From Protein Structure to Function with Bioinformatics.pdf

8 3D Motifs 199Fig. 8.3 The FFF motif for the disulphide oxidoreductase active site is found in many proteins.Illustrated are T4 glutaredoxin, 1aaz, chain A (left), human thioredoxin, 4trx (middle) and prolinedisulphide isomerase, 1dsb, chain A (right). The three key residues which define this FFF are twocysteines (red side chains) and a proline (cyan side chain). The active site structure of these proteinsis conserved, although the rest of the protein structures exhibit some differences. Using thesethree key residues, the active site signature for each protein was identified (fragments shown asblue ribbons in each protein). Global sequence alignment, produced using ClustalW, of these threeproteins shows the location of the key residues (red and cyan, underlined) and the active site signaturefragments (blue) within the whole sequence. The alignment illustrates the lack of overallsequence similarity between the three proteins, even though the active site structure itself is highlyconservedThe program SPASM (SPatial Arrangements of Sidechains and Mainchains)represents each residue in a 3D motif by its alpha-carbon (CA) and/or side chaincentroid (SC) (Kleywegt 1999). The user specifies which residue types areallowed to match each residue in the motif, and hits are identified by a depthfirstexhaustive search. Intra-motif CA-CA and SC-SC distance tolerances areused to eliminate possibilities before the patterns are superimposed to calculateRMSD. Sequence order constraints are optional. Examples included using anactive-site pattern of three acidic residues to recognize a family of glucanases.SPASM executables and related files can be downloaded from the UppsalaSoftware Factory (see Table 8.2).The Babbitt group used SPASM with not only family motifs, each associatedwith a single function (reaction catalyzed), but also superfamily motifs associatedwith a common mechanistic step in different overall reactions (Meng et al. 2004).