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

PDB id:

1jjh

Name:

DNA binding protein

Title:

E2 DNA-binding domain from bovine papillomavirus type 1

Structure:

Regulatory protein e2. Chain: a, b, c. Fragment: DNA-binding domain. Engineered: yes

Source:

Bovine papillomavirus type 1. Organism_taxid: 10559. Gene: e2. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.50Å R-factor: 0.225 R-free: 0.266

Authors:

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

Key ref:

R.S.Hegde et al. (1998). Subunit rearrangement accompanies sequence-specific DNA binding by the bovine papillomavirus-1 E2 protein. J Mol Biol, 276, 797-808. PubMed id: 9500927 DOI: 10.1006/jmbi.1997.1587

Date:

05-Jul-01 Release date: 18-Jul-01

Protein chain

P03122  (VE2_BPV1) -  Regulatory protein E2 from Bovine papillomavirus type 1

Seq: 410 a.a.

Struc: 77 a.a.*

Protein chain

P03122  (VE2_BPV1) -  Regulatory protein E2 from Bovine papillomavirus type 1

Seq: 410 a.a.

Struc: 78 a.a.*

Protein chain

P03122  (VE2_BPV1) -  Regulatory protein E2 from Bovine papillomavirus type 1

Seq: 410 a.a.

Struc: 73 a.a.

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DOI no: 10.1006/jmbi.1997.1587

J Mol Biol 276:797-808 (1998)

PubMed id: 9500927

Subunit rearrangement accompanies sequence-specific DNA binding by the bovine papillomavirus-1 E2 protein.

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

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.

Selected figure(s)

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.

Figures were selected by an automated process.