Journal:Acta Cryst F:S2053230X19000815
From Proteopedia
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<scene name='80/806371/Cv/11'>Cartoon representation showing the domain architecture of Tdi1</scene>. The GAD-like domain and the DUF1851 domain are shown in orange and cyan, respectively. The GAD-like domain structure is composed a seven-stranded twisted antiparallel β-sheet (β1↑-β2↓-β3↑-β4↓-β5↑-β6↓-β7↑) in the N-terminus and a two-stranded antiparallel β-sheet (β10↓-β11↑) in the C-terminus, surrounded by six helices (α1-α5 and η1). The DUF1851 domain is composed of a two-stranded antiparallel β-sheet (β8↓-β9↑) and four helices (η2-η3 and α6-α7). Therefore, the DUF1851 domain probably exists as an insertion of the GAD-like domain rather than an independent domain. | <scene name='80/806371/Cv/11'>Cartoon representation showing the domain architecture of Tdi1</scene>. The GAD-like domain and the DUF1851 domain are shown in orange and cyan, respectively. The GAD-like domain structure is composed a seven-stranded twisted antiparallel β-sheet (β1↑-β2↓-β3↑-β4↓-β5↑-β6↓-β7↑) in the N-terminus and a two-stranded antiparallel β-sheet (β10↓-β11↑) in the C-terminus, surrounded by six helices (α1-α5 and η1). The DUF1851 domain is composed of a two-stranded antiparallel β-sheet (β8↓-β9↑) and four helices (η2-η3 and α6-α7). Therefore, the DUF1851 domain probably exists as an insertion of the GAD-like domain rather than an independent domain. | ||
| - | <scene name='80/806371/Cv/ | + | <scene name='80/806371/Cv/14'>The spacefill representation of Tdi1</scene> (blue, positive; red, negative), colored by its local electrostatic potential. Remarkably, there is a groove that is mainly composed of β7, η1 and α5 in the GAD-like domain and extends to β8 in theDUF1851 domain. Many of the residues constituting the groove are conserved or highly conserved among Tdi1 homologs. Inspection of the surface charge distribution of the groove revealed it is covered with dominantly positive charges, which may be associated with nucleotide-binding. |
The GAD domain exists as an insertion in bacterial aminoacyl-tRNA synthetases (aaRSs), such as aspartyl- and glutamyl-tRNA synthetases (AspRS and GluRS). Structural comparison of Tdi1 with the GAD domain of E. coli AspRS (PDB ID [[1c0a]]) showed they have similar topology structures (with a RMSD of 3.9). <scene name='80/806371/Cv/12'>Structural superposition of Tdi1 with the GAD domain of E. coli AspRS</scene> (PDB ID [[1c0a]], in gray) shown as cartoon. An AMP molecule (shown as green sticks) is bound in ''E. coli'' AspRS. | The GAD domain exists as an insertion in bacterial aminoacyl-tRNA synthetases (aaRSs), such as aspartyl- and glutamyl-tRNA synthetases (AspRS and GluRS). Structural comparison of Tdi1 with the GAD domain of E. coli AspRS (PDB ID [[1c0a]]) showed they have similar topology structures (with a RMSD of 3.9). <scene name='80/806371/Cv/12'>Structural superposition of Tdi1 with the GAD domain of E. coli AspRS</scene> (PDB ID [[1c0a]], in gray) shown as cartoon. An AMP molecule (shown as green sticks) is bound in ''E. coli'' AspRS. | ||
Revision as of 11:13, 23 January 2019
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This page complements a publication in scientific journals and is one of the Proteopedia's Interactive 3D Complement pages. For aditional details please see I3DC.
