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Figure 1.
Figure 1. Structure, Sequence Alignment, and p97
Association of Ufd1
(A) Schematic model of the
Ufd1-Npl4-p97 complex based on the 6-fold symmetry of the p97
AAA-ATPase. See text for the domain names.
(B) Ensemble of
backbone traces of the 15 lowest-energy conformers of Ufd1.
Regular secondary structured regions are aligned and overlaid to
generate the ensemble.
(C) Ribbon diagram of the
lowest-energy conformer of the ensemble showing the presence of
the two separate domains. The Nn subdomain is in red, and the Nc
subdomain is in blue. Secondary structural elements are
numbered. The two psi loops (psi1 and psi2) in the double-psi b
barrel are also labeled. The position of the V94 found in ufd1-1
is shown.
(D) Structure-based sequence alignment of Ufd1,
its orthologs, and the p97 N domain. The alignments within the
Ufd1 orthologs were generated with the ClustalX program. The
alignment of p97 to the rest of the sequences is based on the
experimental structure of S. cerevisiae Ufd1 reported here and
the mouse p97 N domain structure reported previously (Dreveny et
al., 2004) and differs from a previously proposed alignment
(Golbik et al., 1999). The conserved residues are in red and
boxed in blue, with the strictly conserved residues in all of
the sequences in inverse shading in red. The secondary structure
cartoon (red) above the alignment is for the yeast Ufd1, and the
one below (blue) is for p97. The residue numbering above the
alignment is for the S. cerevisiae sequence used in this study.
The gene bank accession numbers of the sequences used are: S.
ser, gi1717964; H. sap, gi12053683; M. mus, gi2501439; C. ele,
gi2501440; A. tha, gi42573225; S. pom, gi3123677; p97,
gi14488635.
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