9BE2
Structure of the E. coli nucleic associated protein, YejK
Summary for 9BE2
| Entry DOI | 10.2210/pdb9be2/pdb |
| Descriptor | Nucleoid-associated protein YejK (1 entity in total) |
| Functional Keywords | nap, nucleoid associated protein, yejk, ndpa, dna binding clamp, non-sequence specific, dna binding protein |
| Biological source | Escherichia coli |
| Total number of polymer chains | 1 |
| Total formula weight | 38145.66 |
| Authors | Schumacher, M.A. (deposition date: 2024-04-13, release date: 2024-05-15, Last modification date: 2024-07-24) |
| Primary citation | Schumacher, M.A.,Singh, R.R.,Salinas, R. Structure of the E. coli nucleoid-associated protein YejK reveals a novel DNA binding clamp. Nucleic Acids Res., 52:7354-7366, 2024 Cited by PubMed Abstract: Nucleoid-associated proteins (NAPs) play central roles in bacterial chromosome organization and DNA processes. The Escherichia coli YejK protein is a highly abundant, yet poorly understood NAP. YejK proteins are conserved among Gram-negative bacteria but show no homology to any previously characterized DNA-binding protein. Hence, how YejK binds DNA is unknown. To gain insight into YejK structure and its DNA binding mechanism we performed biochemical and structural analyses on the E. coli YejK protein. Biochemical assays demonstrate that, unlike many NAPs, YejK does not show a preference for AT-rich DNA and binds non-sequence specifically. A crystal structure revealed YejK adopts a novel fold comprised of two domains. Strikingly, each of the domains harbors an extended arm that mediates dimerization, creating an asymmetric clamp with a 30 Å diameter pore. The lining of the pore is electropositive and mutagenesis combined with fluorescence polarization assays support DNA binding within the pore. Finally, our biochemical analyses on truncated YejK proteins suggest a mechanism for YejK clamp loading. Thus, these data reveal YejK contains a newly described DNA-binding motif that functions as a novel clamp. PubMed: 38832628DOI: 10.1093/nar/gkae459 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (3.56 Å) |
Structure validation
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