6R4U

Crystal structure of the Pri1 subunit of human primase bound to fludarabine triphosphate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural Basis for Inhibition of Human Primase by Arabinofuranosyl Nucleoside Analogues Fludarabine and Vidarabine.

Holzer, S., Rzechorzek, N.J., Short, I.R., Jenkyn-Bedford, M., Pellegrini, L., Kilkenny, M.L.

(2019) ACS Chem Biol 14: 1904-1912

  • DOI: 10.1021/acschembio.9b00367
  • Primary Citation of Related Structures:  
    6RB4, 6R4S, 6R4U, 6R4T, 6R5D, 6R5E

  • PubMed Abstract: 

    • Nucleoside analogues are widely used in clinical practice as chemotherapy drugs. Arabinose nucleoside derivatives such as fludarabine are effective in the treatment of patients with acute and chronic leukemias and non-Hodgkin's lymphomas. Although nucleo ...

    Nucleoside analogues are widely used in clinical practice as chemotherapy drugs. Arabinose nucleoside derivatives such as fludarabine are effective in the treatment of patients with acute and chronic leukemias and non-Hodgkin's lymphomas. Although nucleoside analogues are generally known to function by inhibiting DNA synthesis in rapidly proliferating cells, the identity of their in vivo targets and mechanism of action are often not known in molecular detail. Here we provide a structural basis for arabinose nucleotide-mediated inhibition of human primase, the DNA-dependent RNA polymerase responsible for initiation of DNA synthesis in DNA replication. Our data suggest ways in which the chemical structure of fludarabine could be modified to improve its specificity and affinity toward primase, possibly leading to less toxic and more effective therapeutic agents.

    Organizational Affiliation: 

    Department of Biochemistry , University of Cambridge , 80 Tennis Court Road , Cambridge CB2 1GA , U.K.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA primase small subunit A, E410Homo sapiensMutation(s): 0 
Gene Names: PRIM1
EC: 2.7.7
Find proteins for P49642 (Homo sapiens)
Explore P49642 
Go to UniProtKB:  P49642
NIH Common Fund Data Resources
PHAROS:  P49642
GTEx:  ENSG00000198056
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HFD
Query on HFD
Download Ideal Coordinates CCD File 
A, E
2-fluoro-9-{5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-9H-purin-6-a mine
C10 H15 F N5 O13 P3
PIOKUWLZUXUBCO-FJFJXFQQSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
A, E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
E
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
MN
Query on MN
Download Ideal Coordinates CCD File 
A, E
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.83α = 90
b = 117.57β = 90
c = 148.8γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
Cootmodel building
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom104641/Z/14/Z

Revision History 

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-10-02
    Changes: Data collection, Database references