3CZ4 | pdb_00003cz4

Native AphA class B acid phosphatase/phosphotransferase from E. coli

• PDB DOI: https://doi.org/10.2210/pdb3CZ4/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-04-28 Released: 2008-11-11 
• Deposition Author(s): Leone, R., Cappelletti, E., Benvenuti, M., Lentini, G., Thaller, M.C., Mangani, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.212 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Structural insights into the catalytic mechanism of the bacterial class B phosphatase AphA belonging to the DDDD superfamily of phosphohydrolases.

Leone, R., Cappelletti, E., Benvenuti, M., Lentini, G., Thaller, M.C., Mangani, S.

(2008) J Mol Biology 384: 478-488

• PubMed: 18845157 
• DOI: https://doi.org/10.1016/j.jmb.2008.09.050
• Primary Citation Related Structures: 
  3CZ4


• PubMed Abstract: 
  

  AphA is a magnesium-dependent, bacterial class B acid phosphatase that catalyzes the hydrolysis of a variety of phosphoester substrates and belongs to the DDDD superfamily of phosphohydrolases. The recently reported crystal structure of AphA from Escherichia coli has revealed the quaternary structure of the enzyme together with hints about its catalytic mechanism. The present work reports the crystal structures of AphA from E. coli in complex with substrate, transition-state, and intermediate analogues. The structures provide new insights into the mechanism of the enzyme and allow a revision of some aspects of the previously proposed mechanism that have broader implications for all the phosphatases of the DDDD superfamily.

---

Organizational Affiliation: 
• Dipartimento di Chimica, Università di Siena, Via Aldo Moro 2, I-53100 Siena, Italy.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 24.01 kDa 
• Atom Count: 2,031 
• Modeled Residue Count: 209 
• Deposited Residue Count: 212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Class B acid phosphatase	A	212	Escherichia coli K-12	Mutation(s): 0  Gene Names: aphA, napA, yjbP, b4055, JW4015 EC: 3.1.3.2
UniProt
Find proteins for P0AE22 (Escherichia coli (strain K12)) Explore P0AE22  Go to UniProtKB:  P0AE22

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.212 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.294	α = 90
b = 92.775	β = 90
c = 137.6	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-11 
Deposition Author(s): Leone, R., Cappelletti, E., Benvenuti, M., Lentini, G., Thaller, M.C., Mangani, S.

Revision History  

• Version 1.0: 2008-11-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description