PDBsum entry 1z3a

Hydrolase

PDB id: 1z3a

Contents

Protein chains

156 a.a. *

Metals

_ZN ×2

Waters ×226

* Residue conservation analysis

PDB id:

1z3a

Name:

Hydrolase

Title:

Crystal structure of tRNA adenosine deaminase tada from escherichia coli

Structure:

tRNA-specific adenosine deaminase. Chain: a, b. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: tada. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Dimer (from PQS)

Resolution:

2.03Å R-factor: 0.176 R-free: 0.216

Authors:

V.Malashkevich,J.Kim,M.Lisbin,S.C.Almo,S.K.Burley,New York Sgx Research Center For Structural Genomics (Nysgxrc)

Key ref:

J.Kim et al. (2006). Structural and kinetic characterization of Escherichia coli TadA, the wobble-specific tRNA deaminase. Biochemistry, 45, 6407-6416. PubMed id: 16700551

Date:

10-Mar-05 Release date: 21-Feb-06

Protein chains

P68398  (TADA_ECOLI) -  tRNA-specific adenosine deaminase from Escherichia coli (strain K12)

Seq: 167 a.a.

Struc: 156 a.a.

Enzyme reactions

• Enzyme class: E.C.3.5.4.33 - tRNA(adenine(34)) deaminase.
• Reaction: adenosine₃₄ in tRNA + H2O + H⁺ = inosine₃₄ in tRNA + NH4⁺
• Cofactor: Zn(2+)

Biochemistry 45:6407-6416 (2006)

PubMed id: 16700551

Structural and kinetic characterization of Escherichia coli TadA, the wobble-specific tRNA deaminase.

J.Kim, V.Malashkevich, S.Roday, M.Lisbin, V.L.Schramm, S.C.Almo.

ABSTRACT

The essential tRNA-specific adenosine deaminase catalyzes the deamination of adenosine to inosine at the wobble position of tRNAs. This modification allows for a single tRNA species to recognize multiple synonymous codons containing A, C, or U in the last (3'-most) position and ensures that all sense codons are appropriately decoded. We report the first combined structural and kinetic characterization of a wobble-specific deaminase. The structure of the Escherichia coli enzyme clearly defines the dimer interface and the coordination of the catalytically essential zinc ion. The structure also identifies the nucleophilic water and highlights residues near the catalytic zinc likely to be involved in recognition and catalysis of polymeric RNA substrates. A minimal 19 nucleotide RNA stem substrate has permitted the first steady-state kinetic characterization of this enzyme (k(cat) = 13 +/- 1 min(-)(1) and K(M) = 0.83 +/- 0.22 microM). A continuous coupled assay was developed to follow the reaction at high concentrations of polynucleotide substrates (>10 microM). This work begins to define the chemical and structural determinants responsible for catalysis and substrate recognition and lays the foundation for detailed mechanistic analysis of this essential enzyme.