Figure 1

Structural, phylogenetic, and sequence comparisons of HupF and HypC. A) Overlay of HupF (white) and HypC (blue) predicted structures. Structural predictions were carried out with the UCSF Chimera package from the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco ([26]; supported by NIH P41 RR001081), and were based on the structure of Thermococcus kodakarensis HypC (PDB 2z1c) and on ab initio predictions using the I-TASSER server [27]. Positions of N- and C-termini of each protein are indicated. B) Neighbour-joining phylogenetic tree of HupF and HypC. Sequences derived from the hupF and hypC genes listed in Table 1, along with those from R. leguminosarum (FRleg and CRleg) and R. eutropha (FReut, C1Reut, and C2Reut), were aligned with ClustalX, and the alignment was corrected for multiple substitutions and refined manually. Distances were generated with the same program using the neighbour-joining method, and bootstrapped (1000x). TREEVIEW was used to draw the most likely tree. Sequence names shown in the tree contain a first letter indicating HupF or HypC protein, followed by a number corresponding to that assigned to each species in Table 1. C) Sequence alignment of R. leguminosarum HupF and HypC proteins. Alignment was carried out on a structural basis using I-TASSER. Asterisks indicate conserved residues. Vertical arrow indicates the start point for the C-terminal deletion in HupF_CST.