A common core for binding single‐stranded DNA: structural comparison of the single‐stranded DNA‐binding proteins (SSB) from E. coli and human mitochondria

Abstract

The crystal structure of the DNA‐binding domain of E. coli SSB (EcoSSB) has been determined to a resolution of 2.5 Å. This is the first reported structure of a prokaryotic SSB. The structure of the DNA‐binding domain of the E. coli protein is compared to that of the human mitochondrial SSB (HsmtSSB). In spite of the relatively low sequence identity between them, the two proteins display a high degree of structural similarity. EcoSSB crystallises with two dimers in the asymmetric unit, unlike HsmtSSB which contains only a dimer. This is probably a consequence of the different polypeptide chain lengths in the EcoSSB heterotetramer. Crucial differences in the dimer‐dimer interface of EcoSSB may account for the inability of EcoSSB and HsmtSSB to form cross‐species heterotetramers, in contrast to many bacterial SSBs.

The role of the 6 lysines and the terminal amine of escherichia coli single‐strand binding protein in its binding of single‐stranded DNA

“…Neither the aminoterminus nor Lys 43 are resolved in either E. coli SSB crystal structures, but their locations suggest that both residues are located in flexible solvent-exposed regions of the protein (Raghunathan et al, 1997;Webster et al, 1997). Such well-exposed locations would yield the high reactivities that we observe for these residues.…”

“…Lys 49 is not resolved in one E. coli SSB structure (Raghunathan et al, 1997), indicating that it is disordered and probably highly accessible to solvent. In contrast, Lys 49 is resolved in the other E. coli structure (Webster et al, 1997), points toward the ssDNA binding channel, but is still solvent accessible. Both of these structures predict that Lys 49 should be highly reactive, contrary to our observation.…”

“…SSBs for which this structural similarity has been noted are Pf3 gene 5 protein, Ff gene 5 protein, the major cold shock protein E. coli CspA (Folmer et al, 1994), T4 gene 32 protein (Shamoo et al, 1995a(Shamoo et al, , 1995b, human replication protein A (Bochkarev et al, 1997), and now human mitochondrial SSB (Yang et al, 1997), and E. coli SSB (Raghunathan et al, 1997;Webster et al, 1997). These SSBs share this structural feature even though there is practically no sequence conservation between, or sometimes even within, the families.…”

“…The folded structures of the homotetrameric SSB from E. coli (Raghunathan et al, 1997;Webster et al, 1997) and human mitochondria (Yang et al, 1997) were recently solved using X-ray crystallography. There are 36 identical and 28 highly conserved residues between residues 1 1 and 11 8 of HsmtSSB and 3 and 103 of E. coli SSB (Fig.…”

Crystal structure of a novel single‐stranded DNA binding protein from Mycoplasma pneumoniae

“…Approximately the first 120 N-terminal residues comprise the OB/SSB fold with conserved structure whereas the rest of the protein has been implicated in interacting with other protein partners and in some cases has been disordered in the crystal structures. Numerous prior efforts have reported in detail the crystal structures of functionally annotated SSBs, [12][13][14][15][16][17][18][19][20][21][22][23] presented comparative analysis of homologous SSBs 20,24 and reported on structures of their protein-DNA complexes. 25,26 An electrophoretic mobility shift assay confirmed that MPN554 binds to a 39-mer single-stranded DNA.…”