4LZI | pdb_00004lzi

Characterization of Solanum tuberosum Multicystatin and Significance of Core Domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.279 (Depositor), 0.279 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history

Literature

Characterization of Solanum tuberosum Multicystatin and the Significance of Core Domains.

Green, A.R.Nissen, M.S.Kumar, G.N.Knowles, N.R.Kang, C.

(2013) Plant Cell 25: 5043-5052

  • DOI: https://doi.org/10.1105/tpc.113.121004
  • Primary Citation Related Structures: 
    4LZI

  • PubMed Abstract: 

    Potato (Solanum tuberosum) multicystatin (PMC) is a unique cystatin composed of eight repeating units, each capable of inhibiting cysteine proteases. PMC is a composite of several cystatins linked by trypsin-sensitive (serine protease) domains and undergoes transitions between soluble and crystalline forms. However, the significance and the regulatory mechanism or mechanisms governing these transitions are not clearly established. Here, we report the 2.2-Å crystal structure of the trypsin-resistant PMC core consisting of the fifth, sixth, and seventh domains. The observed interdomain interaction explains PMC's resistance to trypsin and pH-dependent solubility/aggregation. Under acidic pH, weakening of the interdomain interactions exposes individual domains, resulting in not only depolymerization of the crystalline form but also exposure of cystatin domains for inhibition of cysteine proteases. This in turn allows serine protease-mediated fragmentation of PMC, producing ∼ 10-kD domains with intact inhibitory capacity and faster diffusion, thus enhancing PMC's inhibitory ability toward cysteine proteases. The crystal structure, light-scattering experiments, isothermal titration calorimetry, and site-directed mutagenesis confirmed the critical role of pH and N-terminal residues in these dynamic transitions between monomer/polymer of PMC. Our data support a notion that the pH-dependent structural regulation of PMC has defense-related implications in tuber physiology via its ability to regulate protein catabolism.


  • Organizational Affiliation
    • School of Molecular Biosciences, Washington State University, Pullman, Washington 99164.

Macromolecule Content 

  • Total Structure Weight: 32.59 kDa 
  • Atom Count: 2,458 
  • Modeled Residue Count: 277 
  • Deposited Residue Count: 282 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Multicystatin282Solanum tuberosumMutation(s): 0 
UniProt
Find proteins for P37842 (Solanum tuberosum)
Explore P37842 
Go to UniProtKB:  P37842
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37842
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.279 (Depositor), 0.279 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.94α = 90
b = 65.94β = 90
c = 191.85γ = 90
Software Package:
Software NamePurpose
BOSdata collection
PHENIXmodel building
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-26
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Refinement description