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

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

Protein Residues predicted as catalytica Non-detected catalytic residues Commentsb
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
  1. 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.