6K63

The crystal structure of cytidine deaminase from Klebsiella pneumoniae

Summary for 6K63

• Entry DOI: 10.2210/pdb6k63/pdb
• Descriptor: Cytidine deaminase, 1,4-DIETHYLENE DIOXIDE, ZINC ION, ... (4 entities in total)
• Functional Keywords: klebsiella pneumoniae, cytidine deaminase, hydrolase, cda
• Biological source: Klebsiella pneumoniae subsp. pneumoniae MGH 78578
• Total number of polymer chains: 4
• Total formula weight: 127349.55

Authors

Liu, W.,Shang, F.,Lan, J.,Chen, Y.,Wang, L.,Xu, Y. (deposition date: 2019-06-01, release date: 2019-07-31, Last modification date: 2023-11-22)

Primary citation

Liu, W.,Shang, F.,Chen, Y.,Lan, J.,Wang, L.,Chen, J.,Gao, P.,Ha, N.C.,Quan, C.,Nam, K.H.,Xu, Y.
Biochemical and structural analysis of the Klebsiella pneumoniae cytidine deaminase CDA.
Biochem.Biophys.Res.Commun., 519:280-286, 2019

PubMed Abstract: The emergence of drug-resistant strains of Klebsiella pneumoniae, has exacerbated the treatment and control of the disease caused by this bacterium. Cytidine deaminases (CDA) are zinc-dependent enzymes involved in the pyrimidine salvage pathway and catalyze the formation of uridine and deoxyuridine from cytidine and deoxycytidine, respectively. To illustrate the structural basis of CDA for a deeper knowledge of the molecular mechanisms underlying the salvage pathway, we reported here the biochemical and structural analysis of CDA from pathogenic K. pneumonia. KpCDA showed deaminase activity against cytidine as well as its analog cytarabine. The deaminase activity of KpCDA on cytarabine was 1.8 times higher than that on cytidine. KpCDA is composed of an N-terminal catalytic domain and a C-terminal noncatalytic domain. Zinc, which is involved in the activity of the catalytic domain, is coordinated by His102, Cys129, and Cys132, and two 1,4-dioxane molecules were present at the active sites. KpCDA exists as a dimer and shows distinct dimeric interface compared with other CDAs. Our results provide the structural features of KpCDA, and KpCDA might be a potential antibacterial target for the disease caused by K. pneumoniae.

PubMed: 31495495
DOI: 10.1016/j.bbrc.2019.08.167

Experimental method

X-RAY DIFFRACTION (2.073 Å)