Database accession: MF2201002
Name: CBP nuclear coactivator binding domain in complex with p53 TAD
PDB ID: 2l14
Experimental method: NMR
Assembly: heterodimer
Source organism: Mus musculus / Homo sapiens
Primer publication of the structure:
Lee CW, Martinez-Yamout MA, Dyson HJ, Wright PE
Structure of the p53 transactivation domain in complex with the nuclear receptor coactivator binding domain of CREB binding protein.
(2010) Biochemistry 49: 9964-71
PMID: 20961098
Abstract:
The activity and stability of the tumor suppressor p53 are regulated by interactions with key cellular proteins such as MDM2 and CBP/p300. The transactivation domain (TAD) of p53 contains two subdomains (AD1 and AD2) and interacts directly with the N-terminal domain of MDM2 and with several domains of CBP/p300. Here we report the NMR structure of the full-length p53 TAD in complex with the nuclear coactivator binding domain (NCBD) of CBP. Both the p53 TAD and NCBD are intrinsically disordered and fold synergistically upon binding, as evidenced by the observed increase in helicity and increased level of dispersion of the amide proton resonances. The p53 TAD folds to form a pair of helices (denoted Pα1 and Pα2), which extend from Phe19 to Leu25 and from Pro47 to Trp53, respectively. In the complex, the NCBD forms a bundle of three helices (Cα1, residues 2066-2075; Cα2, residues 2081-2092; and Cα3, residues 2095-2105) with a hydrophobic groove into which p53 helices Pα1 and Pα2 dock. The polypeptide chain between the p53 helices remains flexible and makes no detectable intermolecular contacts with the NCBD. Complex formation is driven largely by hydrophobic contacts that form a stable intermolecular hydrophobic core. A salt bridge between D49 of p53 and R2105 of NCBD may contribute to the binding specificity. The structure provides the first insights into simultaneous binding of the AD1 and AD2 motifs to a target protein.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding Interacting selectively and non-covalently with a sequence of DNA that is in the transcription regulatory region for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
RNA polymerase II transcription factor binding Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II.
p53 binding Interacting selectively and non-covalently with one of the p53 family of proteins.
damaged DNA binding Interacting selectively and non-covalently with damaged DNA.
zinc ion binding Interacting selectively and non-covalently with zinc (Zn) ions.
Biological process:
negative regulation of transcription from RNA polymerase II promoter Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
rhythmic process Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
positive regulation of transcription from RNA polymerase II promoter Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
transcription from RNA polymerase II promoter The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
Cellular component:
nuclear chromatin The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
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: 2
Name: CREB-binding protein
Source organism: Mus musculus
Length: 59 residues
Sequence:Sequence according to PDB SEQRESPNRSISPSALQDLLRTLKSPSSPQQQQQVLNILKSNPQLMAAFIKQRTAKYVANQPGMQ
UniProtKB AC: P45481 (positions: 2059-2117) Coverage: 2.4%
UniRef90 AC: UniRef90_Q92793 (positions: 2058-2116)
Name: Cellular tumor antigen p53
Source organism: Homo sapiens
Length: 49 residues
Sequence:Sequence according to PDB SEQRESPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPD
UniProtKB AC: P04637 (positions: 13-61) Coverage: 12.5%
UniRef90 AC: UniRef90_P04637 (positions: 13-61)
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Chain A:
The 2059-2152 region described in DisProt entry DP00348 and the 2057-2117 region described in IDEAL entry IID50008 cover 100% of the sequence present in the structure.
Chain B:
The 1-73 region described in DisProt entry DP00086 and the 1-96 region described in IDEAL entry IID00015 cover 100% of the sequence present in the structure.
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). No related structure was found in the Protein Data Bank.
