5NFG

Structure of recombinant cardosin B from Cynara cardunculus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.375 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Functional and structural characterization of synthetic cardosin B-derived rennet.

Almeida, C.M.Manso, J.A.Figueiredo, A.C.Antunes, L.Cruz, R.Manadas, B.Bur, D.Pereira, P.J.B.Faro, C.Simoes, I.

(2017) Appl. Microbiol. Biotechnol. 101: 6951-6968

  • DOI: 10.1007/s00253-017-8445-8

  • PubMed Abstract: 
  • The potential of using a synthetic cardosin-based rennet in cheese manufacturing was recently demonstrated with the development and optimization of production of a recombinant form of cardosin B in Kluyveromyces lactis. With the goal of providing a m ...

    The potential of using a synthetic cardosin-based rennet in cheese manufacturing was recently demonstrated with the development and optimization of production of a recombinant form of cardosin B in Kluyveromyces lactis. With the goal of providing a more detailed characterization of this rennet, we herein evaluate the impact of the plant-specific insert (PSI) on cardosin B secretion in this yeast, and provide a thorough analysis of the specificity requirements as well as the biochemical and structural properties of the isolated recombinant protease. We demonstrate that the PSI domain can be substituted by different linker sequences without substantially affecting protein secretion and milk clotting activity. However, the presence of small portions of the PSI results in dramatic reductions of secretion yields in this heterologous system. Kinetic characterization and specificity profiling results clearly suggest that synthetic cardosin B displays lower catalytic efficiency and is more sequence selective than native cardosin B. Elucidation of the structure of synthetic cardosin B confirms the canonical fold of an aspartic protease with the presence of two high mannose-type, N-linked glycan structures; however, there are some differences in the conformation of the flap region when compared to cardosin A. These subtle variations in catalytic properties and the more stringent substrate specificity of synthetic cardosin B help to explain the observed suitability of this rennet for cheese production.


    Organizational Affiliation

    Biocant, Biotechnology Innovation Center, Parque Tecnológico de Cantanhede, Núcleo 4 Lote 8, 3060-197, Cantanhede, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Procardosin-B,Procardosin-B
A, B
383Cynara cardunculusMutation(s): 0 
Gene Names: cardB
EC: 3.4.23.-
Find proteins for Q9XFX4 (Cynara cardunculus)
Go to UniProtKB:  Q9XFX4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.375 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 52.580α = 90.00
b = 143.130β = 107.90
c = 64.710γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2017-12-13
    Type: Database references