Domenico:
Both InterproScan and Genthreader back the hypothesis that this target is a geranyltranstransferase. Indeed, the potantial catalytic residues Arg103 and Phe220 are identically or higly conserved between the target and the closest templates.
Besides, this class of enzymes uses Mg as a cofactor, and ten Genthreader's hits are found in complex with this ion. The consensus from such contacts is Asp94, Asp98 and Asp224.
Finally, we need to list the residues in contact with the substrates - geranyl diphosphate and isopentenyl diphosphate. The following residues correspond to amino acids contacting a valid ligand in at least 4 out of 10 templates: Gly54, Lys55, Arg58, His87, Ser90, Leu91, Asp94, Asp98, Arg103, Arg104, Gln159, Lys183, Thr184, Leu187, Gln221, Asp224 and Lys238.

PFRMAT FN
TARGET T0584
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: 54, 55, 58, 87, 90, 91, 94, 98, 103, 104, 159, 183, 184, 187, 220, 221, 224, 238
END

I'm afraid that the list of amino acids that could interact with the substrates includes a number of false positives. We could increase the threshold for consensus from 4/10 to 6/10, and so obtain: Leu91, Asp94, Asp98, Arg103, Gln159, Lys183, Thr184, Gln221, Asp224 and Lys238.

PFRMAT FN
TARGET T0584
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: 91, 94, 98, 103, 159, 183, 184, 220, 221, 224, 238
END

Add new attachment

Only authorized users are allowed to upload new attachments.
« This page (revision-1) was last changed on 28-Jun-2010 23:21 by UnknownAuthor