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 Å
  • R-Value Free: 0.222 
  • R-Value Work: 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.Usa 101: 8114-8119

  • DOI: 10.1073/pnas.0400493101

  • 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
    • 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
    • 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
    • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytidine deaminase
A, B, C, D
142Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CDD1
EC: 3.5.4.5
Find proteins for Q06549 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q06549
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
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 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.188 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 78.520α = 90.00
b = 86.370β = 90.00
c = 156.260γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
SHELXphasing
CNSrefinement
HKL-2000data reduction
RESOLVEphasing
SCALEPACKdata scaling
DMphasing
Omodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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