Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

 3D View: Structure | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 206126.22 
• Atom Count: 14264 
• Residue Count: 1728 
• Unique protein chains: 1

1KBP

KIDNEY BEAN PURPLE ACID PHOSPHATASE

• DOI: 10.2210/pdb1KBP/pdb

• Classification: HYDROLASE (PHOSPHORIC MONOESTER)
• Organism(s): Phaseolus vulgaris


• Deposited: 1995-02-20 Released: 1996-10-14 
• Deposition Author(s): Klabunde, T., Strater, N., Krebs, B.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.233 
• R-Value Work: 0.195 

Literature

Mechanism of Fe(III)-Zn(II) purple acid phosphatase based on crystal structures.

Klabunde, T., Strater, N., Frohlich, R., Witzel, H., Krebs, B.

(1996) J.Mol.Biol. 259: 737-748

• PubMed: 8683579 
• DOI: 10.1006/jmbi.1996.0354
• Primary Citation of Related Structures:  
  4KBP, 3KBP


• PubMed Abstract: 
  

Purple acid phosphatase is a widely distributed non-specific phosphomonoesterase. X-ray structures of the dimeric 111-kDa Fe(III)-Zn(II) kidney bean purple acid phosphatase (kbPAP) complexed with phosphate, the product of the reaction, and with tungstate, a strong inhibitor of the phosphatase activity, were determined at 2.7 and 3.0 angstroms resolution, respectively. Furthermore the resolution of the unligated enzyme, recently solved at 2.9 angstroms could be extended to 2.65 angstroms with completely new data. The binding of both oxoanions is not accompanied by larger conformational changes in the enzyme structure. Small movements with a maximal coordinate shift of 1 angstroms are only observed for the active site residues His295 and His296. In the inhibitor complex as well as in the product complex, the oxoanion binds in a bidentate bridging mode to the two metal ions, replacing two of the presumed solvent ligands present in the unligated enzyme form. As also proposed for the unligated structure a bridging hydroxide ion completes the coordination spheres of both metal ions to octahedral arrangements. All three structures reported herein support a mechanism of phosphate ester hydrolysis involving interaction of the substrate with Zn(II) followed by a nucleophilic attack on the phosphorus by an Fe(III)-coordinated hydroxide ion. The negative charge evolving at the pentacoordinated transition state is probably stabilized by interactions with the divalent zinc and the imidazole groups of His202, His295, and His296, the latter protonating the leaving alcohol group.

---

Related Citations: 

• Crystal Structure of a Purple Acid Phosphatase Containing a Dinuclear Fe(III)-Zn(II) Active Site
  Strater, N.,Klabunde, T.,Tucker, P.,Witzel, H.,Krebs, B.
  (1995) Science 268: 1489




---

Organizational Affiliation: 

Anorganisch-Chemisches Institut, Universität Münster, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PURPLE ACID PHOSPHATASE	A, B, C, D	432	Phaseolus vulgaris	Mutation(s): 0  EC: 3.1.3.2
Find proteins for P80366 (Phaseolus vulgaris) Go to UniProtKB:  P80366

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A, B, C, D	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE	A, B, C, D	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
NAG	A, B, C, D	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.233 
• R-Value Work: 0.195 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 132.700	α = 90.00
b = 347.300	β = 90.00
c = 128.700	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-02-20 
• Released Date: 1996-10-14 
• Deposition Author(s): Klabunde, T., Strater, N., Krebs, B.

Revision History 

• Version 1.0: 1996-10-14
  Type: Initial release
• Version 1.1: 2008-03-03
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Derived calculations, Version format compliance