Biological Assembly 1  

 3D View: Structure | 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: 94.63 kDa 
• Atom Count: 7296 
• Residue Count: 898 
• Unique protein chains: 1

1ELZ

E. COLI ALKALINE PHOSPHATASE MUTANT (S102G)

• DOI: 10.2210/pdb1ELZ/pdb

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


• Deposited: 1998-02-10 Released: 1998-05-27 
• Deposition Author(s): Stec, B., Hehir, M., Brennan, C., Nolte, M., Kantrowitz, E.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.173 
• R-Value Work: 0.138 
• R-Value Observed: 0.138 

Literature

Kinetic and X-ray structural studies of three mutant E. coli alkaline phosphatases: insights into the catalytic mechanism without the nucleophile Ser102.

Stec, B., Hehir, M.J., Brennan, C., Nolte, M., Kantrowitz, E.R.

(1998) J Mol Biol 277: 647-662

• PubMed: 9533886 
• DOI: 10.1006/jmbi.1998.1635
• Primary Citation of Related Structures:  
  1ELZ, 1ELY, 1ELX


• PubMed Abstract: 
  

Escherichia coli alkaline phosphatase (EC 3.1.3.1) is a non-specific phosphomonoesterase that catalyzes the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol. We investigated the nature of the primary nucleophile, fulfilled by the deprotonated Ser102, in the catalytic mechanism by mutating this residue to glycine, alanine and cysteine. The efficiencies of the S102G, S102A and S102C enzymes were 6 x 10(5)-fold, 10(5)-fold and 10(4)-fold lower than the wild-type enzyme, respectively, as measured by the kcat/Km ratio, still substantially higher than the non-catalyzed reaction. In order to investigate the structural details of the altered active site, the enzymes were crystallized and their structures determined. The enzymes crystallized in a new crystal form corresponding to the space group P6322. Each structure has phosphate at each active site and shows little departure from the wild-type model. For the S102G and S102A enzymes, the phosphate occupies the same position as in the wild-type enzyme, while in the S102C enzyme it is displaced by 2.5 A. This kinetic and structural study suggests an explanation for differences in catalytic efficiency of the mutant enzymes and provides a means to study the nature and strength of different nucleophiles in the same environment. The analysis of these results provides insight into the mechanisms of other classes of phosphatases that do not utilize a serine nucleophile.

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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

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Organizational Affiliation: 

Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02167, USA.

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	A, B	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.173 
• R-Value Work: 0.138 
• R-Value Observed: 0.138 
• Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.57	α = 90
b = 164.5	β = 90
c = 138.59	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-02-10 
• Released Date: 1998-05-27 
Deposition Author(s): Stec, B., Hehir, M., Brennan, C., Nolte, M., Kantrowitz, E.R.

Revision History 

• Version 1.0: 1998-05-27
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model