3djl: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,615 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,615 edits
No edit summary
 
(8 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Seed}}
[[Image:3djl.jpg|left|200px]]


<!--
==Crystal structure of alkylation response protein E. coli AidB==
The line below this paragraph, containing "STRUCTURE_3djl", creates the "Structure Box" on the page.
<StructureSection load='3djl' size='340' side='right'caption='[[3djl]], [[Resolution|resolution]] 1.70&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'>[[3djl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DJL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DJL FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
-->
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aidB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
{{STRUCTURE_3djl|  PDB=3djl  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3djl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3djl OCA], [https://pdbe.org/3djl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3djl RCSB], [https://www.ebi.ac.uk/pdbsum/3djl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3djl ProSAT]</span></td></tr>
</table>
== Function ==
[[https://www.uniprot.org/uniprot/AIDB_ECOLI AIDB_ECOLI]] Part of the adaptive DNA-repair response to alkylating agents. Could prevent alkylation damage by protecting DNA and destroying alkylating agents that have yet to reach their DNA target. Binds to double-stranded DNA with a preference for a DNA region that includes its own promoter. Shows weak isovaleryl-CoA dehydrogenase activity in vitro.<ref>PMID:7961409</ref> <ref>PMID:16352838</ref> <ref>PMID:18829440</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/dj/3djl_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=3djl ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Exposure of Escherichia coli to alkylating agents activates expression of AidB in addition to DNA repair proteins Ada, AlkA, and AlkB. AidB was recently shown to possess a flavin adenine dinucleotide (FAD) cofactor and to bind to dsDNA, implicating it as a flavin-dependent DNA repair enzyme. However, the molecular mechanism by which AidB acts to reduce the mutagenic effects of specific DNA alkylators is unknown. We present a 1.7-A crystal structure of AidB, which bears superficial resemblance to the acyl-CoA dehydrogenase superfamily of flavoproteins. The structure reveals a unique quaternary organization and a distinctive FAD active site that provides a rationale for AidB's limited dehydrogenase activity. A highly electropositive C-terminal domain not present in structural homologs was identified by mutational analysis as the DNA binding site. Structural analysis of the DNA and FAD binding sites provides evidence against AidB-catalyzed DNA repair and supports a model in which AidB acts to prevent alkylation damage by protecting DNA and destroying alkylating agents that have yet to reach their DNA target.


===Crystal structure of alkylation response protein E. coli AidB===
Structure and DNA binding of alkylation response protein AidB.,Bowles T, Metz AH, O'Quin J, Wawrzak Z, Eichman BF Proc Natl Acad Sci U S A. 2008 Oct 7;105(40):15299-304. Epub 2008 Sep 30. PMID:18829440<ref>PMID:18829440</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
==About this Structure==
</div>
3DJL is a [[Single protein]] structure of sequence 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=3DJL OCA].
<div class="pdbe-citations 3djl" style="background-color:#fffaf0;"></div>
[[Category: Escherichia coli]]
== References ==
[[Category: Single protein]]
<references/>
[[Category: Bowles, T.]]
__TOC__
[[Category: Eichman, B F.]]
</StructureSection>
[[Category: Metz, A H.]]
[[Category: Bacillus coli migula 1895]]
[[Category: Large Structures]]
[[Category: Bowles, T]]
[[Category: Eichman, B F]]
[[Category: Metz, A H]]
[[Category: Alpha helix]]
[[Category: Alpha helix]]
[[Category: Beta-barrel]]
[[Category: Beta-barrel]]
Line 25: Line 43:
[[Category: Flavoprotein]]
[[Category: Flavoprotein]]
[[Category: Oxidoreductase]]
[[Category: Oxidoreductase]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 24 10:41:05 2008''
Retrieved from "https://proteopedia.org/3djl"