1TJL

Crystal structure of transcription factor DksA from E. coli

Summary for 1TJL

• Entry DOI: 10.2210/pdb1tjl/pdb
• Descriptor: DnaK suppressor protein, ZINC ION (3 entities in total)
• Functional Keywords: dksa, transcription factor, rna polymerase, stringent response, ppgpp, riken structural genomics/proteomics initiative, rsgi, structural genomics, transcription
• Biological source: Escherichia coli
• Cellular location: Cytoplasm: P0ABS1
• Total number of polymer chains: 10
• Total formula weight: 176201.96

Authors

Perederina, A.,Svetlov, V.,Vassylyeva, M.N.,Artsimovitch, I.,Yokoyama, S.,Vassylyev, D.G.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2004-06-06, release date: 2004-09-07, Last modification date: 2024-03-13)

Primary citation

Perederina, A.,Svetlov, V.,Vassylyeva, M.N.,Tahirov, T.H.,Yokoyama, S.,Artsimovitch, I.,Vassylyev, D.G.
Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription
Cell(Cambridge,Mass.), 118:297-309, 2004

PubMed Abstract: Bacterial transcription is regulated by the alarmone ppGpp, which binds near the catalytic site of RNA polymerase (RNAP) and modulates its activity. We show that the DksA protein is a crucial component of ppGpp-dependent regulation. The 2.0 A resolution structure of Escherichia coli DksA reveals a globular domain and a coiled coil with two highly conserved Asp residues at its tip that is reminiscent of the transcript cleavage factor GreA. This structural similarity suggests that DksA coiled coil protrudes into the RNAP secondary channel to coordinate a ppGpp bound Mg2+ ion with the Asp residues, thereby stabilizing the ppGpp-RNAP complex. Biochemical analysis demonstrates that DksA affects transcript elongation, albeit differently from GreA; augments ppGpp effects on initiation; and binds directly to RNAP, positioning the Asp residues near the active site. Substitution of these residues eliminates the synergy between DksA and ppGpp. Thus, the secondary channel emerges as a common regulatory entrance for transcription factors.

PubMed: 15294156
DOI: 10.1016/j.cell.2004.06.030

Experimental method

X-RAY DIFFRACTION (2 Å)