4DWL
Avd molecule from Bordetella bacteriophage DGR
Summary for 4DWL
| Entry DOI | 10.2210/pdb4dwl/pdb |
| Descriptor | Bbp7, PHOSPHATE ION (3 entities in total) |
| Functional Keywords | pentameric four helix bundle, accessory variability determinant from bordetella bacteriophage diversity generating retroelements, reverse transcriptase, phosphate binding protein, nucleic acid binding protein |
| Biological source | Bordetella phage BPP-1 |
| Total number of polymer chains | 5 |
| Total formula weight | 75139.18 |
| Authors | Ghosh, P.,Al-Ayyoubi, M. (deposition date: 2012-02-24, release date: 2013-02-27, Last modification date: 2024-11-06) |
| Primary citation | Alayyoubi, M.,Guo, H.,Dey, S.,Golnazarian, T.,Brooks, G.A.,Rong, A.,Miller, J.F.,Ghosh, P. Structure of the essential diversity-generating retroelement protein bAvd and its functionally important interaction with reverse transcriptase. Structure, 21:266-276, 2013 Cited by PubMed Abstract: 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 Å 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. PubMed: 23273427DOI: 10.1016/j.str.2012.11.016 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.69 Å) |
Structure validation
Download full validation report
