EH, Gowda AS, Spratt TE, Gold B, Eichman BF Nature. 2010 Nov 18;468(7322):406-11. Epub 2010 Oct 3. PMID:20927102<ref>PMID:20927102</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 3jy1" style="background-color:#fffaf0;"></div>
-
==About this Structure==
+
==See Also==
-
3JY1 is a 3 chains structure with sequences from [http://en.wikipedia.org/wiki/Bacillus_cereus_atcc_10987 Bacillus cereus atcc 10987]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JY1 OCA].
+
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
-
[[Category: Bacillus cereus atcc 10987]]
+
== References ==
-
[[Category: Eichman, B F.]]
+
<references/>
-
[[Category: Rubinson, E H.]]
+
__TOC__
-
[[Category: Dna alkylation]]
+
</StructureSection>
-
[[Category: Dna binding]]
+
[[Category: Bacillus cereus ATCC 10987]]
-
[[Category: Dna glycosylase]]
+
[[Category: Large Structures]]
-
[[Category: Heat repeat]]
+
[[Category: Eichman BF]]
-
[[Category: Hydrolase-dna complex]]
+
[[Category: Rubinson EH]]
-
[[Category: Lyase-dna complex]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 22 14:44:13 2010''
+

Current revision

Bacillus cereus Alkylpurine DNA Glycosylase AlkD Bound to DNA Containing an Abasic Site (across from C)

PDB ID 3jy1

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/3jy1"
Personal tools