Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 94921.05 
• Atom Count: 6634 
• Residue Count: 898 
• Unique protein chains: 1

1B8J

ALKALINE PHOSPHATASE COMPLEXED WITH VANADATE

• DOI: 10.2210/pdb1B8J/pdb

• Classification: ALKALINE PHOSPHATASE
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli


• Deposited: 1999-02-01 Released: 1999-02-18 
• Deposition Author(s): Holtz, K.M., Stec, B., Kantrowitz, E.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.196 
• R-Value Work: 0.177 

Literature

A model of the transition state in the alkaline phosphatase reaction.

Holtz, K.M., Stec, B., Kantrowitz, E.R.

(1999) J.Biol.Chem. 274: 8351-8354

• PubMed: 10085061 


• PubMed Abstract: 
  

A high resolution crystal structure of Escherichia coli alkaline phosphatase in the presence of vanadate has been refined to 1.9 A resolution. The vanadate ion takes on a trigonal bipyramidal geometry and is covalently bound by the active site serine nucleophile. A coordinated water molecule occupies the axial position opposite the serine nucleophile, whereas the equatorial oxygen atoms of the vanadate ion are stabilized by interactions with both Arg-166 and the zinc metal ions of the active site. This structural complex supports the in-line displacement mechanism of phosphomonoester hydrolysis by alkaline phosphatase and provides a model for the proposed transition state in the enzyme-catalyzed reaction.

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Related Citations: 

• Reaction Mechanism of Alkaline Phosphatase Based on Crystal Structures. Two- Metal Ion Catalysis
  Kim, E.E.,Wyckoff, H.W.
  (1991) J.Mol.Biol. 218: 449
• Trapping and Visualization of a Covalent Enzyme-Phosphate Intermediate
  Murphy, J.E.,Stec, B.,Ma, L.,Kantrowitz, E.R.
  (1997) Nat.Struct.Mol.Biol. 4: 618




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Organizational Affiliation: 

Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02167, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (ALKALINE PHOSPHATASE)	A, B	449	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: phoA EC: 3.1.3.1
Find proteins for P00634 (Escherichia coli (strain K12)) Go to UniProtKB:  P00634

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SVA	A, B	L-PEPTIDE LINKING	C3 H7 N O7 V		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.196 
• R-Value Work: 0.177 
• Space Group: I 2 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 195.410	α = 90.00
b = 167.810	β = 90.00
c = 76.520	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	model building
SDMS	data reduction
SDMS	data scaling
X-PLOR	refinement
SDMS	data collection
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-02-01 
• Released Date: 1999-02-18 
• Deposition Author(s): Holtz, K.M., Stec, B., Kantrowitz, E.R.

Revision History 

• Version 1.0: 1999-02-18
  Type: Initial release
• Version 1.1: 2007-10-16
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Derived calculations, Version format compliance
• Version 1.3: 2017-10-04
  Type: Refinement description