Primary Citation PubMed: 16021622
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PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics.
(2006) BMC Bioinformatics 7
PubMed: 16460560 | PubMedCentral: PMC1409798 | DOI: 10.1186/1471-2105-7-53
Figure 8 The backbone superposition for 2 deep trefoil knotted TrmD methyltransferases (PDB codes: 1P9P, and 1UAJ) and 4 hypothetical proteins from A. Aureus , E. Coli , T. Maritime and B. Subtilis (P... B codes: 1VH0, 1NS5, 1O6D, and 1TO0, respectively).
We show that 4 hypothetical proteins (with PDB accession codes: 1VH0, 1NS5, 1O6D, and 1TO0), for which standard BLAST tools such as PSI-BLAST or RPS-BLAST failed to assign any function, are probably methyltransferase enzymes.
Publication Year: 2006
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases.
(2007) BMC Bioinformatics 8
PubMed: 17338813 | PubMedCentral: PMC1829167 | DOI: 10.1186/1471-2105-8-73
The available crystal structures of COG1576 members exhibit also the smallest dimerization interface, so small that according to PDB and the Protein Quaternary Structure Database (PQS) 1o6d has been c... assified as a monomer, even though in the crystal it forms protein-protein contacts with its symmetry mate (-X -Y, Z) that are very similar to those found in 1ns5, 1to0, and 1vh0 dimers (data not shown).
However, four crystal structures have been determined by two structural genomics consortia: for YbeA from E. coli (1ns5), YydA from Bacillus subtilis (1to0), SAV0024/SA0023 from S. aureus (1vh0, [ 51 ]), and Tm0844 from T. maritima (1o6d, [ 51 ]).
Publication Year: 2007
3D-Fun: predicting enzyme function from structure.
(2008) Nucleic Acids Res 36
PubMed: 18515349 | PubMedCentral: PMC2447717 | DOI: 10.1093/nar/gkn308
Similar results were obtained in our previous studies, where we showed that four other hypothetical proteins (with the PDB accession codes: 1VH0, 1NS5, 1O6D and 1TO0) are probably also methyltransfera... e enzymes ( 4 ).
Publication Year: 2008
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