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| - | {{Large structure}}
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| | ==Crystal Structure of the E. coli adaptive response protein AidB in the space group P3(2)== | | ==Crystal Structure of the E. coli adaptive response protein AidB in the space group P3(2)== |
| - | <StructureSection load='3u33' size='340' side='right' caption='[[3u33]], [[Resolution|resolution]] 2.80Å' scene=''> | + | <StructureSection load='3u33' size='340' side='right'caption='[[3u33]], [[Resolution|resolution]] 2.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3u33]] is a 12 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=3U33 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3U33 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3u33]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U33 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U33 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3djl|3djl]]</td></tr> | + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3djl|3djl]]</div></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aidB, b4187, JW5867 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr> | + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aidB, b4187, JW5867 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3u33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u33 OCA], [http://pdbe.org/3u33 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3u33 RCSB], [http://www.ebi.ac.uk/pdbsum/3u33 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3u33 ProSAT]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3u33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u33 OCA], [https://pdbe.org/3u33 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u33 RCSB], [https://www.ebi.ac.uk/pdbsum/3u33 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u33 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| - | {{Large structure}} | |
| | == Function == | | == Function == |
| - | [[http://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> | + | [[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> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Ecoli]] | | [[Category: Ecoli]] |
| | + | [[Category: Large Structures]] |
| | [[Category: Drennan, C L]] | | [[Category: Drennan, C L]] |
| | [[Category: Jost, M]] | | [[Category: Jost, M]] |
| Structural highlights
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]
Publication Abstract from PubMed
The process known as "adaptive response" allows Escherichia coli to respond to small doses of DNA-methylating agents by upregulating the expression of four proteins. While the role of three of these proteins in mitigating DNA damage is well understood, the function of AidB is less clear. Although AidB is a flavoprotein, no catalytic role has been established for the bound cofactor. Here we investigate the possibility that flavin plays a structural role in the assembly of the AidB tetramer. We report the generation and biophysical characterization of deflavinated AidB and of an AidB mutant that has greatly reduced affinity for flavin adenine dinucleotide (FAD). Using fluorescence quenching and analytical ultracentrifugation, we find that apo AidB has a high affinity for FAD, as indicated by an apparent dissociation constant of 402.1 +/- 35.1 nM, and that binding of substoichiometric amounts of FAD triggers a transition in the AidB oligomeric state. In particular, deflavinated AidB is dimeric, whereas the addition of FAD yields a tetramer. We further investigate the dimerization and tetramerization interfaces of AidB by determining a 2.8 A resolution crystal structure in space group P3(2) that contains three intact tetramers in the asymmetric unit. Taken together, our findings provide strong evidence that FAD plays a structural role in the formation of tetrameric AidB.
Flavin-Induced Oligomerization in Escherichia coli Adaptive Response Protein AidB.,Hamill MJ, Jost M, Wong C, Elliott SJ, Drennan CL Biochemistry. 2011 Oct 27. PMID:22004173[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
- ↑ Hamill MJ, Jost M, Wong C, Elliott SJ, Drennan CL. Flavin-Induced Oligomerization in Escherichia coli Adaptive Response Protein AidB. Biochemistry. 2011 Oct 27. PMID:22004173 doi:10.1021/bi201340t
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