1SHQ

Crystal structure of shrimp alkaline phosphatase with magnesium in M3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Ligand-binding and metal-exchange crystallographic studies on shrimp alkaline phosphatase.

de Backer, M.M.McSweeney, S.Lindley, P.F.Hough, E.

(2004) Acta Crystallogr.,Sect.D 60: 1555-1561

  • DOI: 10.1107/S0907444904015628
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Alkaline phosphatases (APs) are homodimeric metalloenzymes that catalyze the hydrolysis and transphosphorylation of phosphate monoesters. Each monomer contains a metal-binding triad that for optimal activity is usually occupied by two zinc ions and o ...

    Alkaline phosphatases (APs) are homodimeric metalloenzymes that catalyze the hydrolysis and transphosphorylation of phosphate monoesters. Each monomer contains a metal-binding triad that for optimal activity is usually occupied by two zinc ions and one magnesium ion. The recently determined crystal structure of cold-active shrimp alkaline phosphatase (SAP) was, however, fully occupied by zinc ions. This paper describes a metal-exchange experiment in which the zinc ion in one binding site (referred to as the M3 site) is replaced by magnesium. Crystal structures revealed a concomitant structural change: the metal exchange causes movement of a ligating histidine into a conformation in which it does not coordinate to the metal ion. The M3 site is relevant to catalysis: its occupation by magnesium is postulated to favour catalysis and it has been suggested to be a regulatory site for other APs. Further crystallographic studies show that ligand binding can induce a conformational change of an active-site arginine from a 'non-docked' (non-interacting) to a 'docked' conformation (interacting with the ligand). The first conformation has only been observed in SAP, while the latter is common in available AP structures. The observation that the arginine does not always bind the substrate may explain the increased catalytic efficiency that is generally observed for cold-active enzymes.


    Organizational Affiliation

    European Synchrotron Radiation Facility, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
alkaline phosphatase
A, B
478Pandalus borealisMutation(s): 0 
Gene Names: sap
EC: 3.1.3.1
Find proteins for Q9BHT8 (Pandalus borealis)
Go to UniProtKB:  Q9BHT8
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.215 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 171.007α = 90.00
b = 171.007β = 90.00
c = 84.098γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-31
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance