3WBH

Structural characteristics of alkaline phosphatase from a moderately halophilic bacteria Halomonas sp.593

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural characteristics of alkaline phosphatase from the moderately halophilic bacterium Halomonas sp. 593.

Arai, S., Yonezawa, Y., Ishibashi, M., Matsumoto, F., Adachi, M., Tamada, T., Tokunaga, H., Blaber, M., Tokunaga, M., Kuroki, R.

(2014) Acta Crystallogr D Biol Crystallogr 70: 811-820

  • DOI: 10.1107/S1399004713033609
  • Primary Citation of Related Structures:  
    3WBH

  • PubMed Abstract: 

    • Alkaline phosphatase (AP) from the moderate halophilic bacterium Halomonas sp. 593 (HaAP) catalyzes the hydrolysis of phosphomonoesters over a wide salt-concentration range (1-4 M NaCl). In order to clarify the structural basis of its halophilic char ...

    Alkaline phosphatase (AP) from the moderate halophilic bacterium Halomonas sp. 593 (HaAP) catalyzes the hydrolysis of phosphomonoesters over a wide salt-concentration range (1-4 M NaCl). In order to clarify the structural basis of its halophilic characteristics and its wide-range adaptation to salt concentration, the tertiary structure of HaAP was determined by X-ray crystallography to 2.1 Å resolution. The unit cell of HaAP contained one dimer unit corresponding to the biological unit. The monomer structure of HaAP contains a domain comprised of an 11-stranded β-sheet core with 19 surrounding α-helices similar to those of APs from other species, and a unique `crown' domain containing an extended `arm' structure that participates in formation of a hydrophobic cluster at the entrance to the substrate-binding site. The HaAP structure also displays a unique distribution of negatively charged residues and hydrophobic residues in comparison to other known AP structures. AP from Vibrio sp. G15-21 (VAP; a slight halophile) has the highest similarity in sequence (70.0% identity) and structure (C(α) r.m.s.d. of 0.82 Å for the monomer) to HaAP. The surface of the HaAP dimer is substantially more acidic than that of the VAP dimer (144 exposed Asp/Glu residues versus 114, respectively), and thus may enable the solubility of HaAP under high-salt conditions. Conversely, the monomer unit of HaAP formed a substantially larger hydrophobic interior comprising 329 C atoms from completely buried residues, whereas that of VAP comprised 264 C atoms, which may maintain the stability of HaAP under low-salt conditions. These characteristics of HaAP may be responsible for its unique functional adaptation permitting activity over a wide range of salt concentrations.

    Organizational Affiliation: 

    Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alkaline phosphataseA, B527Halomonas sp. #593Mutation(s): 0 
EC: 3.1.3.1
Find proteins for B5BP20 (Halomonas sp. #593)
Explore B5BP20 
Go to UniProtKB:  B5BP20
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.713α = 90
b = 146.974β = 105.21
c = 58.28γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references