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Review
. 2000;1(1):REVIEWS001.
doi: 10.1186/gb-2000-1-1-reviews001. Epub 2000 Jun 9.

An overview of the structures of protein-DNA complexes

N M Luscombe  1 , S E Austin, H M Berman, J M Thornton
Affiliations
Review

An overview of the structures of protein-DNA complexes

N M Luscombe et al. Genome Biol. 2000.

Abstract

On the basis of a structural analysis of 240 protein-DNA complexes contained in the Protein Data Bank (PDB), we have classified the DNA-binding proteins involved into eight different structural/functional groups, which are further classified into 54 structural families. Here we present this classification and review the functions, structures and binding interactions of these protein-DNA complexes.

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Figures

Box 1
Box 1
Flow diagram showing the selection of the protein-DNA complexes from the PDB (04/01/00). The protein-DNA complexes were grouped into structurally related families using the secondary structure alignment program SSAP (see text).
Figure 1
Figure 1
Group I, HTH proteins. The DNA-binding motif is red. The protein binds as a dimer; one monomer is colored blue and the other yellow. The DNA is shown as a space filling model. Family names and numbers are as listed in Table 2; PDB codes are bracketed.
Figure 2
Figure 2
Group II, zinc-coordinating proteins. Colors, numbers and names are as in Figure 1.
Figure 3
Figure 3
Group III, zipper-type proteins. Colors, numbers and names are as in Figure 1.
Figure 4
Figure 4
Group IV, 'other α helix proteins'. Colors, numbers and names are as in Figure 1.
Figure 5
Figure 5
Group V, β-sheet proteins. Colors, numbers and names are as in Figure 1.
Figure 6
Figure 6
Group VI, the β-hairpin/ribbon proteins. Colors, numbers and names are as in Figure 1.
Figure 7
Figure 7
Group VII, 'other DNA-binding proteins'. Colors, numbers and names are as in Figure 1.
Figure 8
Figure 8
Group VIII, the enzymes. Colors, numbers and names are as in Figure 1.
See this image and copyright information in PMC

References

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