The Crystal Structure of a Hyperthermophilic Archaeal TATA-box Binding Protein

Abstract

This study analyzes the three-dimensional structure of the TATA-box properties. The crystal structure of this hyperthermostable protein was Cambridge University, compared to its mesophilic homologs and analyzed for differences in the Cambridge, CB2 1QR, UK native structure that may contribute to thermostability. Differences found were: (1) a disulfide bond not found in mesophilic counterparts; (2) an increased number of surface electrostatic interactions; (3) more compact protein packing. The presumed DNA binding surface of PwTBP, like its eukaryotic counterparts, is hydrophobic but the electrostatic profile surrounding the protein is relatively neutral compared to the asymmetric positive potential that surrounds eukaryotic TBPs. The total reliance on a hydrophobic interface with DNA may explain the enhanced affinity of PwTBP for its DNA promoter at higher temperatures and increased salt concentration.

Discrepancies between the NMR and X-ray Structures of Uncomplexed Barstar: Analysis Suggests That Packing Densities of Protein Structures Determined by NMR Are Unreliable,

“…We chose proteins for which both the crystal and NMR structures were available, either for the same structure or within the same protein family. Our analysis showed that all the protein structures solved by using crystallographic procedures had packing values lying within the narrow range of 0.34-0.37 ( Figure 5), as pointed out by DeDecker et al (38). The only exceptions were the well-packed hyperthermophilic TBP [packing value ) 0.375 (38)] and a metallothionein (packing value ) 0.25, 4MT2).…”

“…Our analysis showed that all the protein structures solved by using crystallographic procedures had packing values lying within the narrow range of 0.34-0.37 ( Figure 5), as pointed out by DeDecker et al (38). The only exceptions were the well-packed hyperthermophilic TBP [packing value ) 0.375 (38)] and a metallothionein (packing value ) 0.25, 4MT2). The crystal structures of proteins with different sequences but belonging to the same family showed very similar packing values (e.g., myoglobin: average, 0.35; standard deviation, 0.008).…”

“…The average side-chain rmsd for a similar comparison yields values of 1.06 and 1.11 Å, respectively. The main-chain residues of barstar (27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38)(39)(40)(41)(42)(43)(44)) that lie at the binding interface with barnase do not show significant deviations in comparison to the structure in the complex, except for Gly 43 ( Figures 2B, 3A, and 4A). Taking into consideration the resolution of this structure as well as the quality of the electron density map, the side-chain residues in the binding site which show significant changes in C82A when compared to 1BRS are Y29, D35, and D39 ( Figure 4A).…”

“…Model bias in the binding region (27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38)(39)(40)(41)(42)(43)(44) was minimized by rebuilding the region after SA σ Aweighted omit map calculations in X-PLOR. The last stage of refinement used all reflections and included constant temperature torsion angle refinement (500 K), positional refinement, and B-factor refinement with an NCS weight of 100 kcal mol -1 Å -1 .…”

Regulation of putative methyl‐sulphide methyltransferases in Methanosarcina acetivorans C2A

“…2). As is typical for archaeal promoters, the TSS of each gene is a purine residue with an appropriately spaced TATA box centred approximately 25 bp upstream (DeDecker et al, 1996). However, none of the promoters have an obvious purinerich BRE element (Qureshi and Jackson, 1998), instead having pyrimidine-rich (~66%) sequences immediately upstream of the putative TATA boxes.…”