1MAS

PURINE NUCLEOSIDE HYDROLASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Three-dimensional structure of the inosine-uridine nucleoside N-ribohydrolase from Crithidia fasciculata.

Degano, M.Gopaul, D.N.Scapin, G.Schramm, V.L.Sacchettini, J.C.

(1996) Biochemistry 35: 5971-5981

  • DOI: 10.1021/bi952999m

  • PubMed Abstract: 
  • Protozoan parasites rely on the host for purines since they lack a de novo synthetic pathway. Crithidia fasciculata salvages exogenous inosine primarily through hydrolysis of the N-ribosidic bond using several nucleoside hydrolases. The most abundant ...

    Protozoan parasites rely on the host for purines since they lack a de novo synthetic pathway. Crithidia fasciculata salvages exogenous inosine primarily through hydrolysis of the N-ribosidic bond using several nucleoside hydrolases. The most abundant nucleoside hydrolase is relatively nonspecific but prefers inosine and uridine as substrates. Here we report the three-dimensional structure of the inosine-uridine nucleoside hydrolase (IU-NH) from C. fasciculata determined by X-ray crystallography at a nominal resolution of 2.5 A. The enzyme has an open (alpha, beta) structure which differs from the classical dinucleotide binding fold. IU-nucleoside hydrolase is composed of a mixed eight-stranded beta sheet surrounded by six alpha helices and a small C-terminal lobe composed of four alpha helices. Two short antiparallel beta strands are involved in intermolecular contacts. The catalytic pocket is located at the C-terminal end of beta strands beta 1 and beta 4. Four aspartate residues are located at the bottom of the cavity in a geometry which suggests interaction with the ribose moiety of the nucleoside. These groups could provide the catalytically important interactions to the ribosyl hydroxyls and the stabilizing anion for the oxycarbonium-like transition state. Histidine 241, located on the side of the active site cavity, is the proposed proton donor which facilitates purine base departure [Gopaul, D. N., Meyer, S. L., Degano, M., Sacchettini, J. C., & Schramm, V. L. (1996) Biochemistry 35, 5963-5970]. The substrate binding site is unlike that from purine nucleoside phosphorylase, phosphoribosyltransferases, or uracil DNA glycosylase and thus represents a novel architecture for general acid-base catalysis. This detailed knowledge of the architecture of the active site, together with the previous transition state analysis [Horenstein, B. A., Parkin, D. W., Estupiñán, B., & Schramm, V. L. (1991) Biochemistry 30, 10788-10795], allows analysis of the interactions leading to catalysis and an explanation for the tight-binding inhibitors of the enzyme [Schramm, V. L., Horenstein, B. A., & Kline, P. C. (1994) J. Biol. Chem. 269, 18259-18262].


    Related Citations: 
    • Nucleoside Hydrolase from Crithidia Fasciculata
      Parkin, D.W.,Horenstein, B.A.,Abdulah, D.R.,Estupinan, B.,Schramm, V.L.
      (1991) J.Biol.Chem. 266: 20658
    • Transition-State Analysis of Nucleoside Hydrolase from Crithidia Fasciculata
      Horenstein, B.A.,Parkin, D.W.,Estupinan, B.,Schramm, V.L.
      (1991) Biochemistry 30: 10788
    • Inosine-Uridine Nucleoside Hydrolase from Crithidia Fasciculata. Genetic Characterization, Crystallization, and Identification of Histidine 241 as a Catalytic Site Residue
      Gopaul, D.N.,Meyer, S.L.,Degano, M.,Sacchettini, J.C.,Schramm, V.L.
      (1996) Biochemistry 35: 5963


    Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INOSINE-URIDINE NUCLEOSIDE N-RIBOHYDROLASE
A, B
314Crithidia fasciculataGene Names: IUNH
EC: 3.2.2.-
Find proteins for Q27546 (Crithidia fasciculata)
Go to UniProtKB:  Q27546
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.170 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 63.840α = 90.00
b = 131.530β = 90.00
c = 90.100γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
XENGENdata reduction
X-PLORrefinement
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-08-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance