Structure and conformational change of a replication protein A heterotrimer bound to ssDNA

High fidelity homologous DNA recombination depends on mismatch repair (MMR), which antagonizes recombination between divergent sequences by rejecting heteroduplex DNA containing excessive nucleotide mismatches. The hMSH2-hMSH6 heterodimer is the first responder in postreplicative MMR and also plays a prominent role in heteroduplex rejection. Whether a similar molecular mechanism underlies its function in these two processes remains enigmatic. We have determined that hMSH2-hMSH6 efficiently recognizes mismatches within a D-loop recombination initiation intermediate. Mismatch recognition by hMSH2-hMSH6 is not abrogated by human replication protein A (HsRPA) bound to the displaced single-stranded DNA (ssDNA) or by HsRAD51. In addition, ATP-bound hMSH2-hMSH6 sliding clamps that are essential for downstream MMR processes are formed and constrained within the heteroduplex region of the D-loop. Moreover, the hMSH2-hMSH6 sliding clamps are stabilized on the Dloop by HsRPA bound to the displaced ssDNA. Our findings reveal similarities and differences in hMSH2-hMSH6 mismatch recognition and sliding-clamp formation between a D-loop recombination intermediate and linear duplex DNA.

Section: Hmsh2-hmsh6 Sliding Clamp Is Constrained Within the D-loop Butsupporting

confidence: 60%

Mismatch repair protein hMSH2–hMSH6 recognizes mismatches and forms sliding clamps within a D-loop recombination intermediate

Honda

Okuno

Hengel

et al. 2014

“…HsRPA displays a high affinity 30 nt ssDNA binding mode (29), although structural analysis suggests that only 25 nt are actually bound (23). We found that mismatched DNA containing an oligo-dT 30 ssDNA tail prebound by HsRPA significantly increased the lifetime of HsMSH2-HsMSH6 (τ on = 26.2 ± 1.9 s) compared with unblocked dT 10 or dig-antidig blocked dT 10 (Fig.…”

Section: Significancementioning

confidence: 78%

“…S5). The significant differences in extension when ssDNA is bound by EcSSB compared with HsRPA likely reflects distinct binding mechanisms; whereas the EcSSB tetramer fully wraps ∼65 nt of ssDNA in a "baseball seam" structure (22), HsRPA merely bends ∼30 nt of ssDNA (23). Including EcSSB with HsEXOI completely impeded the contraction of mismatched DNA in the smFS system (Fig.…”

Section: Significancementioning

confidence: 99%

Dynamic control of strand excision during human DNA mismatch repair

Jeon

Kim

Martín-López

et al. 2016

Mismatch repair (MMR) is activated by evolutionarily conserved MutS homologs (MSH) and MutL homologs (MLH/PMS). MSH recognizes mismatched nucleotides and form extremely stable sliding clamps that may be bound by MLH/PMS to ultimately authorize strand-specific excision starting at a distant 3′-or 5′-DNA scission. The mechanical processes associated with a complete MMR reaction remain enigmatic. The purified human (Homo sapien or Hs) 5′-MMR excision reaction requires the HsMSH2-HsMSH6 heterodimer, the 5′ → 3′ exonuclease HsEXOI, and the single-stranded binding heterotrimer HsRPA. The HsMLH1-HsPMS2 heterodimer substantially influences 5′-MMR excision in cell extracts but is not required in the purified system. Using real-time single-molecule imaging, we show that HsRPA or Escherichia coli EcSSB restricts HsEXOI excision activity on nicked or gapped DNA. HsMSH2-HsMSH6 activates HsEXOI by overcoming HsRPA/EcSSB inhibition and exploits multiple dynamic sliding clamps to increase tract length. Conversely, HsMLH1-HsPMS2 regulates tract length by controlling the number of excision complexes, providing a link to 5′ MMR.is a highly conserved strand-specific excision-resynthesis process that corrects nucleotide misincorporation errors during replication and nucleotide mismatches arising from recombination between heteroallelic parents or physical damage to the DNA (for review see ref. 1). Mutation of core MMR components results in elevated mutation rates and susceptibility to a variety of cancers (2).MMR has been reconstituted with purified Escherichia coli, Saccharomyces cerevisae, and human proteins (3-6). The core MutS homologs (MSH) and MutL homologs (MLH/PMS) components direct a strand-specific excision reaction, whereas resynthesis appears to be uniquely performed by the replicative polymerase complex (1). In all organisms the excision process is initiated at a single-strand DNA scission (ssDNA/S) that may be located either 3′ or 5′ and hundreds to thousands of base pairs distant from the mismatch (4, 7). An ssDNA/S positioned on the newly replicated strand ensures accurate correction of replication misincorporation errors (1).Excision directionality in γ-proteobacteria (E. coli) is linked to the choice of 3′ or 5′ exonucleases that specifically degrade ssDNA generated by the EcUvrD helicase in concert with EcMutS and EcMutL (1). The lack of a helicase distinguishes yeast and human MMR from γ-proteobacteria. Moreover, the eukaryotic 3′-and 5′-excision reactions require different core MMR components and likely occur by different mechanisms (1). For example, the 3′-MMR excision requires the replicative processivity factor PCNA to activate a cryptic MLH/PMS endonuclease activity (8), whereas 5′ MMR uses the only known MMR exonuclease EXOI (3, 5, 6). Unlike the E. coli ssDNA exonucleases, EXOI will initiate 5′ excision from a ssDNA/S in the absence of a helicase (9). Whereas the purified 5′-MMR reaction does not require MLH/PMS or PCNA, complementation studies with cellular extracts displayed a substantial requirement for...

“…Binding involves the ssDNA wrapping around the homotetramer, although bacterial SSBs exhibit considerable variability in their association. In contrast to bacterial SSBs, eukaryotic SSBs generally function as a heterotrimer consisting of six OB folds distributed among three subunits; however, only four of these OB folds are involved in binding to ssDNA (7), which results in an extended arrangement for the protein-ssDNA complex. Telomere end binding proteins, which safeguard the vulnerable telomere 3′ end of ssDNA, also use different numbers of OB folds to bind with ssDNA (8).…”

mentioning

confidence: 99%

Molecular determinants of the interactions between proteins and ssDNA

Mishra

Levy

2015

ssDNA binding proteins (SSBs) protect ssDNA from chemical and enzymatic assault that can derail DNA processing machinery. Complexes between SSBs and ssDNA are often highly stable, but predicting their structures is challenging, mostly because of the inherent flexibility of ssDNA and the geometric and energetic complexity of the interfaces that it forms. Here, we report a newly developed coarse-grained model to predict the structure of SSBssDNA complexes. The model is successfully applied to predict the binding modes of six SSBs with ssDNA strands of lengths of 6-65 nt. In addition to charge-charge interactions (which are often central to governing protein interactions with nucleic acids by means of electrostatic complementarity), an essential energetic term to predict SSB-ssDNA complexes is the interactions between aromatic residues and DNA bases. For some systems, flexibility is required from not only the ssDNA but also, the SSB to allow it to undergo conformational changes and the penetration of the ssDNA into its binding pocket. The association mechanisms can be quite varied, and in several cases, they involve the ssDNA sliding along the protein surface. The binding mechanism suggests that coarse-grained models are appropriate to study the motion of SSBs along ssDNA, which is expected to be central to the function carried out by the SSBs.ssDNA | protein-DNA interaction | coarse-grained model