Crystal structure of cytidine deaminase from Mycobacterium tuberculosis

Experimental Data Snapshot

  • Resolution: 1.99 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

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Structural and functional analyses of Mycobacterium tuberculosis Rv3315c-encoded metal-dependent homotetrameric cytidine deaminase.

Sanchez-Quitian, Z.A.Schneider, C.Z.Ducati, R.G.de Azevedo, W.F.Bloch, C.Basso, L.A.Santos, D.S.

(2010) J Struct Biol 169: 413-423

  • DOI: https://doi.org/10.1016/j.jsb.2009.12.019
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The emergence of drug-resistant strains of Mycobacterium tuberculosis, the causative agent of tuberculosis, has exacerbated the treatment and control of this disease. Cytidine deaminase (CDA) is a pyrimidine salvage pathway enzyme that recycles cytidine and 2'-deoxycytidine for uridine and 2'-deoxyuridine synthesis, respectively. A probable M. tuberculosis CDA-coding sequence (cdd, Rv3315c) was cloned, sequenced, expressed in Escherichia coli BL21(DE3), and purified to homogeneity. Mass spectrometry, N-terminal amino acid sequencing, gel filtration chromatography, and metal analysis of M. tuberculosis CDA (MtCDA) were carried out. These results and multiple sequence alignment demonstrate that MtCDA is a homotetrameric Zn(2+)-dependent metalloenzyme. Steady-state kinetic measurements yielded the following parameters: K(m)=1004 microM and k(cat)=4.8s(-1) for cytidine, and K(m)=1059 microM and k(cat)=3.5s(-1) for 2'-deoxycytidine. The pH dependence of k(cat) and k(cat)/K(M) for cytidine indicate that protonation of a single ionizable group with apparent pK(a) value of 4.3 abolishes activity, and protonation of a group with pK(a) value of 4.7 reduces binding. MtCDA was crystallized and crystal diffracted at 2.0 A resolution. Analysis of the crystallographic structure indicated the presence of a Zn(2+) coordinated by three conserved cysteines and the structure exhibits the canonical cytidine deaminase fold.

  • Organizational Affiliation

    Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga, 6681, Porto Alegre, RS 90619-900, Brazil.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytidine deaminaseA [auth X]133Mycobacterium tuberculosisMutation(s): 0 
Gene Names: cddMT3416Rv3315c
Find proteins for P9WPH3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPH3 
Go to UniProtKB:  P9WPH3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPH3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
B [auth X]ZINC ION
Experimental Data & Validation

Experimental Data

  • Resolution: 1.99 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.705α = 90
b = 75.338β = 90
c = 55.116γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description