Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 62.47 kDa 
• Atom Count: 4517 
• Modelled Residue Count: 554 
• Deposited Residue Count: 568 
• Unique protein chains: 1

1R5T

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

• PDB DOI: 10.2210/pdb1R5T/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-10-13 Released: 2004-05-25 
• Deposition Author(s): Xie, K., Sowden, M.P., Dance, G.S.C., Torelli, A.T., Smith, H.C., Wedekind, J.E.

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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 

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

• PubMed: 15148397 
• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytidine deaminase	A, B, C, D	142	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: Cdd1p EC: 3.5.4.5
UniProt
Find proteins for Q06549 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06549  Go to UniProtKB:  Q06549

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth B], G [auth C], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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 = 78.52	α = 90
b = 86.37	β = 90
c = 156.26	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
SHELX	phasing
DM	phasing
O	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-10-13 
• Released Date: 2004-05-25 
Deposition Author(s): Xie, K., Sowden, M.P., Dance, G.S.C., Torelli, A.T., Smith, H.C., Wedekind, J.E.

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