3WBH

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

Summary for 3WBH

• Entry DOI: 10.2210/pdb3wbh/pdb
• Descriptor: Alkaline phosphatase, MAGNESIUM ION, ZINC ION, ... (5 entities in total)
• Functional Keywords: crown-domain, hydrolase
• Biological source: Halomonas
• Total number of polymer chains: 2
• Total formula weight: 114499.86

Authors

Arai, S.,Yonezawa, Y.,Ishibashi, M.,Matsumoto, F.,Tamada, T.,Tokunaga, H.,Tokunaga, M.,Kuroki, R. (deposition date: 2013-05-17, release date: 2014-03-12, Last modification date: 2023-11-08)

Primary citation

Arai, S.,Yonezawa, Y.,Ishibashi, M.,Matsumoto, F.,Adachi, M.,Tamada, T.,Tokunaga, H.,Blaber, M.,Tokunaga, M.,Kuroki, R.
Structural characteristics of alkaline phosphatase from the moderately halophilic bacterium Halomonas sp. 593.
Acta Crystallogr.,Sect.D, 70:811-820, 2014

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 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.

PubMed: 24598750
DOI: 10.1107/S1399004713033609

Experimental method

X-RAY DIFFRACTION (2.1 Å)