Database Accession: DI2010005
Name: p53 bound to S100B dimer
PDB ID: 1dt7
Experimental method: NMR
Source organism: Homo sapiens / Rattus norvegicus
Proof of disorder:
Kd: 7.40×10-05 M
Primary publication of the structure:
Rustandi RR, Baldisseri DM, Weber DJ
Structure of the negative regulatory domain of p53 bound to S100B(betabeta).
(2000) Nat. Struct. Biol. 7: 570-4
PMID: 10876243
Abstract:
A Ca2+ dependent conformational change in dimeric S100B(betabeta) is required for it to bind p53 and inhibit phosphorylation of this tumor suppressor in its C-terminal negative regulatory domain. A peptide derived from this region of p53 (residues 367-388) was found to have no regular structure in its native form by NMR spectroscopy, but becomes helical when bound to Ca2+ loaded S100B(betabeta). The three-dimensional structure of this complex reveals several favorable hydrophobic and electrostatic interactions between S100B(betabeta) and the p53 peptide in the binding pocket, where S100B(betabeta) sterically blocks sites of phosphorylation and acetylation on p53 that are important for transcription activation.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
zinc ion binding Interacting selectively and non-covalently with zinc (Zn) ions.
identical protein binding Interacting selectively and non-covalently with an identical protein or proteins.
protein dimerization activity The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
Biological process:
positive regulation of apoptotic process Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
regulation of cell proliferation Any process that modulates the frequency, rate or extent of cell proliferation.
regulation of cellular component organization Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
regulation of biological quality Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc.
positive regulation of intracellular signal transduction Any process that activates or increases the frequency, rate or extent of intracellular signal transduction.
multicellular organism development The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
response to organic substance Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
negative regulation of cellular process Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
Cellular component:
Structural annotations of the participating protein chains.Entry contents: 3 distinct polypeptide molecules
Chains: X, A, B
Notes: Chain Y was removed as chains A, B and X highlight the biologically relevant interaction.
Name: Cellular tumor antigen p53
Source organism: Homo sapiens
Length: 22 residues
Sequence:Sequence according to PDB SEQRESSHLKSKKGQSTSRHKKLMFKTE
UniProtKB AC: P04637 (positions: 367-388) Coverage: 5.6%
UniRef90 AC: UniRef90_P04637 (positions: 367-388)
Name: Protein S100-B
Source organism: Rattus norvegicus
Length: 92 residues
Sequence:Sequence according to PDB SEQRESMSELEKAMVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDEDGDGECDFQEFMAFVSMVTTACHEFFEHE
UniProtKB AC: P04631 (positions: 1-92) Coverage: 100%
UniRef90 AC: UniRef90_P04631 (positions: 1-92)
Name: Protein S100-B
Source organism: Rattus norvegicus
Length: 92 residues
Sequence:Sequence according to PDB SEQRESMSELEKAMVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDEDGDGECDFQEFMAFVSMVTTACHEFFEHE
UniProtKB AC: P04631 (positions: 1-92) Coverage: 100%
UniRef90 AC: UniRef90_P04631 (positions: 1-92)
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Chain X:
The 320-393 region described in DisProt entry DP00086 and the 364-389 region described in IDEAL entry IID00015 cover 100% of the sequence present in the structure.
Chain A:
S100B is known to adopt a stable structure in isolation in dimeric form. A solved structure of the domain dimer without bound ligands is represented by PDB ID 1qlk.
Chain B:
S100B is known to adopt a stable structure in isolation in dimeric form. A solved structure of the domain dimer without bound ligands is represented by PDB ID 1qlk.
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.
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