Problem Summary:
View a structure to examine the
significance of a conserved domain |
| Sample User Question |
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I am looking for a 3D structure that contains a conserved domain
found in the period 2 protein. What conserved domain should I examine? What
structure contains this domain? What can I learn from the structure?
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| Analysis/Comments |
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By finding a conserved domain with an associated structure,
the researcher can learn how related molecules with similar functions might
provide information important to research in circadian rhythms.
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| Flow Chart |
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- Entrez Protein - retrieve the RefSeq protein sequence
record for the PER2 gene with a search such as: period 2[titl] AND
human[orgn]. Limit your results to the RefSeq database. One
entry, NP_073728, includes a LinkOut to "Conserved Domains" (the Conserved Domain Database, CDD). Clicking the Domains link shows that Per2 has a conserved PAS domain. Click on the PAS hyperlink to get to a full description of the PAS conserved domain.
Search for the per2 gene. In the human LocusLink record
(8864), notice in the RefSeq section that this gene contains a PAS domain.
Click on the PAS hyperlink.
- Conserved Domain Database summary page - Click "View 3D Structure"
with
Cn3D chosen from the pulldown menu (default setting).
- 3D view (PAS - Cn3D) - Note that PAS domain is colored (To see how
these options are chosen, go to Style -> Coloring Shortcuts
-> Sequence Conservation -> Weighted variety option. ALSO go to Style
-> Rendering Shortcuts -> Tubes)
- Sequence Viewer (PAS - Sequence/Alignment Viewer) - PAS domain in
caps and colored to correspond to 3D view.
- 3D view - Double click on ligand (six-sided ring) in center of 3D
structure.
- 3D view - Show/Hide -> Select by Distance -> Residues Only ->
Distance: 5,
click OK. Highlighting residues within 5 Angstroms of the ligand allows users
to help identify likely binding sites and/or residues involved in the protein's
active site.
- 3D view - Parts of PAS domain are highlighted. Also areas of
structure in
gray that are NOT part of PAS domain are also highlighted. The corresponding
amino acids are also highlighted in yellow in the Sequence/Alignment
Viewer.
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| Additional Notes |
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Conclusions: Because no structures are currently available for human
PER2, we used this
alternative approach to find related structures. Conserved domains, such as the
PAS
domain in this example, are often shared by related proteins. Learning about
the
structure of a specific domain may provide information about that same domain in
other
proteins.
The 3PYP structure is a bacterial blue-light photoreceptor called photoactive
yellow protein (PYP). A photoreceptor protein may have some properties relevant
to
studies of proteins involved in circadian rhythms. 3PYP contains a PAS domain
(as does
the PER2 protein). The ligand lies in a loop such that roughly half of the loop
is formed
by part of the PAS domain.
Information obtained from the study of the PAS domain in 3PYP and the residues
that may form
the binding site can assist scientists in designing experiments to study related
questions
in the PER2 protein.
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