Database accession: MF2140007
Name: DNA binding domain of the E2 protein (Human papillomavirus type 31)
PDB ID: 1dhm
Experimental method: NMR
Assembly: homodimer
Source organism: Human papillomavirus type 31
Primer publication of the structure:
Liang H, Petros AM, Meadows RP, Yoon HS, Egan DA, Walter K, Holzman TF, Robins T, Fesik SW
Solution structure of the DNA-binding domain of a human papillomavirus E2 protein: evidence for flexible DNA-binding regions.
(1996) Biochemistry 35: 2095-103
PMID: 8652551
Abstract:
The three-dimensional structure of the DNA-binding domain of the E2 protein from human papillomavirus-31 was determined by using multidimensional heteronuclear nuclear magnetic resonance (NMR) spectroscopy. A total of 1429 NMR-derived distance and dihedral angle restraints were obtained for each of the 83-residue subunits of this symmetric dimer. The average root mean square deviations of 20 structures calculated using a distance geometry-simulated annealing protocol are 0.59 and 0.90 angstroms for the backbone and all heavy atoms, respectively, for residues 2-83. The structure of the human virus protein free in solution consists of an eight-stranded beta-barrel and two pairs of alpha-helices. Although the overall fold of the protein is similar to the crystal structure of the bovine papillomavirus-1 E2 protein when complexed to DNA, several small but interesting differences were observed between these two structures at the subunit interface. In addition, a beta-hairpin that contacts DNA in the crystal structure of the protein-DNA complex is disordered in the NMR structures, and steady-state 1H-15N heteronuclear NOE measurements indicate that this region is highly mobile in the absence of DNA. The recognition helix also appears to be flexible, as evidenced by fast amide exchange rates. This phenomenon has also been observed for a number of other DNA-binding proteins and may constitute a common theme in protein/DNA recognition.
Molecular function:
transcription factor activity, sequence-specific DNA binding Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
Biological process:
regulation of transcription, DNA-templated Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
viral DNA genome replication The replication of a viral DNA genome.
regulation of DNA replication Any process that modulates the frequency, rate or extent of DNA replication.
transcription, DNA-templated The cellular synthesis of RNA on a template of DNA.
Cellular component:
Entry contents: 2 distinct polypeptide molecules
Chains: A, B
Notes: No modifications of the original PDB file. Chain identifiers are identical with the PDB's identifiers.
Number of unique protein segments: 1
Name: Regulatory protein E2
Source organism: Human papillomavirus type 31
Length: 83 residues
Sequence:Sequence according to PDB SEQRESMATTPIIHLKGDANILKCLRYRLSKYKQLYEQVSSTWHWTCTDGKHKNAIVTLTYISTSQRDDFLNTVKIPNTVSVSTGYMTI
UniProtKB AC: P17383 (positions: 290-372)
Coverage: 22.3%UniRef90 AC: UniRef90_P17383 (positions: 291-372)
Name: Regulatory protein E2
Source organism: Human papillomavirus type 31
Length: 83 residues
Sequence:Sequence according to PDB SEQRESMATTPIIHLKGDANILKCLRYRLSKYKQLYEQVSSTWHWTCTDGKHKNAIVTLTYISTSQRDDFLNTVKIPNTVSVSTGYMTI
UniProtKB AC: P17383 (positions: 290-372)
Coverage: 22.3%UniRef90 AC: UniRef90_P17383 (positions: 291-372)
Complex evidence:
The DNA binding domain of E2 was shown to exhibit a two-state concerted unfolding and dissociation in denaturation/renaturation experiments (PMID: 8745409, PMID: 8756330).