Comparison of kinase and glutathione synthase folds.
"Open book" ribbon diagrams of PK, PIPK, SAICAR
synthase, and D-ala-D-ala ligase structures are drawn using the program MOLSCRIPT. The N-terminal
domain (bottom row) and the C-terminal domain (top row) are separated from each other for the purposes
of clarity. The domain interface (ATP-binding cleft) is facing up (open book). The N and C termini of the displayed
segment of a protein chain are labeled in roman upper case black letters as well as the numbers of the last and the
first residue in the N-terminal and the C-terminal domain, respectively. Secondary structural elements are labeled by
color-coded italicized letters: lower case is for β-strands and upper case is for α-helices
with letter colors corresponding
to the colors of the structural element. The αββ-unit, essential for ATP-binding is shown
in red. "Cofactor" is
shown in a dark blue wire presentation and is indicated on each domain to mark the binding site. Metal cations are
shown as orange balls. Catalytic, ATP and metal-binding residues are shown in a ball-and-stick representation.
(a) cAMP-dependent protein kinase in complex with adenylyl imidodiphosphate and Mn2+
(1cdk, residues B46-B298). The additional helices are shown in green. (b) Type IIb phosphatidylinositol phosphate
kinase (1bo1, residues B126-B416). (c) SAICAR synthase (1a48, residues 11-272). (d) D-ala-D-ala ligase
in complex with ADP and Mg2+ (2dln, residues 95-292). The N-terminal
domain of ATP-grasp fold (the "central" domain in the protein) is colored differently to emphasize the fold difference.
The additional structural elements in the C-terminal domain (compared to PKs) are shown in purple in (b),
(c) and (d). Dots stand for the disordered regions. (e) Structure-based sequence alignment of 1cdk, 1bo1, 1a48, and
2dln. The alignment was constructed using DALI and corrected manually to incorporate
additional elements and adjust several regions. Color and letter-coding of structural elements in the sequence is as
described for (a), (b), (c) and (d). The chain ID (where available) and the residue number of the first amino acid in
each line and the last amino acid in the alignment are indicated. Numbers in parentheses interrupting the sequence
indicate the number of residues in insertions not displayed in the alignment. Residues disordered in the structure are
shown in lower case letters. Residues that form the conserved hydrophobic core are shown in bold letters. Residues
that participate in catalysis, ATP and metal cation binding (displayed in ball-and-stick models in (a), (b), (c) and (d))
and catalysis are shown in white on black.