3bie

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (05:42, 17 October 2024) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3bie.png|left|200px]]
 
-
<!--
+
==X-ray structure of E coli AlkB bound to dsDNA containing 1meA/T with Mn and 2KG==
-
The line below this paragraph, containing "STRUCTURE_3bie", creates the "Structure Box" on the page.
+
<StructureSection load='3bie' size='340' side='right'caption='[[3bie]], [[Resolution|resolution]] 1.68&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'>[[3bie]] is a 3 chain structure with sequence from [https://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=3BIE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BIE 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]] 1.68&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2YR:2-DEOXY-N-(2-SULFANYLETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>2YR</scene>, <scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MA7:1N-METHYLADENOSINE-5-MONOPHOSPHATE'>MA7</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-
{{STRUCTURE_3bie| PDB=3bie | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bie OCA], [https://pdbe.org/3bie PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bie RCSB], [https://www.ebi.ac.uk/pdbsum/3bie PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bie ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/ALKB_ECOLI ALKB_ECOLI] Dioxygenase that repairs alkylated DNA and RNA containing 3-methylcytosine or 1-methyladenine by oxidative demethylation. Has highest activity towards 3-methylcytosine. Has lower activity towards alkylated DNA containing ethenoadenine, and no detectable activity towards 1-methylguanine or 3-methylthymine. Accepts double-stranded and single-stranded substrates. Requires molecular oxygen, alpha-ketoglutarate and iron. Provides extensive resistance to alkylating agents such as MMS and DMS (SN2 agents), but not to MMNG and MNU (SN1 agents).<ref>PMID:12226668</ref> <ref>PMID:12594517</ref> <ref>PMID:16482161</ref> <ref>PMID:19706517</ref> <ref>PMID:21068844</ref> <ref>PMID:20084272</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/bi/3bie_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3bie 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.
-
===X-ray structure of E coli AlkB bound to dsDNA containing 1meA/T with Mn and 2KG===
+
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>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 3bie" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_18432238}}, adds the Publication Abstract to the page
+
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 18432238 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_18432238}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Escherichia coli K-12]]
-
3BIE is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BIE OCA].
+
[[Category: Large Structures]]
-
 
+
[[Category: Yang C-G]]
-
==Reference==
+
[[Category: Yi C]]
-
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:[http://www.ncbi.nlm.nih.gov/pubmed/18432238 18432238]
+
-
[[Category: Escherichia coli k12]]
+
-
[[Category: Protein complex]]
+
-
[[Category: Yang, C G.]]
+
-
[[Category: Yi, C.]]
+
-
[[Category: Alkylation repair]]
+
-
[[Category: Cross-linking]]
+
-
[[Category: Dioxygenase]]
+
-
[[Category: Oxidoreductase/dna complex]]
+
-
[[Category: Protein dna interaction]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 23 10:04:50 2008''
+

Current revision

X-ray structure of E coli AlkB bound to dsDNA containing 1meA/T with Mn and 2KG

PDB ID 3bie

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/3bie"
Personal tools