PDBsum entry 4lcp

Hydrolase

PDB id: 4lcp

Contents

Protein chains

189 a.a.

Ligands

6AP

Metals

_ZN ×2

Waters ×161

PDB id:

4lcp

Name:

Hydrolase

Title:

Crytsal structure of ne0047 in complex with 2,6-diaminopurine

Structure:

Cytidine and deoxycytidylate deaminase zinc-binding region. Chain: a, b. Engineered: yes

Source:

Nitrosomonas europaea. Organism_taxid: 228410. Strain: atcc 19718 / nbrc 14298. Gene: ne0047. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.00Å R-factor: 0.169 R-free: 0.223

Authors:

A.Bitra,A.Biswas,R.Anand

Key ref:

A.Bitra et al. (2013). Structural basis of the substrate specificity of cytidine deaminase superfamily Guanine deaminase. Biochemistry, 52, 8106-8114. PubMed id: 24083949 DOI: 10.1021/bi400818e

Date:

22-Jun-13 Release date: 22-Jan-14

Protein chains

Q82Y41  (Q82Y41_NITEU) -  Cytidine and deoxycytidylate deaminase zinc-binding region from Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)

Seq: 193 a.a.

Struc: 189 a.a.

Enzyme reactions

• Enzyme class: E.C.3.5.-.-

DOI no: 10.1021/bi400818e

Biochemistry 52:8106-8114 (2013)

PubMed id: 24083949

Structural basis of the substrate specificity of cytidine deaminase superfamily Guanine deaminase.

A.Bitra, A.Biswas, R.Anand.

ABSTRACT

Guanine deaminases (GDs) are important enzymes involved in purine metabolism as well as nucleotide anabolism pathways that exhibit a high degree of fidelity. Here, the structural basis of the substrate specificity of GDs was investigated by determining a series of X-ray structures of NE0047 (GD from Nitrosomonas europaea) with nucleobase analogues and nucleosides. The structures demonstrated that the interactions in the GD active site are tailor-made to accommodate only guanine and any substitutions in the purine ring or introduction of a pyrimidine ring results in rearrangement of the bases in a catalytically unfavorable orientation, away from the proton shuttling residue E143. In addition, X-ray structural studies performed on cytidine revealed that although it binds in an optimal conformation, its deamination does not occur because of the inability of the enzyme to orchestrate the closure of the catalytically important C-terminal loop (residues 181-189). Isothermal calorimetry measurements established that these nucleoside moieties also disrupt the sequential mode of ligand binding, thereby abrogating all intersubunit communication. Intriguingly, it was recently discovered that GDs can also serve as endogenous ammeline deaminases, although it is structurally nonhomologous with guanine. To understand the mechanism of dual-substrate specificity, the structure of NE0047 in complex with ammeline was determined to a resolution of 2.7 Å. The structure revealed that ammeline not only fits in the active site in a catalytically favorable orientation but also allows for closure of the C-terminal loop.