Quaternary structure of E. coli ATCase. (A) Holoenzyme viewed along the threefold axis. Catalytic chains are numbered C1 to C6, and regulatory chains are numbered R1 to R6. The different catalytic and regulatory subunits are indicated by different colors. The aspartate domain of the catalytic chain is designated asp, and the carbamoylphosphate domain is designated cp. The domains of the regulatory chain are named Zn for zinc domain and al for allosteric domain. (B) Binding mode of the bisubstrate analogue PALA (purple) to the active site of ATCase. Side chains are shown as sticks with atoms labeled by color (green, carbon; blue, nitrogen; red, oxygen). Apostrophes after residue numbers indicate the position of the residue in an adjacent polypeptide chain. The figures are based on data for the CTP-liganded structure and the bisubstrate analogue PALA-liganded structure, respectively (35, 51).

Structural prototypes of CM enzymes and binding mode of a stable transition state analogue. (A) Schematic presentations of the structural folds displayed by CMs from B. subtillis (BsCM) (left), E. coli (EcCM) (middle), and ScCM (right). The helix numbers in parentheses indicate the corresponding helices in the yeast enzyme. The polypeptide backbone is displayed in ribbon style, and secondary elements are labeled with red cylinders (α-helices) and yellow bars (β-sheets). N and C termini are indicated, as are structural elements of ScCM (see the text for details). (B) Oligomeric structure of B. subtilis CM (left), E. coli CM (middle), and ScCM (right) in complex with a stable transition state analogue. Monomeric subunits are indicated by different shades of grey. For ScCM, the binding position of the positive effector tryptophan is also shown. (C) Section views of the catalytic sites of E. coli CM (left) and ScCM (right) with the transition state analogue (purple) bound. Side chains are shown as sticks with atoms labeled by colour (green, carbon; blue, nitrogen; red, oxygen). Apostrophes indicate the position of the residue in an adjacent polypeptide chain.

Superposition of the allosteric site in the T and R states of ScCM. The polypeptide backbones of helices H4-H5 and H8 are displayed in ribbon style. The residues necessary for binding of tyrosine (blue) and tryptophan (red) are shown as sticks with atoms labeled by color (green, carbon; blue, nitrogen; red, oxygen). Apostrophes indicate the position of the residue in an adjacent polypeptide chain. The dimer in the T state is superimposed onto the dimer in the R state by using residues 1 to 214 and 224 to 254.

Triads of residues functioning as molecular switches in intramolecular signaling. On the T-R transition, rearrangements occur between residues Glu23, Tyr234, and Arg157 of ScCM (A) and between residues Glu50, Arg167, and Arg234 of ATCase (B). α-Helices and β-strands are outlined as ribbons.

Claisen rearrangement of chorismic acid resulting in prephenic acid. The two conformers of chorismate, as well as the proposed transition state finally leading to prephenate, are shown.

Binding mode of the endo-oxabicyclic inhibitor to the active site of ScCM. The stable transition analogue is highlighted in red, and residues Arg157 and Glu246 are shown in green and blue, respectively. Hydrogen bond interactions are indicated by dotted lines. Corresponding residues of E. coli CM are indicated in parentheses. Apostrophes indicate the position of the residue in an adjacent polypeptide chain.

Intramolecular signaling pathway. A section of the ScCM dimer is presented in the T state (top), R state (middle), or super R state (bottom). The polypeptide backbone is drawn in ribbon style. The residues which change their position during allosteric transition and thereby transduce the signal of effector binding from the allosteric to the active site are shown as stick models (green, carbon; blue, nitrogen; red, oxygen). Hydrogen bonds are indicated by black lines. The position of the catalytic site inhibitor in the T and R state is derived from a superposition with the super R state structure using residues 1 to 214 and 224 to 254. Tyrosine is colored blue, tryptophan is red, and the bicyclic inhibitor is green.