Abstract
Using a recently developed program (SCOPmap) designed to automatically assign new protein structures to existing evolutionary-based classification schemes, we identify a evolutionarily conserved domain (EDD) common to three different folds: mannose transporter EIIA domain (EIIA-man), dihydroxyacetone kinase (Dak), and DegV. Several lines of evidence support unification of these three folds into a single superfamily: statistically significant sequence similarity detected by PSI-BLAST; "closed structural grouping" using DALI Z-scores (each protein inside a group finds all other group members with scores higher than those to proteins outside the group) that includes only these proteins sharing a unique α-helical hairpin at the C-terminus and excludes all other proteins with similar topology; similar domain fusions connect Dak and DegV, and genomic neighborhood organizations connect Dak and EIIA-man. Finally, both Dak and EIIA-man perform similar phosphotransfer reactions, suggesting a phosphotransferase activity for the DegV-like family of proteins, whose function other than lipid binding revealed in the crystal structure remains unknown.
Original language | English (US) |
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Pages (from-to) | 360-367 |
Number of pages | 8 |
Journal | Protein Science |
Volume | 14 |
Issue number | 2 |
DOIs | |
State | Published - Feb 2005 |
Keywords
- Dak1
- Dak2
- DegV
- Dihydroxyacetone kinase
- EDD domain
- Homology detection
- Mannose transporter EIIA
- Protein classification
- SCOPmap
- Structure similarity
ASJC Scopus subject areas
- Biochemistry
- Molecular Biology