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DNA mismatch repair (MMR) ensures replication fidelity by correcting mismatches generated during DNA replication. Although human MMR has been reconstituted in vitro, how MMR occurs in vivo is unknown. Here, we show that an epigenetic histone mark, H3K36me3, is required in vivo to recruit the mismatch recognition protein hMutSα (hMSH2-hMSH6) onto chromatin through direct interactions with the hMSH6...
E. coli DNA Pol II and eukaryotic Rev3 are B-family polymerases that can extend primers past a damaged or mismatched site when the high-fidelity replicative polymerases in the same family are ineffective. We report here the biochemical and structural properties of DNA Pol II that facilitate this translesion synthesis. DNA Pol II can extend primers past lesions either directly or by template skipping,...
The first step in the repair of DNA damage is lesion detection. In this issue, Scrima et al. (2008) report the structure of the complex of DNA Damage-Binding Protein 1 (DDB1) and DDB2 bound to a DNA photodimer, providing critical insight into the repair of DNA damage caused by ultraviolet light.
Helicases use the energy derived from nucleoside triphosphate hydrolysis to unwind double helices in essentially every metabolic pathway involving nucleic acids. Earlier crystal structures have suggested that DNA helicases translocate along a single-stranded DNA in an inchworm fashion. We report here a series of crystal structures of the UvrD helicase complexed with DNA and ATP hydrolysis intermediates...
Many essential functions of living cells are performed by nanoscale protein motors. The best characterized of these is F o F 1 -ATP synthase, the smallest rotary motor. This rotary motor catalyzes the synthesis of ATP with high efficiency under conditions where the reactants (ADP, H 2 PO 4− ) and the product (ATP) are present in the cell at similar concentrations...
RNase H belongs to a nucleotidyl-transferase superfamily, which includes transposase, retroviral integrase, Holliday junction resolvase, and RISC nuclease Argonaute. We report the crystal structures of RNase H complexed with an RNA/DNA hybrid and a mechanism for substrate recognition and two-metal-ion-dependent catalysis. RNase H specifically recognizes the A form RNA strand and the B form DNA strand...
Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) is a DinB homolog that belongs to the recently described Y-family of DNA polymerases, which are best characterized by their low-fidelity synthesis on undamaged DNA templates and propensity to traverse normally replication-blocking lesions. Crystal structures of Dpo4 in ternary complexes with DNA and an incoming nucleotide, either correct or incorrect,...
The kinesin superfamily motor protein KIF1B has been shown to transport mitochondria. Here, we describe an isoform of KIF1B, KIF1Bβ, that is distinct from KIF1B in its cargo binding domain. KIF1B knockout mice die at birth from apnea due to nervous system defects. Death of knockout neurons in culture can be rescued by expression of the β isoform. The KIF1B heterozygotes have a defect in transporting...
The MutL DNA mismatch repair protein has recently been shown to be an ATPase and to belong to an emerging ATPase superfamily that includes DNA topoisomerase II and Hsp90. We report here the crystal structures of a 40 kDa ATPase fragment of E. coli MutL (LN40) complexed with a substrate analog, ADPnP, and with product ADP. More than 60 residues that are disordered in the apoprotein structure become...
MutL and its homologs are essential for DNA mismatch repair. Mutations in genes encoding human homologs of MutL cause multiorgan cancer susceptibility. We have determined the crystal structure of a 40 kDa N-terminal fragment of E. coli MutL that retains all of the conserved residues in the MutL family. The structure of MutL is homologous to that of an ATPase-containing fragment of DNA gyrase. We have...
Integration host factor (IHF) is a small heterodimeric protein that specifically binds to DNA and functions as an architectural factor in many cellular processes in prokaryotes. Here, we report the crystal structure of IHF complexed with 35 bp of DNA. The DNA is wrapped around the protein and bent by >160°, thus reversing the direction of the helix axis within a very short distance. Much of the...
The structure of γδ resolvase complexed with a 34 bp substrate DNA has been determined at 3.0 A resolution. The DNA is sharply bent by 60 o toward the major groove and away from the resolvase catalytic domains at the recombination crossover point. The C-terminal on third of resolvase, which was disordered in the absence of DNA, forms an arm and a 3-helix DNA-binding domain on the opposite...
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