1HO5

5'-NUCLEOTIDASE (E. COLI) IN COMPLEX WITH ADENOSINE AND PHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanism of hydrolysis of phosphate esters by the dimetal center of 5'-nucleotidase based on crystal structures.

Knofel, T.Strater, N.

(2001) J.Mol.Biol. 309: 239-254

  • DOI: 10.1006/jmbi.2001.4656
  • Primary Citation of Related Structures:  1HP1, 1HPU

  • PubMed Abstract: 
  • 5'-Nucleotidase belongs to a large superfamily of distantly related dinuclear metallophosphatases including the Ser/Thr protein phosphatases and purple acid phosphatases. The protein undergoes a 96 degrees domain rotation between an open (inactive) a ...

    5'-Nucleotidase belongs to a large superfamily of distantly related dinuclear metallophosphatases including the Ser/Thr protein phosphatases and purple acid phosphatases. The protein undergoes a 96 degrees domain rotation between an open (inactive) and a closed (active) enzyme form. Complex structures of the closed form with the products adenosine and phosphate, and with the substrate analogue inhibitor alpha,beta-methylene ADP, have been determined at 2.1 A and 1.85 A resolution, respectively. In addition, a complex of the open form of 5'-nucleotidase with ATP was analyzed at a resolution of 1.7 A. These structures show that the adenosine group binds to a specific binding pocket of the C-terminal domain. The adenine ring is stacked between Phe429 and Phe498. The N-terminal domain provides the ligands to the dimetal cluster and the conserved His117, which together form the catalytic core structure. However, the three C-terminal arginine residues 375, 379 and 410, which are involved in substrate binding, may also play a role in transition-state stabilization. The beta-phosphate group of the inhibitor is terminally coordinated to the site 2 metal ion. The site 1 metal ion coordinates a water molecule which is in an ideal position for a nucleophilic attack on the phosphorus atom, assuming an in-line mechanism of phosphoryl transfer. Another water molecule bridges the two metal ions.


    Related Citations: 
    • E. COLI 5'-NUCLEOTIDASE UNDERGOES A HINGE-BENDING DOMAIN ROTATION RESEMBLING A BALL-AND-SOCKET MOTION
      Knoefel, T.,Straeter, N.
      (2001) J.Mol.Biol. 309: 255
    • X-ray structure of the Escherichia coli periplasmic 5'-nucleotidase containing a dimetal catalytic site
      Knoefel, T.,Straeter, N.
      (1999) Nat.Struct.Mol.Biol. 6: 448


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5'-NUCLEOTIDASE
A, B
525Escherichia coli (strain K12)Gene Names: ushA
EC: 3.1.3.5, 3.6.1.45
Find proteins for P07024 (Escherichia coli (strain K12))
Go to UniProtKB:  P07024
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ADN
Query on ADN

Download SDF File 
Download CCD File 
A, B
ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.238 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 69.900α = 90.00
b = 75.700β = 90.00
c = 221.700γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-03-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance