Detection of protein catalytic residues at high precision using local network properties

BMC Bioinformatics

Table 2 Results at the residue scale: detection of catalytic and functional residues over the proteins from the validation set.

Protein	Residues predicted as catalytic^a	Non-detected catalytic residues	Comments^b
TEM β-lactamase	Lys73, Glu166, Asp233, Lys234*	Ser70, Ser130	Lys234 forms H-bond with substrate analogue-binding water
Pancreatic phospholipase	Arg6, Glu46, His48, Asp49, Asp99	Gly30	Asp49 binds Ca
Alkylguanine-transferase	Tyr69, His71, His146, Arg147, Tyr158, Lys165, Glu172	Asn137, Cys145	Glu172→His146 activates Cys145 by deprotonation, Lys165 mutations affect activity
Ubiquitin-conjugating enzyme 1	Lys36, Asp55, Asp72	Cys88	Detected residues define a single site in structure
Phenylalanine hydroxylase	His138, Asp139, His143, Glu184*	Ser203	Asp139 forms H-bond with Fe-bound H₂O
Prolyl-isomerase 1	His59, Glu145, His157	Cys113	Glu145 plays a role in the two-domain arrangement of the protein
Ferric binding protein	His9, Glu57, Arg101, Arg103, Glu144, Glu264	Tyr195, Tyr196	Arg101 (not conserved) interacts with ligand, Glu57 interacts with ligand and binds iron
Bovine β-trypsin	His40, Asp189, Ser190, Asp194, Tyr228, Lys230	His57, Asp102, Gly193, Gly196, Ser214	Asp189 forms H-bond with substrate-bound water, Tyr228 is H-bonded to Asp189 through H₂O

^a All residues predicted using our scoring parameter at threshold MDev1. In bold, those also predicted at threshold MDev2. With * superscript, residues that are 'catalytic' according to CSA definition. Residues that are 'functional' according to our definition (see text) but not 'catalytic' according to CSA are underlined. ^bDerived from the analysis of multiple crystallized states. See text for references.

ISSN: 1471-2105