The human mitochondrial DNA polymerase (pol ␥) is nuclearly encoded and is solely responsible for the replication and repair of the mitochondrial genome. The progressive accumulation of mutations within the mitochondrial genome is thought to be related to aging, and mutations in the pol ␥ gene are responsible for numerous heritable disorders including progressive external opthalmoplegia, Alpers syndrome, and parkinsonism. Here we investigate the kinetic effect of H932Y, a mutation associated with opthalmoplegia. Mutations H932Y and H932A reduce the specificity constant governing correct nucleotide incorporation 150-and 70-fold, respectively, without significantly affecting fidelity of incorporation or the maximum rate of incorporation. However, this leads to only a 2-fold reduction in rate of incorporation at a physiological nucleotide concentration (ϳ100 M). Surprisingly, incorporation of T:T or C:T mismatches catalyzed by either H932Y or H932A mutants was followed by slow pyrophosphate release (or fast pyrophosphate rebinding). Also, H932Y readily catalyzed incorporation of multiple mismatches, which may have a profound physiological impact over time. His-932 is thought to contact the -phosphate of the incoming nucleotide, so it is perhaps surprising that H932Y appears to slow rather than accelerate pyrophosphate release.
Mutations in DNA polymerase ␥ (pol ␥)2 have been linked to several mitochondrial disorders that include progressive external opthalmoplegia (PEO), Alpers syndrome, parkinsonism, male infertility, and SANDO (sensory ataxic neuropathy, dysarthria, and opthalmoparesis) among others (1). The majority of the mutations in pol ␥ are associated with PEO, a mitochondrial disorder associated with accumulation of mitochondrial DNA deletions and mutations. The main clinical manifestation of PEO is progressive weakness of the external eye muscles and is often accompanied by dysphagia and variable weakness of the limb and neck muscles. Neurological symptoms could include depression or avoidant personality (2). Greater than 60 pathogenic mutations in the pol ␥A gene are associated with PEO, including about 14 dominant mutations, 36 recessive mutations, and other mutations of sporadic or unknown origin (1).Recently the crystal structure of the human pol ␥ was solved by Lee et al. (3) and has provided an insight into understanding how processivity is achieved by the holoenzyme. The structure provides a framework to examine the physiological basis of heritable mutations in pol ␥. Pol ␥ is a heterotrimer in which one molecule of the catalytic subunit (pol ␥A) binds to a dimeric pol ␥B. Similar to most DNA polymerases, the structure of pol ␥A resembles a human right hand with "palm," "fingers," and "thumb" domains (4, 5). The palm domain is responsible for the catalysis of the phosphoryl transfer reaction, and the fingers domain is proposed to be involved in binding of the templating base and the incoming nucleotide and governs the fidelity of the DNA polymerase. The structures of the fingers domain differ bet...