1X90 | pdb_00001x90

Crystal structure of mutant form B of a pectin methylesterase inhibitor from Arabidopsis

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 
    0.256 (Depositor), 0.256 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

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

Literature

Structural insights into the target specificity of plant invertase and pectin methylesterase inhibitory proteins

Hothorn, M., Wolf, S., Aloy, P., Greiner, S., Scheffzek, K.

(2004) Plant Cell 16: 3437-3447

  • DOI: https://doi.org/10.1105/tpc.104.025684
  • Primary Citation Related Structures: 
    1X8Z, 1X90, 1X91

  • PubMed Abstract: 

    Pectin methylesterase (PME) and invertase are key enzymes in plant carbohydrate metabolism. Inhibitors of both enzymes constitute a sequence family of extracellular proteins. Members of this family are selectively targeted toward either PME or invertase. In a comparative structural approach we have studied how this target specificity is implemented on homologous sequences. By extending crystallographic work on the invertase inhibitor Nt-CIF to a pectin methylesterase inhibitor (PMEI) from Arabidopsis thaliana, we show an alpha-helical hairpin motif to be an independent and mobile structural entity in PMEI. Removal of this hairpin fully inactivates the inhibitor. A chimera composed of the alpha-hairpin of PMEI and the four-helix bundle of Nt-CIF is still active against PME. By contrast, combining the corresponding segment of Nt-CIF with the four-helix bundle of PMEI renders the protein inactive toward either PME or invertase. Our experiments provide insight in how these homologous inhibitors can make differential use of similar structural modules to achieve distinct functions. Integrating our results with previous findings, we present a model for the PME-PMEI complex with important implications.

    • Organizational Affiliation: 
    • European Molecular Biology Laboratory, Structural and Computational Biology Programme, 69117 Heidelberg, Germany.

Macromolecule Content 

  • Total Structure Weight: 32.61 kDa 
  • Atom Count: 2,242 
  • Modeled Residue Count: 294 
  • Deposited Residue Count: 304 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
invertase/pectin methylesterase inhibitor family protein
A, B
152Arabidopsis thalianaMutation(s): 1 
Gene Names: AT1G48020
UniProt
Find proteins for Q9LNF2 (Arabidopsis thaliana)
Explore Q9LNF2 
Go to UniProtKB:  Q9LNF2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LNF2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free:  0.256 (Depositor), 0.256 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.41α = 90
b = 82.41β = 90
c = 105.41γ = 120
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Data collection, Database references
  • Version 1.4: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-10-16
    Changes: Structure summary