Functional Representation of Enzymes by Specific Peptides
Figure 2
SPs Occurrence on a Spatial Structure of an Enzyme
(A) 3-D display of enzyme P07649 (PDB code 1DJ0), belonging to 5.4.99.12, showing (1) an active site D at sequence location 60; (2) a binding site Y at location 118; (3) a binding site L at location 245. The active site is common to two SPs (4) containing (CAGRT(D)AGVH). Other shown SPs are (5) GQVVH at locations 67–71; (6) FHARF at 107–111, known to be a tentative RNA-binding peptide; (7) ENDFTS at 157–163; and (8) HMVRNI at 201–207, sharing a pocket with the active and binding sites. QVVH and ENDFTS belong to SP3, all other peptides belong to SP4.
(B) A different display of the same enzyme focuses on the pocket containing the active site. The relevant section of the sequence is shown, with red residues signifying active and binding sites, green residues corresponding to other amino acids residing in the pocket, and underlined residues corresponding to SPs.