5NFG | pdb_00005nfg

Structure of recombinant cardosin B from Cynara cardunculus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 
    0.270 (Depositor), 0.273 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

Starting Model: experimental
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This is version 2.2 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: https://doi.org/10.1007/s00253-017-8445-8
  • Primary Citation Related Structures: 
    5NFG

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 86.01 kDa 
  • Atom Count: 5,400 
  • Modeled Residue Count: 661 
  • Deposited Residue Count: 766 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Procardosin-B,Procardosin-B
A, B
383Cynara cardunculusMutation(s): 0 
Gene Names: cardB
EC: 3.4.23
UniProt
Find proteins for Q9XFX4 (Cynara cardunculus)
Explore Q9XFX4 
Go to UniProtKB:  Q9XFX4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XFX4
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, E
6N-Glycosylation
Glycosylation Resources
GlyTouCan: G23622SL
GlyCosmos: G23622SL
GlyGen: G23622SL
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, F
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G22573RC
GlyCosmos: G22573RC
GlyGen: G22573RC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free:  0.270 (Depositor), 0.273 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.58α = 90
b = 143.13β = 107.9
c = 64.71γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2017-12-13
    Changes: Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-11-06
    Changes: Structure summary