Figure 3. with 2 supplements.

Ligand binding modes in E. coli PRPS type A and type B filaments. (A) Hexamer of type A filament. Each chain is marked with a different color. (B) ADP and R5P are identified on the active site of PRPS in type A filament, while allosteric site 1 is bound by Pi and allosteric site 2 is bound by ADP. The residues that interact with ligands are indicated. Residues in chain A number with the ^# symbol and in chain C number with the * symbol. Residues in red are conserved in various organisms. Each chain is marked with a different color(dash lines in cyan indicate hydrogen bonds). (C) Ligands of the active site of type A filament. ADP and Mg²⁺ occupy ATP binding sites at active sites. R5P and Mg²⁺ can also be seen in the active site. Residues in red are conserved in various organisms. Each chain is marked with a different color. (D) ADP in allosteric site 2 of type A filament. Residues in red are conserved in various organisms. Each chain is marked with a different color. (E) Hexamer of type B filament. Each chain is marked with a different color. (F) In type B filament, the ATP binding site of the active site is not bound by any ligand, while the R5P binding site and allosteric site 1 are bound by Pi. Residues in chain A number with the ^# symbol and in chain C number with the * symbol. Residues in red are conserved in various organisms. Each chain is marked with a different color(dash lines in yellow indicate hydrogen bonds).

Figure 3—figure supplement 1. Structure comparison of PRPS in various organisms.

(A) Structural comparison of ecPRPS models in type A and type B polymers, Legionella pneumophila PRPS (6NFE), human PRPS1 (2H06), Bacillus subtilis PRPS (1DKU) bound with phosphomethylphosphonic acid adenosyl ester and methyl phosphonic acid adenosine ester, and Bacillus subtilis PRPS (1DKR) containing sulfate ion. (B and C) Structure comparison of ecPRPS models in type A polymers and human PRPS1(2HCR). Ligands of the active sites and allosteric sites were displayed in (B). In the structure of human PRPS1(2HCR), AMP occupy ATP binding sites, SO₄²⁺ and Cd²⁺ bind in the R5P binding region. SO₄²⁺ can also be seen in the allosteric site 1 and allosteric site 2. In the structure of ecPRPS hexamer in type A polymers, ADP and Mg²⁺ occupy ATP binding sites, R5P and Mg²⁺ bind in the R5P binding region. Pi bind in the allosteric site 1, and ADP can be seen in the allosteric site 2. (C) Structure comparison of the allosteric 2 in ecPRPS type A polymers and human PRPS1. The residues that interact with ligands are indicated. Residues in the human PRPS1 structure number with the ’ symbol.

Figure 3—figure supplement 2. Comparison of PRPS sequences of various organisms.

Sequence alignment of Escherichia coli (strain K12), Salmonella typhimurium (strain LT2 /SGSC1412/ATCC 700720), Bacillus subtilis (strain 168), Mycobacterium tuberculosis (strain ATCC 25618/H37 Rv), Homo sapiens (Human), Mus musculus (Mouse) and Saccharomyces cerevisiae (strain ATCC 204508/S288 c) (Baker’s yeast). The conserved residues are indicated in red, and secondary structure elements are indicated above.