Table 2.
Annotation of uncharacterized proteins based on our ligand-centric approach
| PDB ID | CURRENT ANNOTATION IN PDB | PIRSF ID | TAXONOMY | PREDICTED LIGAND CONFORMATION & CLASS | SUGGESTED NAME |
|---|---|---|---|---|---|
| 2PGX |
Crystal structure of UPF0341 protein yhiQ from E. coli |
SF016106 |
E=0, B=156, A=0, V=0, O=4 |
Type 1 |
Putative SAM dependent r-RNA methyltransferase |
| Class 1a | |||||
| 2O3A |
Crystal structure of a protein AF_0751 from Archaeoglobus fulgidus |
SF016123 |
E=0, B=0, A=134, V=0, O=0 |
Type IV |
Putative SAM dependent t-RNA archaeal methyltransferase |
| Class IV | |||||
| 2B78 |
A putative sam-dependent methyltransferase from Streptococcus mutans |
SF004981 |
E=2, B=403, A=16, V=0, O=5 |
Type 1 |
Putative SAM dependent RNA methyltransferase |
| Class 1a | |||||
| 3DR5 |
Crystal structure of the Q8NRD3_CORGL protein from Corynebacterium glutamicum |
SF005841 |
E=122, B=346, A=6, V=0, O=3 |
Type 1 |
Putative SAM dependent COMT type methyltransferase |
| Class 1b | |||||
| 1XXL |
The crystal structure of YcgJ protein from Bacillus subitilis at 2.1 A resolution |
SF006616 |
E=6, B=130, A=2, V=0, O=4 |
Type 1 |
Putative SAM dependent Class Ib methyltransferase |
| Class 1b | |||||
| 1YB2 |
Structure of a putative methyltransferase from Thermoplasma acidophilum |
SF017269 |
E=227, B=418, A=110, V=0, O=2 |
Type 1 |
Putative SAM dependent t-RNA methyltransferase |
| Class 1a | |||||
| 1JSX |
Crystal Structure of the Escherichia coli Glucose-Inhibited Division Protein B (GidB) |
SF003078 |
E=19, B=4040, A=0, V=0, O=13 |
Type 1 |
Putative SAM dependent r-RNA methyltransferase |
| Class 1b |
Functions are assigned based on the results of the analysis presented in this manuscript. Majority of the structures are from Structural Genomics Initiatives with unassigned functions.