Figure 1.
The Occurrence of Specific Peptides within the EC Hierarchy of Enzymes
(A) A sketch of the EC hierarchy and the assignments of SPs to SP classes. SPs can be compared with those appearing in Figure 1B.
(B) Aligned sequences of two groups of enzymes of level 4 that share the same third-level assignment. Alignment is performed according to SPs. The organisms in the upper group, 5.1.3.20, belong to proteobacteria, while those of the lower group, 5.1.3.2, also contain eukaryotes (ARATH, CYATE, and PEA). Boldfaced substrings denote SPs. Amino acids flanked by spaces denote active sites and binding sites, as indicated above. A list of all SPs and their assignments to SPN classes is presented below the sequences.
Table 1.
Specific Peptides in All Six Classes of Swiss-Prot Release 48.3
Table 2.
Performance of SPs Extracted from the Swiss-Prot 45 Dataset on Novel Enzyme Sequences in Swiss-Prot 48.3
Table 3.
Coverage of a Non-Redundant Test Set by Motifs in SP1, SP2, and SP3
Table 4.
Enzymes with High Sequence Similarity and Different EC Assignments
Table 5.
Occurrence of Specific Peptides on Active Sites
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.
Table 6.
Occurrence of SPs in Spatial Proximity to Active Sites
Table 7.
Small Sets of SPs that Contain Active Sites Suffice To Specify Functionality of Many Enzymes