5CQH

Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 

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This is version 1.6 of the entry. See complete history


Literature

Crystal Structure of the DNA Deaminase APOBEC3B Catalytic Domain.

Shi, K.Carpenter, M.A.Kurahashi, K.Harris, R.S.Aihara, H.

(2015) J Biol Chem 290: 28120-28130

  • DOI: https://doi.org/10.1074/jbc.M115.679951
  • Primary Citation of Related Structures:  
    5CQD, 5CQH, 5CQI, 5CQK

  • PubMed Abstract: 

    Functional and deep sequencing studies have combined to demonstrate the involvement of APOBEC3B in cancer mutagenesis. APOBEC3B is a single-stranded DNA cytosine deaminase that functions normally as a nuclear-localized restriction factor of DNA-based pathogens. However, it is overexpressed in cancer cells and elicits an intrinsic preference for 5'-TC motifs in single-stranded DNA, which is the most frequently mutated dinucleotide in breast, head/neck, lung, bladder, cervical, and several other tumor types. In many cases, APOBEC3B mutagenesis accounts for the majority of both dispersed and clustered (kataegis) cytosine mutations. Here, we report the first structures of the APOBEC3B catalytic domain in multiple crystal forms. These structures reveal a tightly closed active site conformation and suggest that substrate accessibility is regulated by adjacent flexible loops. Residues important for catalysis are identified by mutation analyses, and the results provide insights into the mechanism of target site selection. We also report a nucleotide (dCMP)-bound crystal structure that informs a multistep model for binding single-stranded DNA. Overall, these high resolution crystal structures provide a framework for further mechanistic studies and the development of novel anti-cancer drugs to inhibit this enzyme, dampen tumor evolution, and minimize adverse outcomes such as drug resistance and metastasis.


  • Organizational Affiliation

    Department of Biochemistry, Molecular Biology, and Biophysics; Institute for Molecular Virology; Masonic Cancer Center. Electronic address: rsh@umn.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA dC-dU-editing enzyme APOBEC-3B186Homo sapiensMutation(s): 0 
Gene Names: APOBEC3B
EC: 3.5.4 (PDB Primary Data), 3.5.4.38 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UH17 (Homo sapiens)
Explore Q9UH17 
Go to UniProtKB:  Q9UH17
PHAROS:  Q9UH17
GTEx:  ENSG00000179750 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UH17
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DC
Query on DC

Download Ideal Coordinates CCD File 
C [auth A]2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O7 P
NCMVOABPESMRCP-SHYZEUOFSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.843α = 90
b = 52.448β = 90
c = 68.035γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-07
    Type: Initial release
  • Version 1.1: 2015-10-14
    Changes: Database references
  • Version 1.2: 2015-12-02
    Changes: Database references
  • Version 1.3: 2016-07-20
    Changes: Data collection
  • Version 1.4: 2017-09-27
    Changes: Author supporting evidence, Derived calculations
  • Version 1.5: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.6: 2024-03-06
    Changes: Data collection, Database references