Domenico:
This protein includes a Carbon-nitrogen hydrolase domain at the N-terminus and a NAD synthase domain at the C-terminus. The former domain is expected to bind L-glutamine or ammonia, while the latter should interact with ATP and NAD. Unfortunately, the set of known related structures includes at most two of these substrates or their analogues and they are not equally represented. Though fairly reliable, the following consensus of the protein-ligand interactions in Genthreader's certain hits is likely to miss some crucial information

PFRMAT FN
TARGET T0542
AUTHOR 7656-5034-1890
REMARK Sequence consensus of contacts between homologous structures and ligands
METHOD pGenTHREADER and PDBSum data mining.
MODEL 1
Binding site: 45, 127, 163, 332, 333, 334, 339, 358, 415, 433, 438, 444, 445, 449, 495, 496
END

However, this is a reasonable starting point:
1. The catalytic triad of the N-terminal domain Glu45, Lys127 and Cys163 is well conserved

2. Glutamine or ammonia would probably contact some more residues, but we'd better be conserrvative

3. According to literature, MG interactions with Ser495 and Glu438 are biologically important and it could be worth adding Asp338.

4. NAD binding residues are also expected to be underrepresented. Prediction of the NAD binding site based on 3dla-NXX, 1xng-DND, 2pz8-APC, 3hmqA0-NAD, and 1kqp-ADJ only gives Asn324, Met420, Ser422, His428, Ile429, Glu438, Tyr443, Ser444, Thr445, Asp449, Ala453, Ala496.

5. Following the same strategy, the following ATP contacting residues can be predicted from 1xng-ATP, 3fiu-(AMP,POP) and 1wxi-(AMP+DPO): Gly332, Leu 333, Ser334, Gly336, Ile 337, Asp338, Ser339, Met 360, Arg415, Pro433, Glu438, Asp449, Lys462, Ser495.

Refined prediction:

PFRMAT FN
TARGET T0542
AUTHOR 7656-5034-1890
REMARK Sequence consensus of contacts between homologous structures and ligands
METHOD pGenTHREADER and PDBSum data mining.
MODEL 1
Binding site: 45, 127, 163, 324, 332, 333, 334, 336, 337, 338, 339, 360, 415, 420, 422, 428, 429, 433, 438, 443, 444, 445, 449, 453, 462, 495, 496
END

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