1HP1

5'-NUCLEOTIDASE (OPEN FORM) COMPLEX WITH ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 

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Ligand Structure Quality Assessment 


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:  
    1HO5, 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) and a closed (active) enzyme form ...

    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 Biol 6: 448

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5'-NUCLEOTIDASEA516Escherichia coliMutation(s): 0 
Gene Names: ushA
EC: 3.1.3.5 (PDB Primary Data), 3.6.1.45 (PDB Primary Data)
UniProt
Find proteins for P07024 (Escherichia coli (strain K12))
Explore P07024 
Go to UniProtKB:  P07024
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07024
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
H [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CO3
Query on CO3

Download Ideal Coordinates CCD File 
D [auth A]CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.7α = 90
b = 83.7β = 90
c = 181.8γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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