Variants on protein structures part 5: TP53 R248 and R273 on DNA

The p53 protein, from TP53, is a transcription factor that binds DNA and stops the cell cycle after DNA damage. Most TP53 mutations in tumours are missense changes in its DNA-binding core, and the arginines at residues 175, 248 and 273 change more often than any other residue. We open codons 248 and 273 side by side, beside the crystal structure of the core domain bound to DNA, and read which of the protein's conserved sites each hotspot falls in. We'll:

• open TP53 in the protein browser with structure 1TUP, and pin the human row of the ortholog alignment
• show codons 248 and 273 side by side, highlighted and labelled
• color the genome, the alignment and the structure by the alignment's protein domains and sites, with Arg175 as the comparison

Prerequisites#

• for your own JBrowse, the protein3d and msaview plugins from the plugin store; genomes.jbrowse.org already loads them

The data#

Nothing to download: the protein browser and the plugins read these files by URL.

Opening TP53 on codons 248 and 273#

Part 1 walks through the protein browser's linked session. Open it on TP53 with structure 1TUP:

• open genomes.jbrowse.org/protein-browser/?gene=TP53&ref=9606&structure=1tup and click Open in JBrowse ↗
• close the ClinVar and AlphaMissense tracks with the × on each track's label
• type chr17:7674201-7674239[rev] chr17:7673783-7673821[rev] into the location box, which puts codon 273 beside codon 248
• click Reset Zoom, the circular arrow at the top right of the structure
• pick Use as reference row on the human_query tip of the alignment's tree, so a residue matching human draws as a dot
• drag across the scale bar over codon 248 and pick Highlight region, then over codon 273. Click the link chip at the top of each band, pick Edit label... and type R248 or R273

The link names no residue. With residue=248 in it, the protein browser opens the seed alignment of p53's Pfam family, a few dozen distant relatives, in place of TP53's orthologs.

Hover codon 248 on the gene. The protein view's header reads the residue in both the genome and the crystal, and 1TUP lights the residue in each of its three copies of the core domain.

Every row of the alignment has arginine at 248 and at 273, while several columns from 259 on hold other letters in many rows.

The domains across all three views#

The alignment view fills its rows with NCBI's conserved domains and sites, and the genome view and the structure read them from the alignment:

• in the alignment view's menu, click Show domains on the genome, which adds a domain track to the genome view
• in the genome view's menu, untick Show... → CDS reading frame colors
• in the protein view's palette menu, pick Domains from the alignment
• type chr17:7675069-7675107[rev] chr17:7674201-7674239[rev] chr17:7673783-7673821[rev] into the location box, which puts codon 175 before codons 248 and 273, and highlight it as R175

Codons 248 and 273 both sit inside NCBI's DNA binding site of the P53 domain, and on the structure both side chains reach the DNA. Arg175, the third hotspot, sits in none of the sites and away from the DNA.

Part 1 found the opposite at HBB codon 7: the sickle position lies outside the globin domain and every site, and the orthologs vary there.

Your own gene#

• any gene the protein browser opens takes the same steps, and the chain picker in the protein view's header chooses among the copies in a crystal
• Launch protein view in a gene's right-click menu picks another structure, and TP53 from prediction to crystal lays several of p53's side by side

See also#

• Tutorial: Variants on protein structures part 1: sickle cell from GWAS hit to haemoglobin S
• Tutorial: Variants on protein structures part 4: KRAS G12 in the GTP pocket
• Tutorial: Variants on protein structures part 6: BRAF V600 in the activation loop
• Tutorial: TP53 from prediction to crystal
• User guide: Highlights

External links#

• Protein browser
• NCBI Conserved Domain Database
• jbrowse-plugin-protein3d
• jbrowse-plugin-msaview

Citations#

• Cho Y, Gorina S, Jeffrey PD, Pavletich NP. Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations. Science 1994;265:346-355. https://doi.org/10.1126/science.8023157

Feedback on this tutorial is welcome: contact us.