1QFC | pdb_00001qfc

STRUCTURE OF RAT PURPLE ACID PHOSPHATASE

• PDB DOI: https://doi.org/10.2210/pdb1QFC/pdb

• Classification: HYDROLASE
• Organism(s): Rattus norvegicus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 1999-04-08 Released: 2000-04-10 
• Deposition Author(s): Uppenberg, J., Lindqvist, F., Svensson, C., Ek-Rylander, B., Andersson, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.281 (Depositor) 
• R-Value Work: 
  0.234 (Depositor), 0.287 (DCC) 

Literature

Crystal structure of a mammalian purple acid phosphatase.

Uppenberg, J., Lindqvist, F., Svensson, C., Ek-Rylander, B., Andersson, G.

(1999) J Mol Biology 290: 201-211

• PubMed: 10388567 
• DOI: https://doi.org/10.1006/jmbi.1999.2896
• Primary Citation Related Structures: 
  1QFC


• PubMed Abstract: 
  

  Tartrate-resistant acid phosphatase (TRAP) is a mammalian di-iron- containing enzyme that belongs to the family of purple acid phosphatases (PAP). It is highly expressed in a limited number of tissues, predominantly in bone-resorbing osteoclasts and in macrophages of spleen. We have determined the crystal structure of rat TRAP in complex with a phosphate ion to 2.7 A resolution. The fold resembles that of the catalytic domain of kidney bean purple acid phosphatase (KBPAP), although the sequence similarity is limited to the active site residues. A surface loop near the active site is absent due to proteolysis, leaving the active-site easily accessible from the surrounding solvent. This, we believe, gives a structural explanation for the observed proteolytic activation of TRAP. The current structure was determined at a relatively high pH and without any external reducing agents. It is likely that it represents an oxidized and therefore catalytically inactive form of the enzyme.

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Organizational Affiliation: 
• Department of Structural Chemistry, Pharmacia and Upjohn, Lindhagensgatan 133, Stockholm, S-112 87, Sweden. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.82 kDa 
• Atom Count: 2,290 
• Modeled Residue Count: 287 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PURPLE ACID PHOSPHATASE)	A	306	Rattus norvegicus	Mutation(s): 0  EC: 3.1.3.2
UniProt
Find proteins for P29288 (Rattus norvegicus) Explore P29288  Go to UniProtKB:  P29288
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P29288-1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
FE	C [auth A], D [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.281 (Depositor) 
• R-Value Work:  0.234 (Depositor), 0.287 (DCC) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.38	α = 90
b = 116.38	β = 90
c = 63.27	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
SHARP	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-04-10 
Deposition Author(s): Uppenberg, J., Lindqvist, F., Svensson, C., Ek-Rylander, B., Andersson, G.

Revision History  

• Version 1.0: 2000-04-10
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Structure summary
• Version 1.5: 2024-11-13
  Changes: Structure summary