6X91

Crystal structure of MBP-fused human APOBEC1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.278 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The structure of APOBEC1 and insights into its RNA and DNA substrate selectivity.

Wolfe, A.D.Li, S.Goedderz, C.Chen, X.S.

(2020) NAR Cancer 2: zcaa027-zcaa027

  • DOI: 10.1093/narcan/zcaa027
  • Primary Citation of Related Structures:  
    6X91

  • PubMed Abstract: 
  • APOBEC1 (APO1), a member of AID/APOBEC nucleic acid cytosine deaminase family, can edit apolipoprotein B mRNA to regulate cholesterol metabolism. This APO1 RNA editing activity requires a cellular cofactor to achieve tight regulation. However, no cofactors are required for deamination on DNA by APO1 and other AID/APOBEC members, and aberrant deamination on genomic DNA by AID/APOBEC deaminases has been linked to cancer ...

    APOBEC1 (APO1), a member of AID/APOBEC nucleic acid cytosine deaminase family, can edit apolipoprotein B mRNA to regulate cholesterol metabolism. This APO1 RNA editing activity requires a cellular cofactor to achieve tight regulation. However, no cofactors are required for deamination on DNA by APO1 and other AID/APOBEC members, and aberrant deamination on genomic DNA by AID/APOBEC deaminases has been linked to cancer. Here, we present the crystal structure of APO1, which reveals a typical APOBEC deaminase core structure, plus a unique well-folded C-terminal domain that is highly hydrophobic. This APO1 C-terminal hydrophobic domain (A1HD) interacts to form a stable dimer mainly through hydrophobic interactions within the dimer interface to create a four-stranded β-sheet positively charged surface. Structure-guided mutagenesis within this and other regions of APO1 clarified the importance of the A1HD in directing RNA and cofactor interactions, providing insights into the structural basis of selectivity on DNA or RNA substrates.


    Organizational Affiliation

    Genetics, Molecular and Cellular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
593Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 9 
Gene Names: DAH37_23060APOBEC1
EC: 3.5.4.36
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for P41238 (Homo sapiens)
Explore P41238 
Go to UniProtKB:  P41238
PHAROS:  P41238
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0AEX9P41238
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
I, J, K, L, M, N, O, P, Q, R, S, T, U, V
I, J, K, L, M, N, O, P, Q, R, S, T, U, V
2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAC
Query on CAC

Download Ideal Coordinates CCD File 
BA [auth C],
DA [auth D],
FA [auth E],
HA [auth F],
JA [auth G],
BA [auth C],
DA [auth D],
FA [auth E],
HA [auth F],
JA [auth G],
LA [auth H],
X [auth A],
Z [auth B]
CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth C],
CA [auth D],
EA [auth E],
GA [auth F],
IA [auth G],
AA [auth C],
CA [auth D],
EA [auth E],
GA [auth F],
IA [auth G],
KA [auth H],
W [auth A],
Y [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900001
Query on PRD_900001
I, J, K, L, M, N, O, P, Q, R, S, T, U, Valpha-maltoseOligosaccharide / Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.278 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 177.715α = 90
b = 179.209β = 90
c = 210.505γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release