5TZB | pdb_00005tzb

Burkholderia sp. beta-aminopeptidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.238 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Crystal structure of a beta-aminopeptidase from an Australian Burkholderia sp.

John-White, M.Dumsday, G.J.Johanesen, P.Lyras, D.Drinkwater, N.McGowan, S.

(2017) Acta Crystallogr F Struct Biol Commun 73: 386-392

  • DOI: https://doi.org/10.1107/S2053230X17007737
  • Primary Citation Related Structures: 
    5TZB

  • PubMed Abstract: 

    β-Aminopeptidases are a unique group of enzymes that have the unusual capability to hydrolyze N-terminal β-amino acids from synthetic β-peptides. β-Peptides can form secondary structures mimicking α-peptide-like structures that are resistant to degradation by most known proteases and peptidases. These characteristics of β-peptides give them great potential as peptidomimetics. Here, the X-ray crystal structure of BcA5-BapA, a β-aminopeptidase from a Gram-negative Burkholderia sp. that was isolated from activated sludge from a wastewater-treatment plant in Australia, is reported. The crystal structure of BcA5-BapA was determined to a resolution of 2.0 Å and showed a tetrameric assembly typical of the β-aminopeptidases. Each monomer consists of an α-subunit (residues 1-238) and a β-subunit (residues 239-367). Comparison of the structure of BcA5-BapA with those of other known β-aminopeptidases shows a highly conserved structure and suggests a similar proteolytic mechanism of action.


  • Organizational Affiliation
    • Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Melbourne, VIC 3800, Australia.

Macromolecule Content 

  • Total Structure Weight: 320.86 kDa 
  • Atom Count: 22,172 
  • Modeled Residue Count: 2,834 
  • Deposited Residue Count: 3,112 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
D-aminopeptidase389Burkholderia sp. LK4Mutation(s): 0 
Gene Names: VK92_01140

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free:  0.238 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.451α = 90
b = 133.26β = 91.61
c = 117.068γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-12
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-29
    Changes: Derived calculations
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description