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| | ==Avd molecule from Bordetella bacteriophage DGR== | | ==Avd molecule from Bordetella bacteriophage DGR== |
| - | <StructureSection load='4dwl' size='340' side='right' caption='[[4dwl]], [[Resolution|resolution]] 2.69Å' scene=''> | + | <StructureSection load='4dwl' size='340' side='right'caption='[[4dwl]], [[Resolution|resolution]] 2.69Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4dwl]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpbpp Bpbpp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DWL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DWL FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4dwl]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Bordetella_virus_BPP1 Bordetella virus BPP1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DWL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DWL FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.69Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bbp7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=194699 BPBPP])</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=4dwl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dwl OCA], [https://pdbe.org/4dwl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dwl RCSB], [https://www.ebi.ac.uk/pdbsum/4dwl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dwl ProSAT]</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=4dwl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dwl OCA], [http://pdbe.org/4dwl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dwl RCSB], [http://www.ebi.ac.uk/pdbsum/4dwl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dwl ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q775D7_BPBPP Q775D7_BPBPP] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bpbpp]] | + | [[Category: Bordetella virus BPP1]] |
| - | [[Category: Al-Ayyoubi, M]] | + | [[Category: Large Structures]] |
| - | [[Category: Ghosh, P]] | + | [[Category: Al-Ayyoubi M]] |
| - | [[Category: Accessory variability determinant from bordetella bacteriophage diversity generating retroelement]] | + | [[Category: Ghosh P]] |
| - | [[Category: Nucleic acid binding protein]]
| + | |
| - | [[Category: Pentameric four helix bundle]]
| + | |
| - | [[Category: Phosphate binding protein]]
| + | |
| - | [[Category: Reverse transcriptase]]
| + | |
| Structural highlights
Function
Q775D7_BPBPP
Publication Abstract from PubMed
Diversity-generating retroelements (DGRs) are the only known source of massive protein sequence variation in prokaryotes. These elements transfer coding information from a template region (TR) through an RNA intermediate to a protein-encoding variable region. This retrohoming process is accompanied by unique adenine-specific mutagenesis and, in the prototypical BPP-1 DGR, requires a reverse transcriptase (bRT) and an accessory variability determinant (bAvd) protein. To understand the role of bAvd, we determined its 2.69 A resolution structure, which revealed a highly positively charged pentameric barrel. In accordance with its charge, bAvd bound both DNA and RNA, albeit without a discernable sequence preference. We found that the coding sequence of bAvd functioned as part of TR but identified means to mutate bAvd without affecting TR. This mutational analysis revealed a strict correspondence between retrohoming and interaction of bAvd with bRT, suggesting that the bRT-bAvd complex is important for DGR retrohoming.
Structure of the essential diversity-generating retroelement protein bAvd and its functionally important interaction with reverse transcriptase.,Alayyoubi M, Guo H, Dey S, Golnazarian T, Brooks GA, Rong A, Miller JF, Ghosh P Structure. 2013 Feb 5;21(2):266-76. doi: 10.1016/j.str.2012.11.016. Epub 2012 Dec, 27. PMID:23273427[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Alayyoubi M, Guo H, Dey S, Golnazarian T, Brooks GA, Rong A, Miller JF, Ghosh P. Structure of the essential diversity-generating retroelement protein bAvd and its functionally important interaction with reverse transcriptase. Structure. 2013 Feb 5;21(2):266-76. doi: 10.1016/j.str.2012.11.016. Epub 2012 Dec, 27. PMID:23273427 doi:http://dx.doi.org/10.1016/j.str.2012.11.016
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