General Information

Database accession: MF2140007

Name: DNA binding domain of the E2 protein (Human papillomavirus type 31)

PDB ID: 1dhm PDB

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 PubMed

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.


Function and Biology Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown.

Molecular function:

DNA binding Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GeneOntology

nucleotide binding Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. GeneOntology

protein binding Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules). GeneOntology

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. GeneOntology

Biological process:

regulation of transcription, DNA-templated Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. GeneOntology

viral DNA genome replication The replication of a viral DNA genome. GeneOntology

regulation of DNA replication Any process that modulates the frequency, rate or extent of DNA replication. GeneOntology

transcription, DNA-templated The cellular synthesis of RNA on a template of DNA. GeneOntology

Cellular component:

host cell nucleus A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction. GeneOntology

Structure Summary Structural annotations of the participating protein chains.

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


Chain A

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) UniProt Coverage: 22.3%

UniRef90 AC: UniRef90_P17383 (positions: 291-372) UniRef90

Chain B

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) UniProt Coverage: 22.3%

UniRef90 AC: UniRef90_P17383 (positions: 291-372) UniRef90

Evidence Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding.

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).

Related Structure(s) Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap).

There is 1 related structure in the Protein Data Bank:





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