1WS7

Crystal Structure of Mavicyanin from Cucurbita pepo medullosa (Zucchini)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

Structural reorganization of the copper binding site involving Thr15 of mavicyanin from Cucurbita pepo medullosa (zucchini) upon reduction.

Xie, Y.Inoue, T.Miyamoto, Y.Matsumura, H.Kataoka, K.Yamaguchi, K.Nojini, M.Suzuki, S.Kai, Y.

(2005) J Biochem 137: 455-461

  • DOI: https://doi.org/10.1093/jb/mvi062
  • Primary Citation of Related Structures:  
    1WS7, 1WS8

  • PubMed Abstract: 

    Mavicyanin, a glycosylated protein isolated from Cucurbita pepo medullosa (zucchini), is a member of the phytocyanin subfamily containing one polypeptide chain of 109 amino residues and an unusual type-I Cu site in which the copper ligands are His45, Cys86, His91, and Gln96. The crystal structures of oxidized and reduced mavicyanin were determined at 1.6 and 1.9 A resolution, respectively. Mavicyanin has a core structure of seven polypeptide beta-strands arranged as a beta-sandwich organized into two beta-sheets, and the structure considerably resembles that of stellacyanin from cucumber (CST) or cucumber basic protein (CBP). A flexible region was not observed on superimpositioning of the oxidized and reduced mavicyanin structures. However, the Cu(II)-epsilon-O-Gln96 bond length was extended by 0.47 A, and the Thr15 residue was rotated by 60.0 degrees and O-gamma1-Thr15 moved from a distance of 4.78 to 2.58 A from the ligand Gln96 forming a new hydrogen bond between O-gamma1-Thr15 and epsilon-O-Gln96 upon reduction. The reorganization of copper coordination geometry of mavicyanin upon reduction arouses reduction potential decreased above pH 8 [Battistuzzi et al. (2001) J. Inorg. Biochem. 83, 223-227]. The rotation of Thr15 and the hydrogen bonding with the ligand Gln96 may constitute structural evidence of the decrease in the reduction potential at high pH.


  • Organizational Affiliation

    Department of Materials Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mavicyanin
A, B, C, D
109Cucurbita pepoMutation(s): 0 
UniProt
Find proteins for P80728 (Cucurbita pepo)
Explore P80728 
Go to UniProtKB:  P80728
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80728
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.66α = 90
b = 62.66β = 90
c = 244.86γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-23
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-07-11
    Changes: Data collection
  • Version 1.4: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-11-13
    Changes: Structure summary