Crystal Structure of Mouse Cytidine Deaminase Complexed with Tetrahydrouridine

Experimental Data Snapshot

  • Resolution: 1.48 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

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The 1.48 A Resolution Crystal Structure of the Homotetrameric Cytidine Deaminase from Mouse

Teh, A.H.Kimura, M.Yamamoto, M.Tanaka, N.Yamaguchi, I.Kumasaka, T.

(2006) Biochemistry 45: 7825-7833

  • DOI: https://doi.org/10.1021/bi060345f
  • Primary Citation of Related Structures:  
    1ZAB, 2FR5, 2FR6

  • PubMed Abstract: 

    Cytidine deaminase (CDA) is a zinc-dependent enzyme that catalyzes the deamination of cytidine or deoxycytidine to form uridine or deoxyuridine. Here we present the crystal structure of mouse CDA (MmCDA), complexed with either tetrahydrouridine (THU), 3-deazauridine (DAU), or cytidine. In the MmCDA-DAU complex, it clearly demonstrates that cytidine is distinguished from uridine by its 4-NH(2) group that acts as a hydrogen bond donor. In the MmCDA-cytidine complex, cytidine, unexpectedly, binds as the substrate instead of the deaminated product in three of the four subunits, and in the remaining subunit it binds as the product uridine. Furthermore, the charge-neutralizing Arg68 of MmCDA has also exhibited two alternate conformations, I and II. In conformation I, the only conformation observed in the other structurally known homotetrameric CDAs, Arg68 hydrogen bonds Cys65 and Cys102 to modulate part of their negative charges. However, in conformation II the side chain of Arg68 rotates about 130 degrees around the Cgamma-Cdelta bond and abolishes these hydrogen bonds. The lack of hydrogen bonding may indirectly weaken the zinc-product interaction by increased electron donation from cysteine to the zinc ion, suggesting a novel product-expelling mechanism. On the basis of known structures, structural analysis further reveals two subclasses of homotetrameric CDAs that can be identified according to the position of the charge-neutralizing arginine residue. Implications for CDA-RNA interaction have also been considered.

  • Organizational Affiliation

    Department of Life Science, Tokyo Institute of Technology, 4259-B-6 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytidine deaminase
A, B, C, D
146Mus musculusMutation(s): 0 
Find proteins for P56389 (Mus musculus)
Explore P56389 
Go to UniProtKB:  P56389
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56389
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on TYU

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
K [auth C],
M [auth D]
C9 H16 N2 O6
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth C],
L [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.48 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.238α = 90
b = 93.403β = 90
c = 180.743γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
PDB_EXTRACTdata extraction
BBSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2006-07-11 
  • Deposition Author(s): Teh, A.H.

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-11
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description