3djl

From Proteopedia

(Difference between revisions)

Revision as of 09:24, 14 November 2018

Crystal structure of alkylation response protein E. coli AidB

Structural highlights

3djl is a 1 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Gene:	aidB ("Bacillus coli" Migula 1895)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.^[1] ^[2] ^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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.

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^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Landini P, Hajec LI, Volkert MR. Structure and transcriptional regulation of the Escherichia coli adaptive response gene aidB. J Bacteriol. 1994 Nov;176(21):6583-9. PMID:7961409
↑ Rohankhedkar MS, Mulrooney SB, Wedemeyer WJ, Hausinger RP. The AidB component of the Escherichia coli adaptive response to alkylating agents is a flavin-containing, DNA-binding protein. J Bacteriol. 2006 Jan;188(1):223-30. PMID:16352838 doi:http://dx.doi.org/10.1128/JB.188.1.223-230.2006
↑ Bowles T, Metz AH, O'Quin J, Wawrzak Z, Eichman BF. Structure and DNA binding of alkylation response protein AidB. Proc Natl Acad Sci U S A. 2008 Oct 7;105(40):15299-304. Epub 2008 Sep 30. PMID:18829440 doi:10.1073/pnas.0806521105
↑ Bowles T, Metz AH, O'Quin J, Wawrzak Z, Eichman BF. Structure and DNA binding of alkylation response protein AidB. Proc Natl Acad Sci U S A. 2008 Oct 7;105(40):15299-304. Epub 2008 Sep 30. PMID:18829440 doi:10.1073/pnas.0806521105

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3djl"

@@ Line 1: / Line 1: @@
 ==Crystal structure of alkylation response protein E. coli AidB==
 <StructureSection load='3djl' size='340' side='right' caption='[[3djl]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
@@ Line 5: / Line 6: @@
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3djl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3djl OCA], [http://pdbe.org/3djl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3djl RCSB], [http://www.ebi.ac.uk/pdbsum/3djl PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3djl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3djl OCA], [http://pdbe.org/3djl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3djl RCSB], [http://www.ebi.ac.uk/pdbsum/3djl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3djl ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 13: / Line 14: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dj/3djl_consurf.spt"</scriptWhenChecked>
+    <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>

3djl

From Proteopedia

Revision as of 09:24, 14 November 2018

Crystal structure of alkylation response protein E. coli AidB

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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