1JTK
Crystal structure of cytidine deaminase from Bacillus subtilis in complex with the inhibitor tetrahydrodeoxyuridine
Summary for 1JTK
| Entry DOI | 10.2210/pdb1jtk/pdb |
| Descriptor | cytidine deaminase, ZINC ION, TETRAHYDRODEOXYURIDINE, ... (4 entities in total) |
| Functional Keywords | cytidine deaminase, cda, pyrimidine salvage pathway, hydrolase |
| Biological source | Bacillus subtilis |
| Total number of polymer chains | 2 |
| Total formula weight | 30329.28 |
| Authors | Johansson, E.,Mejlhede, N.,Neuhard, J.,Larsen, S. (deposition date: 2001-08-21, release date: 2002-04-10, Last modification date: 2023-10-25) |
| Primary citation | Johansson, E.,Mejlhede, N.,Neuhard, J.,Larsen, S. Crystal structure of the tetrameric cytidine deaminase from Bacillus subtilis at 2.0 A resolution. Biochemistry, 41:2563-2570, 2002 Cited by PubMed Abstract: Cytidine deaminases (CDA, EC 3.5.4.5) are zinc-containing enzymes in the pyrimidine salvage pathway that catalyze the formation of uridine and deoxyuridine from cytidine and deoxycytidine, respectively. Two different classes have been identified in the CDA family, a homodimeric form (D-CDA) with two zinc ions per dimer and a homotetrameric form (T-CDA) with four zinc ions per tetramer. We have determined the first structure of a T-CDA from Bacillus subtilis. The active form of T-CDA is assembled of four identical subunits with one active site apiece. The subunit of D-CDA is composed of two domains each exhibiting the same fold as the T-CDA subunits, but only one of them contains zinc in the active site. The similarity results in a conserved structural core in the two CDA forms. An intriguing difference between the two CDA structures is the zinc coordinating residues found at the N-terminal of two alpha-helices: three cysteine residues in the tetrameric form and two cysteine residues and one histidine residue in the dimeric form. The role of the zinc ion is to activate a water molecule and thereby generate a hydroxide ion. How the zinc ion in T-CDA surrounded with three negatively charged residues can create a similar activity of T-CDA compared to D-CDA has been an enigma. However, the structure of T-CDA reveals that the negative charge caused by the three ligands is partly neutralized by (1) an arginine residue hydrogen-bonded to two of the cysteine residues and (2) the dipoles of two alpha-helices. PubMed: 11851403DOI: 10.1021/bi011849a PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.04 Å) |
Structure validation
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