General Information

Database accession: MF2140009

Name: DNA binding domain of the E2 protein (Bovine papillomavirus type 1)

PDB ID: 1dbd PDB

Experimental method: NMR

Assembly: homodimer

Source organism: Bovine papillomavirus type 1

Primer publication of the structure:

Veeraraghavan S, Mello CC, Androphy EJ, Baleja JD
Structural correlates for enhanced stability in the E2 DNA-binding domain from bovine papillomavirus.
(1999) Biochemistry 38: 16115-24

PMID: 10587434 PubMed

Abstract:

Papillomaviral E2 proteins participate in viral DNA replication and transcriptional regulation. We have solved the solution structure of the DNA-binding domain of the E2 protein from bovine papillomavirus (BPV-1). The structure calculation used 2222 distance and 158 dihedral angle restraints for the homodimer (202 residues in total), which were derived from homonuclear and heteronuclear multidimensional nuclear magnetic resonance (NMR) spectroscopic data. The root-mean-square deviation for structured regions of the monomer when superimposed to the average is 0.73 +/- 0.10 A for backbone atoms and 1.42 +/- 0.16 A for heavy atoms. The 101 residue construct used in this study (residues 310-410) is about 4.5 kcal/mol more stable than a minimal domain comprising the C-terminal 85 amino acid residues (residues 326-410). The structure of the core domain contained within BPV-1 E2 is similar to the corresponding regions of other papilloma viral E2 proteins. Here, however, the extra N-terminal 16 residues form a flap that covers a cavity at the dimer interface and play a role in DNA binding. Interactions between residues in the N-terminal extension and the core domain correlate with the greater stability of the longer form of the protein relative to the minimal domain.


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

Molecular function:

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

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

DNA binding Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). 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 DNA replication Any process that modulates the frequency, rate or extent of DNA replication. GeneOntology

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

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: Bovine papillomavirus type 1

Length: 100 residues

Sequence:Sequence according to PDB SEQRESRRTTNDGFHLLKAGGSCFALISGTANQVKCYRFRVKKNHRHRYENCTTTWFTVADNGAERQGQAQILITFGSPSQRQDFLKHVPLPPGMNISGFTASLDF

UniProtKB AC: P03122 (positions: 311-410) UniProt Coverage: 24.4%

UniRef90 AC: UniRef90_P03122 (positions: 311-410) UniRef90

Chain B

Name: Regulatory protein E2

Source organism: Bovine papillomavirus type 1

Length: 100 residues

Sequence:Sequence according to PDB SEQRESRRTTNDGFHLLKAGGSCFALISGTANQVKCYRFRVKKNHRHRYENCTTTWFTVADNGAERQGQAQILITFGSPSQRQDFLKHVPLPPGMNISGFTASLDF

UniProtKB AC: P03122 (positions: 311-410) UniProt Coverage: 24.4%

UniRef90 AC: UniRef90_P03122 (positions: 311-410) 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 are 2 related structures in the Protein Data Bank:











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