1R5T

The Crystal Structure of Cytidine Deaminase CDD1, an Orphan C to U editase from Yeast


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The structure of a yeast RNA-editing deaminase provides insight into the fold and function of activation-induced deaminase and APOBEC-1.

Xie, K.Sowden, M.P.Dance, G.S.Torelli, A.T.Smith, H.C.Wedekind, J.E.

(2004) Proc Natl Acad Sci U S A 101: 8114-8119

  • DOI: 10.1073/pnas.0400493101
  • Primary Citation of Related Structures:  
    1R5T

  • PubMed Abstract: 
  • Activation-induced deaminase (AID) uses base deamination for class-switch recombination and somatic hypermutation and is related to the mammalian RNA-editing enzyme apolipoprotein B editing catalytic subunit 1 (APOBEC-1). CDD1 is a yeast ortholog of ...

    Activation-induced deaminase (AID) uses base deamination for class-switch recombination and somatic hypermutation and is related to the mammalian RNA-editing enzyme apolipoprotein B editing catalytic subunit 1 (APOBEC-1). CDD1 is a yeast ortholog of APOBEC-1 that exhibits cytidine deaminase and RNA-editing activity. Here, we present the crystal structure of CDD1 at 2.0-A resolution and its use in comparative modeling of APOBEC-1 and AID. The models explain dimerization and the need for trans-acting loops that contribute to active site formation. Substrate selectivity appears to be regulated by a central active site "flap" whose size and flexibility accommodate large substrates in contrast to deaminases of pyrimidine metabolism that bind only small nucleosides or free bases. Most importantly, the results suggested both AID and APOBEC-1 are equally likely to bind single-stranded DNA or RNA, which has implications for the identification of natural AID targets.


    Related Citations: 
    • Activation induced deaminase: the importance of being specific
      Smith, H.C., Bottaro, A., Sowden, M.P., Wedekind, J.E.
      (2004) Trends Genet 20: 224
    • Messenger RNA editing in mammals: new members of the APOBEC family seeking roles in the family business
      Wedekind, J.E., Dance, G.S., Sowden, M.P., Smith, H.C.
      (2003) Trends Genet 19: 207
    • Identification of the Yeast Cytidine Deaminase CDD1 as an Orphan C-to-U RNA Editase
      Dance, G.S., Beemiller, P., Yang, Y., Mater, D.V., Mian, I.S., Smith, H.C.
      (2001) Nucleic Acids Res 29: 1772
    • APOBEC-1 Dependent Cytidine to Uridine Editing of Apolipoprotein B RNA in Yeast
      Dance, G.S., Sowden, M.P., Yang, Y., Smith, H.C.
      (2000) Nucleic Acids Res 28: 424

    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytidine deaminaseA, B, C, D142Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: Cdd1p
EC: 3.5.4.5
Find proteins for Q06549 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06549 
Go to UniProtKB:  Q06549
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.52α = 90
b = 86.37β = 90
c = 156.26γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
SHELXphasing
DMphasing
Omodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-25
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description