7Z1U | pdb_00007z1u

Biochemical implications of the substitution of a unique cysteine residue in sugar beet phytoglobin BvPgb 1.2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 
    0.288 (Depositor), 0.294 (DCC) 
  • R-Value Work: 
    0.263 (Depositor), 0.266 (DCC) 
  • R-Value Observed: 
    0.264 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Oxidative Implications of Substituting a Conserved Cysteine Residue in Sugar Beet Phytoglobin BvPgb 1.2.

Christensen, S.Groth, L.Leiva-Eriksson, N.Nyblom, M.Bulow, L.

(2022) Antioxidants (Basel) 11

  • DOI: https://doi.org/10.3390/antiox11081615
  • Primary Citation Related Structures: 
    7Z1U, 7ZOS

  • PubMed Abstract: 

    Phytoglobins (Pgbs) are plant-originating heme proteins of the globin superfamily with varying degrees of hexacoordination. Pgbs have a conserved cysteine residue, the role of which is poorly understood. In this paper, we investigated the functional and structural role of cysteine in BvPgb1.2, a Class 1 Pgb from sugar beet ( Beta vulgaris ), by constructing an alanine-substituted mutant (Cys86Ala). The substitution had little impact on structure, dimerization, and heme loss as determined by X-ray crystallography, size-exclusion chromatography, and an apomyoglobin-based heme-loss assay, respectively. The substitution significantly affected other important biochemical properties. The autoxidation rate increased 16.7- and 14.4-fold for the mutant versus the native protein at 25 °C and 37 °C, respectively. Thermal stability similarly increased for the mutant by ~2.5 °C as measured by nano-differential scanning fluorimetry. Monitoring peroxidase activity over 7 days showed a 60% activity decrease in the native protein, from 33.7 to 20.2 U/mg protein. When comparing the two proteins, the mutant displayed a remarkable enzymatic stability as activity remained relatively constant throughout, albeit at a lower level, ~12 U/mg protein. This suggests that cysteine plays an important role in BvPgb1.2 function and stability, despite having seemingly little effect on its tertiary and quaternary structure.


  • Organizational Affiliation
    • Pure and Applied Biochemistry, Department of Chemistry, Lund University, 22100 Lund, Sweden.

Macromolecule Content 

  • Total Structure Weight: 39.68 kDa 
  • Atom Count: 2,389 
  • Modeled Residue Count: 289 
  • Deposited Residue Count: 342 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Non-symbiotic hemoglobin class 1
A, B
171Beta vulgarisMutation(s): 1 
Gene Names: Bv9_224250_aayd.t2
UniProt
Find proteins for V5QR23 (Beta vulgaris subsp. vulgaris)
Explore V5QR23 
Go to UniProtKB:  V5QR23
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV5QR23
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free:  0.288 (Depositor), 0.294 (DCC) 
  • R-Value Work:  0.263 (Depositor), 0.266 (DCC) 
  • R-Value Observed: 0.264 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.85α = 90
b = 73.92β = 105.05
c = 62.83γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
autoPROCdata processing
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--
The Swedish Foundation for Strategic ResearchSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-07
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description