4P87

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.999 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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.,Sect.D 70: 2455-2466

  • DOI: 10.1107/S1399004714015272
  • Primary Citation of Related Structures:  

  • 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 determi ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Est-Y29
A, B
401N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4NP
Query on 4NP

Download SDF File 
Download CCD File 
A, B
4-NITROPHENYL PHOSPHATE
C6 H6 N O6 P
XZKIHKMTEMTJQX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.999 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.178 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 121.731α = 90.00
b = 121.731β = 90.00
c = 155.829γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-10
    Type: Initial release
  • Version 1.1: 2014-09-24
    Type: Database references
  • Version 1.2: 2014-12-17
    Type: Database references