PDBsum entry 1kic

Hydrolase

PDB id: 1kic

Contents

Protein chains

317 a.a. *

Ligands

NOS ×4

Metals

_CA ×2

_NI

Waters ×631

* Residue conservation analysis

PDB id:

1kic

Name:

Hydrolase

Title:

Inosine-adenosine-guanosine preferring nucleoside hydrolase from trypanosoma vivax: asp10ala mutant in complex with inosine

Structure:

Inosine-adenosine-guanosine preferring nucleoside hydrolase. Chain: a, b. Synonym: iag-nucleoside hydrolase, iag-nh. Engineered: yes. Mutation: yes

Source:

Trypanosoma vivax. Organism_taxid: 5699. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.60Å R-factor: 0.176 R-free: 0.194

Authors:

W.Versees,K.Decanniere,E.Van Holsbeke,N.Devroede,J.Steyaert

Key ref:

W.Versées et al. (2002). Enzyme-substrate interactions in the purine-specific nucleoside hydrolase from Trypanosoma vivax. J Biol Chem, 277, 15938-15946. PubMed id: 11854281 DOI: 10.1074/jbc.M111735200

Date:

03-Dec-01 Release date: 15-May-02

Protein chains

Q9GPQ4  (Q9GPQ4_TRYVI) -  IAG-nucleoside hydrolase from Trypanosoma vivax

Seq: 327 a.a.

Struc: 317 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.2.2.1 - purine nucleosidase.
• Reaction: a purine D-ribonucleoside + H2O = a purine nucleobase + D-ribose

purine D-ribonucleoside + H2O = purine nucleobase + D-ribose (Bound ligand (Het Group name = NOS) matches with 45.00% similarity)

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

Key reference

DOI no: 10.1074/jbc.M111735200

J Biol Chem 277:15938-15946 (2002)

PubMed id: 11854281

Enzyme-substrate interactions in the purine-specific nucleoside hydrolase from Trypanosoma vivax.

W.Versées, K.Decanniere, E.Van Holsbeke, N.Devroede, J.Steyaert.

ABSTRACT

Nucleoside hydrolases are key enzymes in the purine salvage pathway of Trypanosomatidae and are considered as targets for drug design. We previously reported the first x-ray structure of an inosine-adenosine-guanosine preferring nucleoside hydrolase (IAG-NH) from Trypanosoma vivax (). Here we report the 2.0-A crystal structure of the slow D10A mutant in complex with the inhibitor 3-deaza-adenosine and the 1.6-A crystal structure of the same enzyme in complex with a genuine substrate inosine. The enzyme-substrate complex shows the substrate bound to the enzyme in a different conformation from 3-deaza-adenosine and provides a snapshot along the reaction coordinate of the enzyme-catalyzed reaction. The chemical groups on the substrate important for binding and catalysis are mapped. The 2'-OH, 3'-OH, and 5'-OH contribute 4.6, 7.5, and 5.4 kcal/mol to k(cat)/K(m), respectively. Specific interactions with the exocyclic groups on the purine ring are not required for catalysis. Site-directed mutagenesis indicates that the purine specificity of the IAG-NHs is imposed by a parallel aromatic stacking interaction involving Trp(83) and Trp(260). The pH profiles of k(cat) and k(cat)/K(m) indicate the existence of one or more proton donors, possibly involved in leaving group activation. However, mutagenesis of the active site residues around the nucleoside base and an alanine scan of a flexible loop near the active site fail to identify this general acid. The parallel aromatic stacking seems to provide the most likely alternative mechanism for leaving group activation.

Selected figure(s)

Figure 2.
Fig. 2. Structure of the D10A mutant of the IAG-NH from T. vivax in complex with inosine. The inosine molecules located in each active site of the IAG-NH dimer are shown as ball-and-stick models, the calcium ions are depicted as blue spheres. Amino acids 245-256 were excluded from the model. Arrows indicate the position of the flexible loop containing these amino acids in one of the subunits of the IAG-NH dimer.

Figure 4.
Fig. 4. F[o] F[c] map around an inosine in one of the active sites of the D10A IAG-NH. A, F[o] F[c] map contoured at 3 . B, F[o] F[c] map contoured at 4.5 . The C-4' endo envelope conformation of the ribose is shown.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 15938-15946) copyright 2002.

Figures were selected by an automated process.