1USH

5'-NUCLEOTIDASE FROM E. COLI

• PDB DOI: https://doi.org/10.2210/pdb1USH/pdb

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


• Deposited: 1998-09-16 Released: 1999-06-15 
• Deposition Author(s): Knofel, T., Strater, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.219 
• R-Value Work: 0.180 
• R-Value Observed: 0.180 

Starting Model: experimental

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.

Macromolecule Content

• Total Structure Weight: 61.47 kDa 
• Atom Count: 4,629 
• Modelled Residue Count: 515 
• Deposited Residue Count: 550 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-NUCLEOTIDASE	A	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CO3	D [auth A]	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.219 
• R-Value Work: 0.180 
• R-Value Observed: 0.180 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.61	α = 90
b = 83.61	β = 90
c = 181.63	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

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: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-16
  Changes: Structure summary