PDBsum entry 3ws5

Hydrolase

PDB id: 3ws5

Contents

Protein chains

357 a.a.

Metals

_CL ×3

_SR

_CA

Waters ×89

PDB id:

3ws5

Name:

Hydrolase

Title:

N288q-n321q mutant beta-lactamase derived from chromohalobacter sp.560 (condition-2b)

Structure:

Beta-lactamase. Chain: a, b, c. Fragment: unp residues 22-388. Engineered: yes. Mutation: yes

Source:

Chromohalobacter sp. 560. Organism_taxid: 169132. Gene: bla. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.80Å R-factor: 0.177 R-free: 0.207

Authors:

S.Arai,Y.Yonezawa,N.Okazaki,F.Matsumoto,R.Shimizu,M.Yamada,M.Adachi, T.Tamada,H.Tokunaga,M.Ishibashi,M.Tokunaga,R.Kuroki

Key ref:

S.Arai et al. (2015). Structure of a highly acidic β-lactamase from the moderate halophile Chromohalobacter sp. 560 and the discovery of a Cs(+)-selective binding site. Acta Crystallogr D Biol Crystallogr, 71, 541-554. PubMed id: 25760604 DOI: 10.1107/S1399004714027734

Date:

28-Feb-14 Release date: 04-Mar-15

Protein chains

Q76LX5  (Q76LX5_9GAMM) -  Beta-lactamase from Chromohalobacter sp. 560

Seq: 388 a.a.

Struc: 357 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.5.2.6 - beta-lactamase.
• Pathway: Penicillin Biosynthesis and Metabolism
• Reaction: a beta-lactam + H2O = a substituted beta-amino acid
• Cofactor: Zn(2+)

DOI no: 10.1107/S1399004714027734

Acta Crystallogr D Biol Crystallogr 71:541-554 (2015)

PubMed id: 25760604

Structure of a highly acidic β-lactamase from the moderate halophile Chromohalobacter sp. 560 and the discovery of a Cs(+)-selective binding site.

S.Arai, Y.Yonezawa, N.Okazaki, F.Matsumoto, C.Shibazaki, R.Shimizu, M.Yamada, M.Adachi, T.Tamada, M.Kawamoto, H.Tokunaga, M.Ishibashi, M.Blaber, M.Tokunaga, R.Kuroki.

ABSTRACT

Environmentally friendly absorbents are needed for Sr(2+) and Cs(+), as the removal of the radioactive Sr(2+) and Cs(+) that has leaked from the Fukushima Nuclear Power Plant is one of the most important problems in Japan. Halophilic proteins are known to have many acidic residues on their surface that can provide specific binding sites for metal ions such as Cs(+) or Sr(2+). The crystal structure of a halophilic β-lactamase from Chromohalobacter sp. 560 (HaBLA) was determined to resolutions of between 1.8 and 2.9 Å in space group P31 using X-ray crystallography. Moreover, the locations of bound Sr(2+) and Cs(+) ions were identified by anomalous X-ray diffraction. The location of one Cs(+)-specific binding site was identified in HaBLA even in the presence of a ninefold molar excess of Na(+) (90 mM Na(+)/10 mM Cs(+)). From an activity assay using isothermal titration calorimetry, the bound Sr(2+) and Cs(+) ions do not significantly affect the enzymatic function of HaBLA. The observation of a selective and high-affinity Cs(+)-binding site provides important information that is useful for the design of artificial Cs(+)-binding sites that may be useful in the bioremediation of radioactive isotopes.