Domenico:
This target belongs to the Pyridoxal phosphate-dependent transferase family. There's strong consensus on the binding site for PLP, which would include Tyr73, Gly109, Thr110, Gln111, Tyr135, Ser185, Asn189, Asp217, Leu219, Tyr220, Ser251, Lys252 and Arg260.
The potential catalytic residues would be Arg77, Tyr135, Asp217 and Lys252. However, Arg77 is likely to be a false positive, because it comes from homology-inferred sites in bifunctional enzymes or with rather different EC numbers - the target is expected to be in 2.6.1.1 while many annotations come from 4.x.x.x or 3.x.x.x. The remaining three amino acids match those of enzymes in the class 2.6.1.57, which makes more sense. I think we need to find a better way to parse CSA annotations, in case we want to set up a web server for the inference of ligand binding sites.
Contacts from metals are invalid and those from peptides are not enough for a reliable prediction.

PFRMAT FN
TARGET T0591
AUTHOR 7656-5034-1890
REMARK Sequence consensus of contacts between homologous structures and ligands
METHOD pGenTHREADER and PDBSum and CSA data mining.
MODEL 1
Binding site: 73, 109, 110, 111, 135, 185, 189, 217, 219, 220, 251, 252, 260
END

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« This page (revision-1) was last changed on 04-Jul-2010 19:26 by UnknownAuthor