This is annotated as Histidyl-tRNA synthetase in Swissprot, which acts on ATP, L-histidine and tRNA(His) - so no need to consider metal ions. Besides, we should list binding residues for the first two substrates only, as tRNA molecules will unlikely be considered heteroatoms. On the contrary, individual amino acids are considered ligands in the PDB - see entry 3lc0, for instance.
Arg131 is evolutionarily conserved and has a catalytic role.
Three certain hits are in complex with amino acids, but we can make use of 3lc0A0 only, because 1nyrA0 is complexed with Thr and 1usyA0 is an enzyme in a different EC class. Based on Genthreader alignment, the following residues would contact histidine: Asp101, Thr103, Gln145, Asp147, Asp149, Leu303, Tyr305, Tyr306, Cys325, Arg329, Gly346, Ile347 and Ser348. However, Cys325 and Arg329 match a Glycine and a Tyrosine in the template, and their side chains are unlikely to contact the substrate, given their orientation in our manual model. All the remaining residues are either identically or similarly conserved. Maybe David's tool can help us spot additional false positives?
Finally, the consensus of residues binding nucleotides or their analogues in certain templates includes: Asp101, Tyr103, Arg131, Glu133, Arg139, Phe140, Phe143, Gln145, Tyr306, Thr307, Ile324, Ser348, Ile349, Gly350 and Arg353. However, Thr307 is unlikely to bind any ligand, if we believe in our manual model. Again, it would be useful to double check this list with the output of David's program.

After considering sequence conservation and discarding those positions with a score lower than 7, we came up with this prediction:

AUTHOR 7656-5034-1890
REMARK Sequence consensus of contacts between homologous structures and ligands
METHOD pGenTHREADER and PDBSum and CSA data mining.
Binding site: 101, 103, 131, 133, 139, 143, 145, 147, 149, 303, 305, 306, 346, 350, 353

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« This page (revision-1) was last changed on 30-Jun-2010 15:44 by UnknownAuthor