Biological Assembly 1  

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Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 137883.25 
• Atom Count: 9616 
• Residue Count: 1256 
• Unique protein chains: 1

2MAS

PURINE NUCLEOSIDE HYDROLASE WITH A TRANSITION STATE INHIBITOR

• DOI: 10.2210/pdb2MAS/pdb

• Classification: HYDROLASE
• Organism(s): Crithidia fasciculata
• Expression System: Escherichia coli


• Deposited: 1996-10-17 Released: 1997-08-12 
• Deposition Author(s): Degano, M., Schramm, V.L., Sacchettini, J.C.

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Experimental Data Snapshot

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

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

• PubMed: 9572842 
• 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 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.

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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




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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
Molecule	Chains	Sequence Length	Organism	Details
INOSINE-URIDINE NUCLEOSIDE N-RIBOHYDROLASE	A, B, C, D	314	Crithidia fasciculata	Gene Names: IUNH EC: 3.2.2.-
Find proteins for Q27546 (Crithidia fasciculata) Go to UniProtKB:  Q27546

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CA	A, B, C, D	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
PIR	A, B, C, D	2-(4-AMINO-PHENYL)-5-HYDROXYMETHYL-PYRROLIDINE-3,4-DIOL C11 H16 N2 O3 SQENVZNKXLCDLF-YTWAJWBKSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
PIR	Kd: 30 nM BINDINGMOAD
PIR	Kd: 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 = 120.630	α = 90.00
b = 159.760	β = 90.00
c = 206.380	γ = 90.00

Software Package:

Software Name	Purpose
SAINT	data reduction
SAINT	data scaling
X-PLOR	refinement
X-PLOR	model building
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-10-17 
• Released Date: 1997-08-12 
• Deposition Author(s): Degano, M., Schramm, V.L., Sacchettini, J.C.

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