5U6K

Crystal structure of TopBP1 BRCT4/5 in complex with a BLM phosphopeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Insight into BLM Recognition by TopBP1.

Sun, L.Huang, Y.Edwards, R.A.Yang, S.Blackford, A.N.Niedzwiedz, W.Glover, J.N.M.

(2017) Structure 25: 1582-1588.e3

  • DOI: 10.1016/j.str.2017.08.005

  • PubMed Abstract: 
  • Topoisomerase IIβ binding protein 1 (TopBP1) is a critical protein-protein interaction hub in DNA replication checkpoint control. It was proposed that TopBP1 BRCT5 interacts with Bloom syndrome helicase (BLM) to regulate genome stability through eith ...

    Topoisomerase IIβ binding protein 1 (TopBP1) is a critical protein-protein interaction hub in DNA replication checkpoint control. It was proposed that TopBP1 BRCT5 interacts with Bloom syndrome helicase (BLM) to regulate genome stability through either phospho-Ser304 or phospho-Ser338 of BLM. Here we show that TopBP1 BRCT5 specifically interacts with the BLM region surrounding pSer304, not pSer338. Our crystal structure of TopBP1 BRCT4/5 bound to BLM reveals recognition of pSer304 by a conserved pSer-binding pocket, and interactions between an FVPP motif N-terminal to pSer304 and a hydrophobic groove on BRCT5. This interaction utilizes the same surface of BRCT5 that recognizes the DNA damage mediator, MDC1; however the binding orientations of MDC1 and BLM are reversed. While the MDC1 interactions are largely electrostatic, the interaction with BLM has higher affinity and relies on a mix of electrostatics and hydrophobicity. We suggest that similar evolutionarily conserved interactions may govern interactions between TopBP1 and 53BP1.


    Organizational Affiliation

    Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA topoisomerase 2-binding protein 1
A, B, C, D, E, F, G, H
200Mus musculusMutation(s): 0 
Gene Names: Topbp1 (Kiaa0259)
Find proteins for Q6ZQF0 (Mus musculus)
Go to UniProtKB:  Q6ZQF0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Bloom Sydrome recQ helicase like protein (BLM)
L, M, N, O
13Homo sapiensMutation(s): 0 
Gene Names: BLM (RECQ2, RECQL3)
EC: 3.6.4.12
Find proteins for P54132 (Homo sapiens)
Go to Gene View: BLM
Go to UniProtKB:  P54132
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
L, M, N, O
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 98.164α = 90.00
b = 96.817β = 94.25
c = 127.050γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesPO1CA092584
Canadian Institutes of Health ResearchCanada114975
Natural Sciences and Engineering Research Council (Canada)CanadaDiscovery grant 2016-05163

Revision History 

  • Version 1.0: 2017-10-04
    Type: Initial release
  • Version 1.1: 2017-10-25
    Type: Database references