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Figure 3.
Figure 3. Structural comparison between the URN1FF domain and
other related structures. (A) Structure-based alignment of FF
and SURP aligned profiles. Conserved residues between the two
profiles are indicated with red gradient (FFs) and blue gradient
(SURPs) backgrounds according to the degree of conservation
(dark is the most conserved). For instance, in the FF family the
Phe in the first helix (the one corresponding to the first Phe
in the name FF) is conserved in all sequences, while the SURP
family contains an Ala at this equivalent position. Both
families have a pair of hydrophobic semiconserved residues in
position +3 with respect to this Phe/Ala highly conserved
residue. Similarly, in the last helix there are four positions
conserved in each family, but not between the families.
Secondary structure elements for each profile and residue
numbers of the distinct domains are indicated. (B) Left and
right: URN1FF domain (in orange) superimposed to either DEK
C-term structure (in green, PDB code 1Q1V) or the SF3a120SURP1
structure (in blue, PDB code 2DT6). Representations show the
superimpositions according to the  1-
3
fittings using the optAlign alignment script. Secondary
structure elements are indicated. (C) RMSD of the family
representatives for another 3-helical bundle fold, as well as
for the SF3a120SURP1 domain (in bold) with respect to the
URN1FF. Fittings were generated taking either the secondary
structure elements 1-
3
helices or the whole molecules (Global). PDB codes: C-term S/T
phosphatase 2C-1A6Q, B-form DNA-mimic Ocr-1S7Z, DEK-C-term-1Q1V,
IscX protein-1UJ8, SF3a120SURP1-2DT6.
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