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see that in this crystal structure, the protein is complexed with a single-stranded
oligonucleotide. We also see that the protein has five 3D Domains. Three CDs align to
the sequence as well, and two of these overlap with one another at the N-terminus of the
protein in the region corresponding to 3D domains 1-3.
Analyzing CDs Found in a Protein.
The Structure summary page displays only
the CDs that give the best match to the protein sequence. To see all of the matching CDs,
we can easily perform a full CD-Search. Select the
Protein
link to the left of the graphic
to reveal the flat file for the record. Then follow the
Domains
link in the
Link
menu on
the right to view the results of the CD-Search. Select
Show Details
to see all CDs
matching the query sequence. We find that nine CDs match this sequence, and that the
statistics of each match are shown below the alignment graphic. The CDs are listed by
database, with curated CDs at the top, followed by SMART, Pfam, and COG records. We
see that the protein contains two domains, an N-terminal TOPRIM domain and a C-
terminal Topoisomerase, subtype IA domain. We can learn more about these CDs by
studying the pairwise alignments at the bottom of the page and by studying their CD
Summary pages, reached by selecting the links to their left
.
Finding Other Proteins with Similar Domain Architecture.
We now would like to
find human proteins that have these same CDs. To perform a CDART search, simply
select the
Show Domain Relatives
button. To limit these results to human proteins, we
select the
Subset by Taxonomy
button. A taxonomic tree is then displayed, and we next
check the box for
Mammal
, the lowest taxa including
Homo sapiens
. Selecting
Choose
then displays a Common Tree, and by clicking on the appropriate “scissor” icons, we can
cut away all branches except the one leading to
H. sapiens
. We can execute this
taxonomic restriction by selecting
Go back
, and we now find a much shorter list of
CDART results. In the second group of proteins, we find two members, one of which is
NP_004609. Selecting the
more>
link for this record shows the CD-Search results for
this human protein. Interestingly, we find that the topoisomerase is very well conserved,
whereas only a portion of the TOPRIM domain has been retained.
Viewing a CD Alignment with a 3D Structure .
We now would like to view the
alignment of the topoisomerase in the human protein to other members of this CD. On the
CD-Search page, select the colored bar of this CD to see a CD-Browser window
displaying the alignment. Because this is a curated CD record, we are able to view
functional features of the protein domain on a structural template. The rightmost menu in
the View Alignment bar shows the available features for this domain, whereas the
topmost row in the alignment itself marks the residues involved in this feature with #
symbols. The second row of the alignment is the consensus sequence of the CD record,
whereas the third row contains the NP_004609 sequence, labeled “query”. At the bottom
of the page, buttons allow Cn3D to be launched with various structural features
highlighted. For example, if we are interested in nucleotide binding site II, Cn3D will
launch with the view depicted in Figure 7, showing the bound nucleotide in orange.
Additonal Cn3D windows not shown in Figure 7 allow one to highlight the binding site
residues yellow as shown, and these highlights also appear in the sequence window. In
this figure, the NP_004609 sequence has been merged into the alignment (bottom row)
using tools within Cn3D, and the result shows that this human protein closely conserves
these important functional residues.
