We apologize for Proteopedia being slow to respond. For the past two years, a new implementation of Proteopedia has been being built. Soon, it will replace this 18-year old system. All existing content will be moved to the new system at a date that will be announced here.

3bi3

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "3bi3" [edit=sysop:move=sysop])
Line 1: Line 1:
-
[[Image:3bi3.png|left|200px]]
+
==X-ray structure of AlkB protein bound to dsDNA containing 1meA/A with cofactors==
 +
<StructureSection load='3bi3' size='340' side='right' caption='[[3bi3]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[3bi3]] is a 3 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=3BI3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BI3 FirstGlance]. <br>
 +
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene><br>
 +
<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2YR:2-DEOXY-N-(2-SULFANYLETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>2YR</scene>, <scene name='pdbligand=MA7:1N-METHYLADENOSINE-5-MONOPHOSPHATE'>MA7</scene></td></tr>
 +
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2fd8|2fd8]], [[2bhz|2bhz]], [[2iuw|2iuw]], [[3bhz|3bhz]]</td></tr>
 +
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">alkB, aidD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
 +
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3bi3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bi3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bi3 RCSB], [http://www.ebi.ac.uk/pdbsum/3bi3 PDBsum]</span></td></tr>
 +
<table>
 +
== 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/bi/3bi3_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/chain_selection.php?pdb_ID=2ata ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Escherichia coli AlkB and its human homologues ABH2 and ABH3 repair DNA/RNA base lesions by using a direct oxidative dealkylation mechanism. ABH2 has the primary role of guarding mammalian genomes against 1-meA damage by repairing this lesion in double-stranded DNA (dsDNA), whereas AlkB and ABH3 preferentially repair single-stranded DNA (ssDNA) lesions and can repair damaged bases in RNA. Here we show the first crystal structures of AlkB-dsDNA and ABH2-dsDNA complexes, stabilized by a chemical cross-linking strategy. This study reveals that AlkB uses an unprecedented base-flipping mechanism to access the damaged base: it squeezes together the two bases flanking the flipped-out one to maintain the base stack, explaining the preference of AlkB for repairing ssDNA lesions over dsDNA ones. In addition, the first crystal structure of ABH2, presented here, provides a structural basis for designing inhibitors of this human DNA repair protein.
-
{{STRUCTURE_3bi3| PDB=3bi3 | SCENE= }}
+
Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA.,Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice PA, He C Nature. 2008 Apr 24;452(7190):961-5. PMID:18432238<ref>PMID:18432238</ref>
-
===X-ray structure of AlkB protein bound to dsDNA containing 1meA/A with cofactors===
+
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-
 
+
</div>
-
{{ABSTRACT_PUBMED_18432238}}
+
== References ==
-
 
+
<references/>
-
==About this Structure==
+
__TOC__
-
[[3bi3]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BI3 OCA].
+
</StructureSection>
-
 
+
[[Category: Ecoli]]
-
==Reference==
+
-
<ref group="xtra">PMID:018432238</ref><references group="xtra"/>
+
-
[[Category: Escherichia coli k-12]]
+
[[Category: Yang, C G.]]
[[Category: Yang, C G.]]
[[Category: Yi, C.]]
[[Category: Yi, C.]]

Revision as of 06:49, 21 May 2014

X-ray structure of AlkB protein bound to dsDNA containing 1meA/A with cofactors

3bi3, resolution 1.90Å

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/3bi3"
Views
Personal tools
Navigation
Toolbox