Structure of reverse gyrase with a minimal latch that supports ATP-dependent positive supercoiling without specific interactions with the topoisomerase domain

Mhaindarkar, V.P.; Rasche, R.; Kümmel, D.; Rudolph, M.G.; Klostermeier, D.

doi:10.1107/S2059798323002565

Figure 5
Properties of the reverse gyrase latch regions. (a) Length distribution. The horizontal axis is given in bin widths of five residues. A single number or a smaller bin width is stated if the actual sequence lengths in that bin were narrower than the bin width (for example the first cluster has only three sequences, all of which comprise 13 residues and belong to Thermosipho). The number on top of the bars states the number of members per bin. The lengths of the latch regions of 184 reverse gyrases fall into three clusters, which are colored differently. (b) Phylogenetic tree of 184 reverse gyrases. The latch length clusters, highlighted in red (13 residues), blue (59–82) and black (89–119), are also clustered when reverse gyrases are grouped in terms of evolutionary relationship. The single exception in this set, marked with a red dot, is reverse gyrase from an as yet unclassified Thermotogae bacterium with a latch length of only 59 residues. The three main clades of the tree are color-coded in gray (1), light blue (2) and blue (3). The branch within clade 2 containing T. africanus reverse gyrase is highlighted in red. The reverse gyrases that were selected for further structural analysis (Fig. 6

) are labelled. A.fu., A. fulgidus; C.te., Caldanaerobacter subterraneus subsp. tengcongensis; D.am., Desulfurococcus amylolyticus; P.ca., Pyrobaculum calidifontis; P.fu., Pyrococcus furiosus; S.so., Saccharolobus solfataricus; S.to., Sulfurisphaera tokodaii; T.af., Thermosipho africanus; T.ma., T. maritima. An annotated version of the tree is given in Supplementary Fig. S3. (c) Electrostatics. The overall charge of the latch at neutral pH, calculated as stated in Section 2

and divided by the length of the latch, is plotted against latch length. Almost two thirds (62%) of the latch regions have an overall positive charge. The red data points (two at zero and one at −0.15) belong to the three Thermosipho sequences of only 13 residues.

STRUCTURAL
BIOLOGY

ISSN: 2059-7983

Volume 79| Part 6| June 2023| Pages 498-507

https://doi.org/10.1107/S2059798323002565

Open

access

Search IUCr Journals		doi		Advanced search
Author		volume	page