Protein Family Models

DksA is a transcription factor that directly binds RNA polymerase and controls the bacteria response to stress and starvation. DksA is all helical and comprises a coiled-coil (CC) and globular domains [1-4]. This is the N-terminal domain which extends through the secondary channel toward the RNAP active site and serves as a conduit for the substrate NTPs. This domain consists of two helices arranged in an antiparallel alpha-hairpin with left-handed twist. Paper describing PDB structure 1tjl. [1]. 15294156. Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription. Perederina A, Svetlov V, Vassylyeva MN, Tahirov TH, Yokoyama S, Artsimovitch I, Vassylyev DG;. Cell. 2004;118:297-309. Paper describing PDB structure 3h3p. [2]. 19906921. Interactions between lipids and human anti-HIV antibody 4E10 can be reduced without ablating neutralizing activity. Xu H, Song L, Kim M, Holmes MA, Kraft Z, Sellhorn G, Reinherz EL, Stamatatos L, Strong RK;. J Virol. 2010;84:1076-1088. Paper describing PDB structure 4ijj. [3]. 23416301. DksA2, a zinc-independent structural analog of the transcription factor DksA. Furman R, Biswas T, Danhart EM, Foster MP, Tsodikov OV, Artsimovitch I;. FEBS Lett. 2013;587:614-619. Paper describing PDB structure 5vsw. [4]. 29478808. Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA. Molodtsov V, Sineva E, Zhang L, Huang X, Cashel M, Ades SE, Murakami KS;. Mol Cell. 2018;69:828-839. (from Pfam)

Date:

2024-10-16

Date:

2024-08-14

DksA (DnaK suppressor A) is a small, pleiotropic protein that binds RNA polymerase. It helps the signaling molecule ppGpp mediate the stringent response, causing changes in transcription initiation rates such as a dramatic decrease for rRNA. While forms of DksA are found broadly in bacteria, this HMM largely describes DksA as found in Proteobacteria.

Gene:

dksA

Date:

2024-06-04

RNA polymerase-binding protein DksA is required for negative regulation of rRNA expression and positive regulation of several amino acid biosynthesis promoters

Date:

2022-09-30