PDBsum entry 1jtk

Hydrolase

PDB id: 1jtk

Contents

Protein chains

131 a.a. *

Ligands

THU ×2

Metals

_ZN ×2

Waters ×183

* Residue conservation analysis

PDB id:

1jtk

Name:

Hydrolase

Title:

Crystal structure of cytidine deaminase from bacillus subtilis in complex with the inhibitor tetrahydrodeoxyuridine

Structure:

Cytidine deaminase. Chain: a, b. Engineered: yes

Source:

Bacillus subtilis. Organism_taxid: 1423. Gene: cdd. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.04Å R-factor: 0.207 R-free: 0.232

Authors:

E.Johansson,N.Mejlhede,J.Neuhard,S.Larsen

Key ref:

E.Johansson et al. (2002). Crystal structure of the tetrameric cytidine deaminase from Bacillus subtilis at 2.0 A resolution. Biochemistry, 41, 2563-2570. PubMed id: 11851403 DOI: 10.1021/bi011849a

Date:

21-Aug-01 Release date: 10-Apr-02

Protein chains

P19079  (CDD_BACSU) -  Cytidine deaminase from Bacillus subtilis (strain 168)

Seq: 136 a.a.

Struc: 131 a.a.

Enzyme reactions

• Enzyme class: E.C.3.5.4.5 - cytidine deaminase.
• Reaction:
  1. cytidine + H2O + H⁺ = uridine + NH4⁺
  2. 2'-deoxycytidine + H2O + H⁺ = 2'-deoxyuridine + NH4⁺

cytidine + H2O + H(+) = uridine + NH4(+) (Bound ligand (Het Group name = THU) matches with 94.12% similarity)

2'-deoxycytidine + H2O + H(+) = 2'-deoxyuridine (Bound ligand (Het Group name = THU) corresponds exactly) + NH4(+)

• Cofactor: Zn(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1021/bi011849a

Biochemistry 41:2563-2570 (2002)

PubMed id: 11851403

Crystal structure of the tetrameric cytidine deaminase from Bacillus subtilis at 2.0 A resolution.

E.Johansson, N.Mejlhede, J.Neuhard, S.Larsen.

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.