4P85

Crystal structure of Est-Y29, a novel penicillin-binding protein/beta-lactamase homolog from a metagenomic library

Summary for 4P85

• Entry DOI: 10.2210/pdb4p85/pdb
• Related: 4P6B
• Descriptor: Est-Y29, DIETHYL PHOSPHONATE (3 entities in total)
• Functional Keywords: hydrolase, penicillin-binding protein, beta-lactamase, metagenome
• Biological source: metagenome
• Total number of polymer chains: 2
• Total formula weight: 88827.13

Authors

Ngo, T.D.,Ryu, B.H.,Ju, H.S.,Jang, E.J.,Kim, K.K.,Kim, D.H. (deposition date: 2014-03-30, release date: 2014-09-10, Last modification date: 2024-10-16)

Primary citation

Ngo, T.D.,Ryu, B.H.,Ju, H.,Jang, E.J.,Kim, K.K.,Kim, T.D.
Crystallographic analysis and biochemical applications of a novel penicillin-binding protein/ beta-lactamase homologue from a metagenomic library.
Acta Crystallogr.,Sect.D, 70:2455-2466, 2014

PubMed Abstract: Interest in penicillin-binding proteins and β-lactamases (the PBP-βL family) is increasing owing to their biological and clinical significance. In this study, the crystal structure of Est-Y29, a metagenomic homologue of the PBP-βL family, was determined at 1.7 Å resolution. In addition, complex structures of Est-Y29 with 4-nitrophenyl phosphate (4NP) and with diethyl phosphonate (DEP) at 2.0 Å resolution were also elucidated. Structural analyses showed that Est-Y29 is composed of two domains: a β-lactamase fold and an insertion domain. A deep hydrophobic patch between these domains defines a wide active site, and a nucleophilic serine (Ser58) residue is located in a groove defined primarily by hydrophobic residues between the two domains. In addition, three hydrophobic motifs, which make up the substrate-binding site, allow this enzyme to hydrolyze a wide variety of hydrophobic compounds, including fish and olive oils. Furthermore, cross-linked Est-Y29 aggregates (CLEA-Est-Y29) significantly increase the stability of the enzyme as well as its potential for extensive reuse in various deactivating conditions. The structural features of Est-Y29, together with biochemical and biophysical studies, could provide a molecular basis for understanding the properties and regulatory mechanisms of the PBP-βL family and their potential for use in industrial biocatalysts.

PubMed: 25195758
DOI: 10.1107/S1399004714015272

Experimental method

X-RAY DIFFRACTION (2 Å)