ITPA variants

Description

ITPA is a pyrophosphatase that hydrolyses inosine triphosphate with a magnesium cofactor.

The mutations discussed in the paper are:

D72G (wild-type/mutant/overlay) The residue Asp72 is likely the catalytic residue that attacks the phosphate. So any mutation would result in a loss of function. It is slightly destabilising due to the loss of the water network (∆∆G: +4.5 kcal/mol)
P84T (wild-type/mutant/overlay) The residue Pro84 preceeds a turn for which flexible residues like proline are key, making the mutation destabilising (∆∆G: +6.9 kcal/mol)
G85S (wild-type/mutant/overlay) The residue Gly85 is part of a turn and the mutation pushes nearby sidechains away, making the mutation highly destabilising (∆∆G: +48 kcal/mol)
F91L (wild-type/mutant/overlay) The residue Phe91 is buried. This mutation loses two π-π interactions and distorts the neighbourhood (0.5 Å RSMD heavy atoms 10Å around), making the mutation destabilising (∆∆G: +7.0 kcal/mol)
W151G (wild-type/mutant/overlay) The Trp151 and Phe149 residues π-π stack with the nucleobase, so are key in substrate binding. This mutation therefore results in a loss of affinity for ITP (+12 kcal/mol)
T163M (wild-type/mutant/overlay) The residue Thr163 is buried. This mutation to a bulkier residue distorts the neighbourhood (+6 kcal/mol)
R178C (wild-type/mutant/overlay) The residue Arg178 coordinates other residues in the binding site. This mutation loses several bonds (+5 kcal/mol)
L182P (wild-type/mutant/overlay) The residue Leu182 is part of a helix. Proline breaks helices due to its inability to hydrogen bond with its backbone nitrogen (+32 kcal/mol)

Specificity

ITPA acts on a specific substrate, ITP, by recognising inosine nucleobase via Arg178, Lys172 and Asp152. Non-destabilising mutations to these residues would result in reactivity towards ATP, GTP, CTP and UTP, which would be catastrophic metabolically. None of the missense alleles present in the human population (gnomAD) affect any of these residues.

missense alleles in the human population

The most common missense alleles in gnomAD are neutral (>5 kcal/mol), with the possible exception of C57Y (wild-type/mutant/overlay) at 1 in 10,000 that is highly destabilising (+30 kcal/mol).

Methods

Show is a hybrid of PDB:2J4E and PDB:2CAR. More details in GitHub repo.