PDBsum entry 1jjh

DNA binding protein

PDB id: 1jjh

Contents

Protein chains

77 a.a. *

78 a.a. *

73 a.a. *

Waters ×62

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Subunit rearrangement accompanies sequence-Specific DNA binding by the bovine papillomavirus-1 e2 protein.

Authors

R.S.Hegde, A.F.Wang, S.S.Kim, M.Schapira.

Ref.

J Mol Biol, 1998, 276, 797-808. [DOI no: 10.1006/jmbi.1997.1587]

PubMed id

9500927

Abstract

The 2.5 A crystal structures of the DNA-binding domain of the E2 protein from bovine papillomavirus strain 1 and its complex with DNA are presented. E2 is a transcriptional regulatory protein that is also involved in viral DNA replication. It is the structural prototype for a novel class of DNA-binding proteins: dimeric beta-barrels with surface alpha-helices that serve as recognition helices. These helices contain the amino-acid residues involved in sequence-specifying interactions. The E2 proteins from different papillomavirus strains recognize and bind to the same consensus 12 base-pair DNA sequence. However, recent evidence from solution studies points to differences in the mechanisms by which E2 from the related viral strains bovine papillomavirus-1 and human papillomavirus-16 discriminate between DNA targets based on non-contacted nucleotide sequences. This report provides evidence that sequence-specific DNA-binding is accompanied by a rearrangement of protein subunits and deformation of the DNA. These results suggest that, along with DNA sequence-dependent conformational properties, protein subunit orientation plays a significant role in the mechanisms of target selection utilized by E2.

Figure 4.
Figure 4. Amino acid side-chains at the BPV-E2/D dimer interface. View is looking down the protein β-barrel axis. Free BPV-E2/D is shown in red and the two representations of the BPV-E2/D-DNA complex are shown in blue and green.

Figure 5.
Figure 5. (a) Stereo view of a 3F[o] − 2F[c] map calculated around residue Trp360 at the dimer interface of the BPV-E2/D structure. The map is contoured at 1.5σ and viewed using the program O [Jones et al 1991]. (b) Stereo view of a 3F[o] − 2F[c]map calculated at the protein-DNA interface of the BPV-E2/D-DNA co-crystal structure. The map is contoured at 1.25σ and viewed using the program O [Jones et al 1991].

The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 276, 797-808) copyright 1998.