7AUD

Structure of an engineered helicase domain construct for human Bloom syndrome protein (BLM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Uncovering an allosteric mode of action for a selective inhibitor of human Bloom syndrome protein.

Chen, X.Ali, Y.I.Fisher, C.E.Arribas-Bosacoma, R.Rajasekaran, M.B.Williams, G.Walker, S.Booth, J.R.Hudson, J.J.Roe, S.M.Pearl, L.H.Ward, S.E.Pearl, F.M.Oliver, A.W.

(2021) Elife 10

  • DOI: https://doi.org/10.7554/eLife.65339
  • Primary Citation of Related Structures:  
    7AUC, 7AUD

  • PubMed Abstract: 

    BLM (Bloom syndrome protein) is a RECQ-family helicase involved in the dissolution of complex DNA structures and repair intermediates. Synthetic lethality analysis implicates BLM as a promising target in a range of cancers with defects in the DNA damage response; however, selective small molecule inhibitors of defined mechanism are currently lacking. Here, we identify and characterise a specific inhibitor of BLM's ATPase-coupled DNA helicase activity, by allosteric trapping of a DNA-bound translocation intermediate. Crystallographic structures of BLM-DNA-ADP-inhibitor complexes identify a hitherto unknown interdomain interface, whose opening and closing are integral to translocation of ssDNA, and which provides a highly selective pocket for drug discovery. Comparison with structures of other RECQ helicases provides a model for branch migration of Holliday junctions by BLM.


  • Organizational Affiliation

    Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, United Kingdom.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bloom syndrome protein,Bloom syndrome protein
A, B, C, D, E
A, B, C, D, E, F
563Homo sapiensMutation(s): 0 
Gene Names: BLMRECQ2RECQL3
EC: 3.6.4.12 (PDB Primary Data), 5.6.2.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P54132 (Homo sapiens)
Explore P54132 
Go to UniProtKB:  P54132
PHAROS:  P54132
GTEx:  ENSG00000197299 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54132
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*TP*AP*CP*CP*CP*GP*AP*TP*GP*TP*GP*T)-3')15synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
BA [auth D]
FA [auth E]
JA [auth F]
N [auth A]
S [auth B]
BA [auth D],
FA [auth E],
JA [auth F],
N [auth A],
S [auth B],
W [auth C]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
RY8 (Subject of Investigation/LOI)
Query on RY8

Download Ideal Coordinates CCD File 
CA [auth D]
GA [auth E]
KA [auth F]
O [auth A]
T [auth B]
CA [auth D],
GA [auth E],
KA [auth F],
O [auth A],
T [auth B],
X [auth C]
N-(2,3-dimethyl-5-sulfamoylphenyl)-4-(2-methylthiazol-4-yl)benzamide
C19 H19 N3 O3 S2
GGIKQVGRVUTAKR-UHFFFAOYSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
DA [auth D]
HA [auth E]
P [auth A]
Q [auth A]
U [auth B]
DA [auth D],
HA [auth E],
P [auth A],
Q [auth A],
U [auth B],
Y [auth C],
Z [auth C]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth D]
EA [auth E]
IA [auth F]
M [auth A]
R [auth B]
AA [auth D],
EA [auth E],
IA [auth F],
M [auth A],
R [auth B],
V [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
LA [auth F]
MA [auth M]
NA [auth N]
OA [auth P]
PA [auth Q]
LA [auth F],
MA [auth M],
NA [auth N],
OA [auth P],
PA [auth Q],
QA [auth Q]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.916α = 72.64
b = 111.709β = 80.18
c = 132.344γ = 79.22
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC302/A24386
Wellcome TrustUnited Kingdom110578/Z/15/Z

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-16
    Type: Initial release
  • Version 1.1: 2021-03-17
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Advisory, Data collection, Database references, Refinement description