2MAS

PURINE NUCLEOSIDE HYDROLASE WITH A TRANSITION STATE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Trypanosomal nucleoside hydrolase. A novel mechanism from the structure with a transition-state inhibitor.

Degano, M.Almo, S.C.Sacchettini, J.C.Schramm, V.L.

(1998) Biochemistry 37: 6277-6285

  • DOI: 10.1021/bi973012e
  • Also Cited By: 3MKM, 3B9X, 1YOE

  • PubMed Abstract: 
  • Nucleoside N-ribohydrolases are targets for disruption of purine salvage in the protozoan parasites. The structure of a trypanosomal N-ribohydrolase in complex with a transition-state inhibitor is reported at 2.3 A resolution. The nonspecific nucleos ...

    Nucleoside N-ribohydrolases are targets for disruption of purine salvage in the protozoan parasites. The structure of a trypanosomal N-ribohydrolase in complex with a transition-state inhibitor is reported at 2.3 A resolution. The nonspecific nucleoside hydrolase from Crithidia fasciculata cocrystallized with p-aminophenyliminoribitol reveals tightly bound Ca2+ as a catalytic site ligand. The complex with the transition-state inhibitor is characterized by (1) large protein conformational changes to create a hydrophobic leaving group site (2) C3'-exo geometry for the inhibitor, typical of a ribooxocarbenium ion (3) stabilization of the ribooxocarbenium analogue between the neighboring group 5'-hydroxyl and bidentate hydrogen bonds to Asn168; and (4) octacoordinate Ca2+ orients a catalytic site water and is liganded to two hydroxyls of the inhibitor. The mechanism is ribooxocarbenium stabilization with weak leaving group activation and is a departure from glucohydrolases which use paired carboxylates to achieve the transition state.


    Related Citations: 
    • 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


    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, C, D
314Crithidia fasciculataGene Names: IUNH
EC: 3.2.2.-
Find proteins for Q27546 (Crithidia fasciculata)
Go to UniProtKB:  Q27546
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
PIR
Query on PIR

Download SDF File 
Download CCD File 
A, B, C, D
2-(4-AMINO-PHENYL)-5-HYDROXYMETHYL-PYRROLIDINE-3,4-DIOL
C11 H16 N2 O3
SQENVZNKXLCDLF-YTWAJWBKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PIRKd: 30 nM BINDINGMOAD
PIRKd: 30 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.205 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 120.630α = 90.00
b = 159.760β = 90.00
c = 206.380γ = 90.00
Software Package:
Software NamePurpose
SAINTdata reduction
SAINTdata scaling
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-08-12
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance