4OFB

Crystal structure of human BRCA1 BRCT in complex with nonphosphopeptide inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Peptide Library Approach to Uncover Phosphomimetic Inhibitors of the BRCA1 C-Terminal Domain.

White, E.R., Sun, L., Ma, Z., Beckta, J.M., Danzig, B.A., Hacker, D.E., Huie, M., Williams, D.C., Edwards, R.A., Valerie, K., Glover, J.N., Hartman, M.C.

(2015) Acs Chem.Biol. 10: 1198-1208

  • DOI: 10.1021/cb500757u

  • PubMed Abstract: 

    • Many intracellular protein-protein interactions are mediated by the phosphorylation of serine, and phosphoserine-containing peptides can inhibit these interactions. However, hydrolysis of the phosphate by phosphatases, and the poor cell permeability ...

    Many intracellular protein-protein interactions are mediated by the phosphorylation of serine, and phosphoserine-containing peptides can inhibit these interactions. However, hydrolysis of the phosphate by phosphatases, and the poor cell permeability associated with phosphorylated peptides has limited their utility in cellular and in vivo contexts. Compounding the problem, strategies to replace phosphoserine in peptide inhibitors with easily accessible mimetics (such as Glu or Asp) routinely fail. Here, we present an in vitro selection strategy for replacement of phosphoserine. Using mRNA display, we created a 10 trillion member structurally diverse unnatural peptide library. From this library, we found a peptide that specifically binds to the C-terminal domain (BRCT)2 of breast cancer associated protein 1 (BRCA1) with an affinity comparable to phosphorylated peptides. A crystal structure of the peptide bound reveals that the pSer-x-x-Phe motif normally found in BRCA1 (BRCT)2 binding partners is replaced by a Glu-x-x-4-fluoroPhe and that the peptide picks up additional contacts on the protein surface not observed in cognate phosphopeptide binding. Expression of the peptide in human cells led to defects in DNA repair by homologous recombination, a process BRCA1 is known to coordinate. Overall, this work validates a new in vitro selection approach for the development of inhibitors of protein-protein interactions mediated by serine phosphorylation.

    Organizational Affiliation: 

    †Department of Chemistry, Virginia Commonwealth University (VCU), 1001 West Main Street, P.O. Box 842006, Richmond, Virginia 23284, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Breast cancer type 1 susceptibility protein
A
214Homo sapiensMutation(s): 0 
Gene Names: BRCA1 (RNF53)
EC: 2.3.2.27
Find proteins for P38398 (Homo sapiens)
Go to Gene View: BRCA1
Go to UniProtKB:  P38398
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
nonphosphopeptide inhibitor
B
14N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
B
NON-POLYMERH2 N

--

PFF
Query on PFF
B
L-PEPTIDE LINKINGC9 H10 F N O2PHE
ACE
Query on ACE
B
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.210 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 37.811α = 90.00
b = 37.811β = 90.00
c = 175.993γ = 90.00
Software Package:
Software NamePurpose
MxDCdata collection
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-15
    Type: Initial release
  • Version 1.1: 2015-05-27
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description