5KEG

Crystal structure of APOBEC3A in complex with a single-stranded DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity.

Kouno, T.Silvas, T.V.Hilbert, B.J.Shandilya, S.M.D.Bohn, M.F.Kelch, B.A.Royer, W.E.Somasundaran, M.Kurt Yilmaz, N.Matsuo, H.Schiffer, C.A.

(2017) Nat Commun 8: 15024-15024

  • DOI: 10.1038/ncomms15024
  • Primary Citation of Related Structures:  
    5KEG

  • PubMed Abstract: 
  • Nucleic acid editing enzymes are essential components of the immune system that lethally mutate viral pathogens and somatically mutate immunoglobulins, and contribute to the diversification and lethality of cancers. Among these enzymes are the seven human APOBEC3 deoxycytidine deaminases, each with unique target sequence specificity and subcellular localization ...

    Nucleic acid editing enzymes are essential components of the immune system that lethally mutate viral pathogens and somatically mutate immunoglobulins, and contribute to the diversification and lethality of cancers. Among these enzymes are the seven human APOBEC3 deoxycytidine deaminases, each with unique target sequence specificity and subcellular localization. While the enzymology and biological consequences have been extensively studied, the mechanism by which APOBEC3s recognize and edit DNA remains elusive. Here we present the crystal structure of a complex of a cytidine deaminase with ssDNA bound in the active site at 2.2 Å. This structure not only visualizes the active site poised for catalysis of APOBEC3A, but pinpoints the residues that confer specificity towards CC/TC motifs. The APOBEC3A-ssDNA complex defines the 5'-3' directionality and subtle conformational changes that clench the ssDNA within the binding groove, revealing the architecture and mechanism of ssDNA recognition that is likely conserved among all polynucleotide deaminases, thereby opening the door for the design of mechanistic-based therapeutics.


    Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA dC->dU-editing enzyme APOBEC-3AA203Homo sapiensMutation(s): 2 
Gene Names: APOBEC3A
EC: 3.5.4 (PDB Primary Data), 3.5.4.38 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P31941 (Homo sapiens)
Explore P31941 
Go to UniProtKB:  P31941
PHAROS:  P31941
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*TP*CP*TP*T)-3')B15synthetic construct
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    C [auth A]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    CA
    Query on CA

    Download Ideal Coordinates CCD File 
    D [auth A]CALCIUM ION
    Ca
    BHPQYMZQTOCNFJ-UHFFFAOYSA-N
     Ligand Interaction
    CL
    Query on CL

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

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.20 Å
    • R-Value Free: 0.225 
    • R-Value Work: 0.177 
    • Space Group: I 2 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 56.583α = 90
    b = 72.666β = 90
    c = 114.971γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-3000data reduction
    HKL-3000data scaling
    PHENIXphasing

    Structure Validation

    View Full Validation Report




    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM091743

    Revision History  (Full details and data files)

    • Version 1.0: 2017-05-10
      Type: Initial release
    • Version 1.1: 2017-09-13
      Changes: Author supporting evidence
    • Version 1.2: 2019-12-25
      Changes: Author supporting evidence