Hidden Relationship between Conserved Residues and Locally Conserved Phosphate-Binding Structures in NAD(P)-Binding Proteins

A one-dimensional (1D) motif usually comprises conserved
essential
residues involved in catalysis, ligand binding, or maintaining a specific
structure. However, it cannot be easily detected in proteins with
low sequence identity because it is difficult to (1) identify protein
sequences suspected to contain the motif, and (2) align sequences
with little sequence identity to spot the conserved residues. Here,
we present a strategy for discovering phosphate-binding 1D motifs
in NAD­(P)-binding proteins sharing low sequence identity that overcomes
these two hurdles by determining all distinct locally conserved pyrophosphate-binding
structures and aligning the same-length sequences comprising each
of these structures to identify the conserved residues. We show that
the sequence motifs derived from the distinct pyrophosphate-binding
structures yield different numbers/spacing of conserved Gly residues.
We also show that they depend on the side chain orientations and cofactor
type (NAD or NADP). Thus, sequence motifs derived from local similarity
of backbone structures without consideration of the cofactor type
and/or side chain orientations would reduce their reliability in annotating
protein function from sequence alone. The three-dimensional (3D) and
1D motifs comprising conserved residues in nonredundant proteins reveal
hidden relationships between the protein structure/function and sequence
as well as protein–cofactor interactions.