3IJF

Crystal structure of cytidine deaminase from Mycobacterium tuberculosis

Summary for 3IJF

• Entry DOI: 10.2210/pdb3ijf/pdb
• Related: 2fr5
• Descriptor: Cytidine deaminase, ZINC ION (3 entities in total)
• Functional Keywords: mycobacterium tuberculosis, cytidine deaminase, drug target, hydrolase
• Biological source: Mycobacterium tuberculosis
• Total number of polymer chains: 1
• Total formula weight: 14153.55

Authors

De Azevedo Jr., W.F.,Basso, L.A.,Santos, D.S. (deposition date: 2009-08-04, release date: 2010-03-02, Last modification date: 2023-09-06)

Primary citation

Sanchez-Quitian, Z.A.,Schneider, C.Z.,Ducati, R.G.,de Azevedo, W.F.,Bloch, C.,Basso, L.A.,Santos, D.S.
Structural and functional analyses of Mycobacterium tuberculosis Rv3315c-encoded metal-dependent homotetrameric cytidine deaminase.
J.Struct.Biol., 169:413-423, 2010

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.

PubMed: 20035876
DOI: 10.1016/j.jsb.2009.12.019

Experimental method

X-RAY DIFFRACTION (1.99 Å)