Figure 3

A novel CP family detected by CPSARST. Entries 2b4lA ([PDB:2B4L], chain A), 1r9lA ([PDB:1R9L], chain A) and 1sw1A ([PDB:1SW1], chain A) are GBBPs. Entries 1atg ([PDB:1ATG]) and 1amf ([PDB:1AMF]) are molybdate-binding proteins (MoBPs) and 1al3 ([PDB:1AL3]) is the cysteine regulon transcriptional activator CysB from Klebsiella aerogenes. Any pair of these proteins share < 24% sequence identity (calculated by FASTA [48]). (a) Multiple sequence alignment of these GBBPs, MoBPs and CysB does not well reveal their functional and evolutionary relationships. Residues interacting with the ligands [65-67] are colored red; they are rather scattered. GBBPs and MoBPs are basically ligand transporters while CysB is a transcriptional regulator; however, the phylogram tree built from this alignment correlates CysB and MoBPs into the same branch and the three GBBPs are separated into two branches; these evolutionary relationships do not agree with their functional relatedness. (b) Multiple circularly permuted sequence alignment and structural superimposition of these six proteins. The numbers after '_cp' following PDB entry IDs stand for the residue numbers of the new amino termini after circular permutations, which are indicated by colored arrows. The ligand-interacting residues are better clustered in this alignment (gray regions) and the phylogram tree agrees well with the functional relatedness. The image of the superimposed proteins shows that these proteins have similar overall structures and the positions of their ligand-binding pockets are conserved (ligands are shown as yellow stick models); the colors used in this image are the same as in the alignment text and phylogram tree. Structures shown in this report were all drawn by using PyMOL [68]. Multiple sequence alignments and the tree building were performed by Clustal W [69].