3n97 | pdb_00003n97

RNA polymerase alpha C-terminal domain (E. coli) and sigma region 4 (T. aq. mutant) bound to (UP,-35 element) DNA

spinqualitylabelsall models 3n97, resolution 3.25Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3n97 is a 6 chain structure with sequence from Escherichia coli K-12 and Thermus aquaticus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 3.252Å Ligands: ACT Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function SIGA_THEAQ Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the primary sigma factor during exponential growth.[HAMAP-Rule:MF_00963] Publication Abstract from PubMed We demonstrate here that the alpha subunit C-terminal domain of Escherichia coli RNA polymerase (alphaCTD) recognizes the upstream promoter (UP) DNA element via its characteristic minor groove shape and electrostatic potential. In two compositionally distinct crystallized assemblies, a pair of alphaCTD subunits bind in tandem to the UP element consensus A-tract that is 6 bp in length (A6-tract), each with their arginine 265 guanidinium group inserted into the minor groove. The A6-tract minor groove is significantly narrowed in these crystal structures, as well as in computationally predicted structures of free and bound DNA duplexes derived by Monte Carlo and molecular dynamics simulations, respectively. The negative electrostatic potential of free A6-tract DNA is substantially enhanced compared to that of generic DNA. Shortening the A-tract by 1 bp is shown to "knock out" binding of the second alphaCTD through widening of the minor groove. Furthermore, in computationally derived structures with arginine 265 mutated to alanine in either alphaCTD, either with or without the "knockout" DNA mutation, contact with the DNA is perturbed, highlighting the importance of arginine 265 in achieving alphaCTD-DNA binding. These results demonstrate that the importance of the DNA shape in sequence-dependent recognition of DNA by RNA polymerase is comparable to that of certain transcription factors. The RNA Polymerase alpha Subunit Recognizes the DNA Shape of the Upstream Promoter Element.,Lara-Gonzalez S, Dantas Machado AC, Rao S, Napoli AA, Birktoft J, Di Felice R, Rohs R, Lawson CL Biochemistry. 2020 Dec 8;59(48):4523-4532. doi: 10.1021/acs.biochem.0c00571. Epub, 2020 Nov 18. PMID:33205945 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also RNA polymerase 3D structures Sigma factor 3D structures

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