Metagenomic cytidine deaminase Cdd

Experimental Data Snapshot

  • Resolution: 1.20 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Cytidine deaminases catalyze the conversion of N ( S , O ) 4 -substituted pyrimidine nucleosides.

Urbeliene, N.Tiskus, M.Tamulaitiene, G.Gasparaviciute, R.Lapinskaite, R.Jauniskis, V.Sudzius, J.Meskiene, R.Tauraite, D.Skrodenyte, E.Urbelis, G.Vaitekunas, J.Meskys, R.

(2023) Sci Adv 9: eade4361-eade4361

  • DOI: https://doi.org/10.1126/sciadv.ade4361
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Cytidine deaminases (CDAs) catalyze the hydrolytic deamination of cytidine and 2'-deoxycytidine to uridine and 2'-deoxyuridine. Here, we report that prokaryotic homo-tetrameric CDAs catalyze the nucleophilic substitution at the fourth position of N 4 -acyl-cytidines, N 4 -alkyl-cytidines, and N 4 -alkyloxycarbonyl-cytidines, and S 4 -alkylthio-uridines and O 4 -alkyl-uridines, converting them to uridine and corresponding amide, amine, carbamate, thiol, or alcohol as leaving groups. The x-ray structure of a metagenomic CDA_F14 and the molecular modeling of the CDAs used in this study show a relationship between the bulkiness of a leaving group and the volume of the binding pocket, which is partly determined by the flexible β3α3 loop of CDAs. We propose that CDAs that are active toward a wide range of substrates participate in salvage and/or catabolism of variously modified pyrimidine nucleosides. This identified promiscuity of CDAs expands the knowledge about the cellular turnover of cytidine derivatives, including the pharmacokinetics of pyrimidine-based prodrugs.

  • Organizational Affiliation

    Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av., 10257 Vilnius, Lithuania.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Metagenomic cytidine deaminase Cdd
A, B, C, D, E
A, B, C, D, E, F, G, H
140uncultured bacteriumMutation(s): 0 
Gene Names: cdd
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MPD

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth F]
DA [auth G]
EA [auth G]
GA [auth H]
AA [auth F],
BA [auth F],
DA [auth G],
EA [auth G],
GA [auth H],
HA [auth H],
J [auth A],
K [auth A],
M [auth B],
N [auth B],
P [auth C],
Q [auth C],
S [auth D],
T [auth D],
V [auth E],
W [auth E]
C6 H14 O2
Query on SO4

Download Ideal Coordinates CCD File 
X [auth E],
Y [auth E]
O4 S
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
CA [auth G]
FA [auth H]
I [auth A]
L [auth B]
O [auth C]
CA [auth G],
FA [auth H],
I [auth A],
L [auth B],
O [auth C],
R [auth D],
U [auth E],
Z [auth F]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.20 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.484α = 90
b = 128.899β = 90.02
c = 97.259γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other governmentLithuania01.2.2-LMT-K-718-03-0082

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-01
    Type: Initial release
  • Version 1.1: 2023-02-15
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description