PDBsum entry 1hoz

Hydrolase

PDB id: 1hoz

Contents

Protein chains

316 a.a. *

Ligands

GOL ×8

Metals

_CA ×2

Waters ×424

* Residue conservation analysis

PDB id:

1hoz

Name:

Hydrolase

Title:

Crystal structure of an inosine-adenosine-guanosine-preferring nucleoside hydrolase from trypanosoma vivax

Structure:

Inosine-adenosine-guanosine-preferring nucleoside hydrolase. Chain: a, b. Fragment: iag-nucleoside hydrolase, iag-nh. Engineered: 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: 0.186 R-free: 0.210

Authors:

W.Versees,K.Decanniere,R.Pelle,J.Depoorter,D.W.Parkin,J.Steyaert

Key ref:

W.Versées et al. (2001). Structure and function of a novel purine specific nucleoside hydrolase from Trypanosoma vivax. J Mol Biol, 307, 1363-1379. PubMed id: 11292348 DOI: 10.1006/jmbi.2001.4548

Date:

12-Dec-00 Release date: 12-Dec-01

Protein chains

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

Seq: 327 a.a.

Struc: 316 a.a.*

* PDB and UniProt seqs differ at 2 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 = GOL) matches with 60.00% similarity)

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

Key reference

DOI no: 10.1006/jmbi.2001.4548

J Mol Biol 307:1363-1379 (2001)

PubMed id: 11292348

Structure and function of a novel purine specific nucleoside hydrolase from Trypanosoma vivax.

W.Versées, K.Decanniere, R.Pellé, J.Depoorter, E.Brosens, D.W.Parkin, J.Steyaert.

ABSTRACT

The purine salvage pathway of parasitic protozoa is currently considered as a target for drug development because these organisms cannot synthesize purines de novo. Insight into the structure and mechanism of the involved enzymes can aid in the development of potent inhibitors, leading to new curative drugs. Nucleoside hydrolases are key enzymes in the purine salvage pathway of Trypanosomatidae, and they are especially attractive because they have no equivalent in mammalian cells. We cloned, expressed and purified a nucleoside hydrolase from Trypanosoma vivax. The substrate activity profile establishes the enzyme to be a member of the inosine-adenosine-guanosine-preferring nucleoside hydrolases (IAG-NH). We solved the crystal structure of the enzyme at 1.6 A resolution using MAD techniques. The complex of the enzyme with the substrate analogue 3-deaza-adenosine is presented. These are the first structures of an IAG-NH reported in the literature. The T. vivax IAG-NH is a homodimer, with each subunit consisting of ten beta-strands, 12 alpha-helices and three small 3(10)-helices. Six of the eight strands of the central beta-sheet form a motif resembling the Rossmann fold. Superposition of the active sites of this IAG-NH and the inosine-uridine-preferring nucleoside hydrolase (IU-NH) of Crithidia fasciculata shows the molecular basis of the different substrate specificity distinguishing these two classes of nucleoside hydrolases. An "aromatic stacking network" in the active site of the IAG-NH, absent from the IU-NH, imposes the purine specificity. Asp10 is the proposed general base in the reaction mechanism, abstracting a proton from a nucleophilic water molecule. Asp40 (replaced by Asn39 in the IU-NH) is positioned appropriately to act as a general acid and to protonate the purine leaving group. The second general acid, needed for full enzymatic activity, is probably part of a flexible loop located in the vicinity of the active site.

Selected figure(s)

Figure 3.
Figure 3. Representative section of the electron density map (b-strand 10; Leu304-Arg309) of uncomplexed T. vivax IAG-NH, contoured at 1 s. (a) Experimental map at 1.6 Å resolution after density modification with DM. (b) The 2F[o] - F[c] map after refinement at a resolution of 1.6 Å. The Figure was made with CONSCRIPT[69] and MOLSCRIPT. [70]

Figure 5.
Figure 5. Two orientations of a T. vivax IAG-NH subunit. 3-Deaza-adenosine is represented as ball-and-stick model, the calcium ion and the catalytic water molecule are depicted as dark and light blue spheres, respectively. The substrate analogue 3-deaza-adenosine is bound at the C terminus of the eight-stranded central b-sheet. The amino acid residues between His247 and Asp253 are missing from the model. The Figure was prepared with MOLSCRIPT.[70]

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 307, 1363-1379) copyright 2001.

Figures were selected by an automated process.