2USH

5'-NUCLEOTIDASE FROM E. COLI

• PDB DOI: https://doi.org/10.2210/pdb2USH/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-09-24 Released: 1999-06-15 
• Deposition Author(s): Knofel, T., Strater, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.254 
• R-Value Work: 0.198 
• R-Value Observed: 0.198 

Literature

X-ray structure of the Escherichia coli periplasmic 5'-nucleotidase containing a dimetal catalytic site.

Knofel, T., Strater, N.

(1999) Nat Struct Biol 6: 448-453

• PubMed: 10331872 
• DOI: https://doi.org/10.1038/8253
• Primary Citation of Related Structures:  
  1USH, 2USH


• PubMed Abstract: 
  

  The crystal structure of 5'-nucleotidase (5'-NT) from E. coli, also known as UDP-sugar hydrolase, has been determined at 1.7 A resolution. Two zinc ions are present in the active site, which is located in a cleft between two domains. The dimetal center and a catalytic Asp-His dyad are the main players in the catalytic mechanism. Structure-based sequence comparisons show that the structure also provides a model for animal 5'-NTs, which together with other ectonucleotidases terminate the action of nucleotides as extracellular signaling substances in the nervous system.

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Organizational Affiliation: 

Institut für Kristallographie, Abteilung Saenger, Freie Universität Berlin, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 123.37 kDa 
• Atom Count: 8,180 
• Modelled Residue Count: 1,026 
• Deposited Residue Count: 1,100 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-NUCLEOTIDASE	A, B	550	Escherichia coli K-12	Mutation(s): 0  Gene Names: USHA EC: 3.1.3.5 (PDB Primary Data), 3.6.1.45 (UniProt)
UniProt
Find proteins for P07024 (Escherichia coli (strain K12)) Explore P07024  Go to UniProtKB:  P07024

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WO4	E [auth A], F [auth A], L [auth B], M [auth B]	TUNGSTATE(VI)ION O4 W PBYZMCDFOULPGH-UHFFFAOYSA-N
ZN	C [auth A], D [auth A], G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], N [auth B], O [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.254 
• R-Value Work: 0.198 
• R-Value Observed: 0.198 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.21	α = 90
b = 116.29	β = 90
c = 132.77	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
DM	model building
MLPHARE	phasing
SHARP	phasing
X-PLOR	refinement
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-06-15 
Deposition Author(s): Knofel, T., Strater, N.

Revision History  

• Version 1.0: 1999-06-15
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary