Launch guide window

Launch NCBI Home Page

Goals

• Locate conserved domains in a protein
• Align the protein to a curated CD
• Predict functional and structural sites in the protein based on this alignment

Steps

1. Retrieve a protein sequence using Entrez
   
   • Find accession XP_001350573 in Entrez protein.
   • Open the record and review its annotation.
   • What is known about the function of this protein?

2. Locate Conserved Domains (CDs) in the sequence
   
   • Click the Conserved Domains link to search for CDs in the protein sequence.
   • Click the Full Result button to see all aligned domains.

3. Analyze the CD-Search results
   
   • What CD is the best hit? Is there a curated CD (cd*****)?
   • What function might this protein perform, and where in the sequence is this functional domain located?

4. Align the query sequence to a CD
   
   • Click the red bar corresponding to the curated CD.
   • Find the alignment row labeled query, representing XP_001350573.
   • What residues of XP_001350573 align to this CD? Residue numbers are in green at the ends of each aligned row.

5. Locate functional residues in the domain
   
   • Locate the Feature Display box near the top of the page.
   • The first feature (active site) is currently annotated in the alignment in the top row labeled "Feature 1". The residues involved in this feature are indicated by a "#" sign above them.
   • What residues are they? Does XP_001350573 conserve these residues?

6. View the alignment in Cn3D
   
   • Click the "Structure View" button to launch Cn3D.
   • Locate the query sequence and the master sequence (top sequence with structure) in the alignment.

7. Highlight functional features on the structure
   
   • In the CDD Descriptive Items window, click "Show Annotations Panel".
   • Select the first feature and click Highlight.
   • Does the query conserve these residues? Do the other sequences conserve them?
   • Use the annotations panel to locate the active site residue. Is the active site residue conserved?

8. View structure evidence for an annotation
   
   • Use the annotations panel to highlight the interdomain interaction site.
   • Click the structure evidence from the right window in the panel and click Show.
   • What region is now highlighted in the structure?

9. Explore the location of functional features
   
   • Chose Show/Hide / Show Everything to display the entire structure
   • Study the distinctive shape of the domain by rendering it as a space filling model (use Style / Edit Global Style).
   • Color the molecule by molecule (use Style / Coloring shortcuts) to see the dimeric structure.
   • Highlight the active site, then the metal binding site. How exposed are these sites? How would a ligand/substrate access them?

Revised January 7, 2008