Model of MiaA.
MiaA (E.C. 188.8.131.52) is a prenyltransferase, which is responsible for introducing posttranscriptional modification N6-(?2-isopentenyl)adenosine (i6A) in position 37 in tRNA. MiaA is related to P-loop NTPases, a large class of proteins with diverse structures and functions. At the stage of our researches no structural information about enzymes from this family was available. However, we constructed a structural model of EcMiaA (Escherichia coli MiaA enzyme) with a respect to known experimental data and predictions of fold-recognition methods. Not long after the acceptance of the final version of our manuscript , the crystal structure of BsMiaA (Bacillus subtilis) was published  giving a possibility for direct comparison of our model with the native structure. Our modeling appeared to be fairly successful and predicted correct protein topology and reviled the structure of regions which were not present in a crystal structure of native protein.
1. Kaminska KH, Baraniak U, Boniecki M, Nowaczyk K, Czerwoniec A, Bujnicki JM. Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms(2)io(6)A37 in tRNA. Proteins. 2008 Jan 1;70(1):1-18.
2. Forouhar F, Neely H, Abashidze M, Seetharaman J, Shastry R, Janjua H, Cunningham K, Ma L-C, Xiao R, Liu J, Baran MC, Acton TB, Rost B, Montelione GT, Tong L, Hunt JF. Crystal structure of tRNA isopentenylpyrophosphate transferase (BH2366) from Bacillus halodurans. To be Published.
Read our manuscript:
Comparison of structures of our model and the native structure (PDB code: 2QGN). Structures are colored according to the sequence index (N-terminus - blue, C-terminus - red). The model is of good quality in regions of catalytic core.
Regions with corresponding secondary structure elements are colored in the same way. The structure of regions which were not present in a crystal structure are colored in a dark gray.
Correctly predicted functionally important residues of MiaA. Amino acids predicted to bind tRNA are colored in blue, catalytic residues are colored in red, DMAPP molecule is colored in purple.