2fd8: Difference between revisions

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{{Seed}}
[[Image:2fd8.png|left|200px]]


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==Crystal Structure of AlkB in complex with Fe(II), 2-oxoglutarate, and methylated trinucleotide T-meA-T==
The line below this paragraph, containing "STRUCTURE_2fd8", creates the "Structure Box" on the page.
<StructureSection load='2fd8' size='340' side='right'caption='[[2fd8]], [[Resolution|resolution]] 2.30&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'>[[2fd8]] is a 2 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=2FD8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FD8 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]] 2.3&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=MA7:1N-METHYLADENOSINE-5-MONOPHOSPHATE'>MA7</scene></td></tr>
{{STRUCTURE_2fd8| PDB=2fd8 |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2fd8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fd8 OCA], [https://pdbe.org/2fd8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fd8 RCSB], [https://www.ebi.ac.uk/pdbsum/2fd8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fd8 ProSAT], [https://www.topsan.org/Proteins/NESGC/2fd8 TOPSAN]</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/fd/2fd8_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=2fd8 ConSurf].
<div style="clear:both"></div>


===Crystal Structure of AlkB in complex with Fe(II), 2-oxoglutarate, and methylated trinucleotide T-meA-T===
==See Also==
 
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
 
== References ==
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<references/>
The line below this paragraph, {{ABSTRACT_PUBMED_16482161}}, adds the Publication Abstract to the page
__TOC__
(as it appears on PubMed at http://www.pubmed.gov), where 16482161 is the PubMed ID number.
</StructureSection>
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[[Category: Escherichia coli K-12]]
{{ABSTRACT_PUBMED_16482161}}
[[Category: Large Structures]]
 
[[Category: Benach J]]
==About this Structure==
[[Category: Edstrom WC]]
2FD8 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FD8 OCA].
[[Category: Gibney BR]]
 
[[Category: Hunt JF]]
==Reference==
[[Category: Yu B]]
<ref group="xtra">PMID:16482161</ref><references group="xtra"/>
[[Category: Escherichia coli]]
[[Category: Benach, J.]]
[[Category: Edstrom, W C.]]
[[Category: Gibney, B R.]]
[[Category: Hunt, J F.]]
[[Category: NESG, Northeast Structural Genomics Consortium.]]
[[Category: Yu, B.]]
[[Category: Beta jellyroll]]
[[Category: Nesg]]
[[Category: Northeast structural genomics consortium]]
[[Category: Protein structure initiative]]
[[Category: Psi]]
[[Category: Structural genomic]]
 
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Retrieved from "https://proteopedia.org/2fd8"