MF2140007
DNA binding domain of the E2 protein (Human papillomavirus type 31)
1dhm
NMR
homodimer
Human papillomavirus type 31
8652551
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.
Biochemistry
1996
7
35
2095-103
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.
GO:0003677
DNA binding
GO:0000166
nucleotide binding
GO:0005515
protein binding
GO:0003700
transcription factor activity, sequence-specific DNA binding
GO:0006355
regulation of transcription, DNA-templated
GO:0039693
viral DNA genome replication
GO:0006275
regulation of DNA replication
GO:0006351
transcription, DNA-templated
GO:0042025
host cell nucleus
No modifications of the original PDB file. Chain identifiers are identical with the PDB's identifiers.
2
1
Other
E2 dimer
A
Regulatory protein E2
Human papillomavirus type 31
MATTPIIHLKGDANILKCLRYRLSKYKQLYEQVSSTWHWTCTDGKHKNAIVTLTYISTSQRDDFLNTVKIPNTVSVSTGYMTI
83
P17383
290
372
22.3%
UniRef90_P17383
291
372
secondary structure
beta
294
299
secondary structure
helix
302
314
secondary structure
beta
321
322
secondary structure
beta
326
326
secondary structure
beta
339
343
secondary structure
helix
347
356
secondary structure
beta
364
369
pfam
PF00511.14
PPV_E2_C
294
370
B
Regulatory protein E2
Human papillomavirus type 31
MATTPIIHLKGDANILKCLRYRLSKYKQLYEQVSSTWHWTCTDGKHKNAIVTLTYISTSQRDDFLNTVKIPNTVSVSTGYMTI
83
P17383
290
372
22.3%
UniRef90_P17383
291
372
secondary structure
beta
294
299
secondary structure
helix
302
314
secondary structure
beta
321
322
secondary structure
beta
326
326
secondary structure
beta
339
343
secondary structure
helix
347
356
secondary structure
beta
364
369
pfam
PF00511.14
PPV_E2_C
294
370
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).
1a7g