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

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

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This is version 1.4 of the entry. See complete history


Crystallographic analysis and biochemical applications of a novel penicillin-binding protein/ beta-lactamase homologue from a metagenomic library.

Ngo, T.D.Ryu, B.H.Ju, H.Jang, E.J.Kim, K.K.Kim, T.D.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2455-2466

  • DOI: https://doi.org/10.1107/S1399004714015272
  • Primary Citation of Related Structures:  
    4P6B, 4P85, 4P87

  • 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.

  • Organizational Affiliation

    Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
390metagenomeMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.541α = 90
b = 121.541β = 90
c = 155.173γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-10
    Type: Initial release
  • Version 1.1: 2014-09-24
    Changes: Database references
  • Version 1.2: 2014-12-17
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Derived calculations, Refinement description, Source and taxonomy
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references