Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 81.30 kDa 
• Atom Count: 5839 
• Modelled Residue Count: 692 
• Deposited Residue Count: 750 
• Unique protein chains: 1

2W5V

Structure of TAB5 alkaline phosphatase mutant His 135 Asp with Mg bound in the M3 site.

• PDB DOI: 10.2210/pdb2W5V/pdb

• Classification: HYDROLASE
• Organism(s): Antarctic bacterium TAB5
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-12-15 Released: 2009-11-24 
• Deposition Author(s): Koutsioulis, D., Lyskowski, A., Maki, S., Guthrie, E., Feller, G., Bouriotis, V., Heikinheimo, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.199 
• R-Value Work: 0.159 
• R-Value Observed: 0.161 

Literature

Coordination Sphere of the Third Metal Site is Essential to the Activity and Metal Selectivity of Alkaline Phosphatases.

Koutsioulis, D., Lyskowski, A., Maki, S., Guthrie, E., Feller, G., Bouriotis, V., Heikinheimo, P.

(2010) Protein Sci 19: 75

• PubMed: 19916164 
• DOI: 10.1002/pro.284
• Primary Citation of Related Structures:  
  2W5V, 2W5W, 2W5X


• PubMed Abstract: 
  

Alkaline phosphatases (APs) are commercially applied enzymes that catalyze the hydrolysis of phosphate monoesters by a reaction involving three active site metal ions. We have previously identified H135 as the key residue for controlling activity of the psychrophilic TAB5 AP (TAP). In this article, we describe three X-ray crystallographic structures on TAP variants H135E and H135D in complex with a variety of metal ions. The structural analysis is supported by thermodynamic and kinetic data. The AP catalysis essentially requires octahedral coordination in the M3 site, but stability is adjusted with the conformational freedom of the metal ion. Comparison with the mesophilic Escherichia coli, AP shows differences in the charge transfer network in providing the chemically optimal metal combination for catalysis. Our results provide explanation why the TAB5 and E. coli APs respond in an opposite way to mutagenesis in their active sites. They provide a lesson on chemical fine tuning and the importance of the second coordination sphere in defining metal specificity in enzymes. Understanding the framework of AP catalysis is essential in the efforts to design even more powerful tools for modern biotechnology.

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Organizational Affiliation: 

New England Biolabs Inc., Ipswich, Massachusetts 01938-2723, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALKALINE PHOSPHATASE	A, B	375	Antarctic bacterium TAB5	Mutation(s): 1  Gene Names: phoA EC: 3.1.3.1
UniProt
Find proteins for Q9KWY4 (Antarctic bacterium TAB5) Explore Q9KWY4  Go to UniProtKB:  Q9KWY4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	E [auth A], F [auth A], I [auth B], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A, B	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.199 
• R-Value Work: 0.159 
• R-Value Observed: 0.161 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.32	α = 90
b = 173.02	β = 90
c = 54.97	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-12-15 
• Released Date: 2009-11-24 
Deposition Author(s): Koutsioulis, D., Lyskowski, A., Maki, S., Guthrie, E., Feller, G., Bouriotis, V., Heikinheimo, P.

Revision History  

• Version 1.0: 2009-11-24
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance