4BFH | pdb_00004bfh

Crystal structure of alpha-amylase inhibitor wrightide R1 (wR1) peptide from Wrightia religiosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 
    0.159 (Depositor), 0.161 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.158 (DCC) 
  • R-Value Observed: 
    0.158 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.6 of the entry. See complete history

Literature

Discovery and Characterization of Pseudocyclic Cystine-Knot Alpha-Amylase Inhibitors with High Resistance to Heat and Proteolytic Degradation.

Nguyen, P.Q.Wang, S.Kumar, A.Yap, L.J.Luu, T.T.Lescar, J.Tam, J.P.

(2014) FEBS J 281: 4351

  • DOI: https://doi.org/10.1111/febs.12939
  • Primary Citation Related Structures: 
    2MAU, 4BFH

  • PubMed Abstract: 

    Obesity and type 2 diabetes are chronic metabolic diseases, and those affected could benefit from the use of α-amylase inhibitors to manage starch intake. The pseudocyclics, wrightides Wr-AI1 to Wr-AI3, isolated from an Apocynaceae plant show promise for further development as orally active α-amylase inhibitors. These linear peptides retain the stability known for cystine-knot peptides in the presence of harsh treatment. They are resistant to heat treatment and endopeptidase and exopeptidase degradation, which is characteristic of cyclic cystine-knot peptides. Our NMR and crystallography analysis also showed that wrightides, which are currently the smallest proteinaceous α-amylase inhibitors reported, contain the backbone-twisting cis-proline, which is preceded by a nonaromatic residue rather than a conventional aromatic residue. The modeled structure and a molecular dynamics study of Wr-AI1 in complex with yellow mealworm α-amylase suggested that, despite having a similar structure and cystine-knot fold, the knottin-type α-amylase inhibitors may bind to insect α-amylase via a different set of interactions. Finally, we showed that the precursors of pseudocyclic cystine-knot α-amylase inhibitors and their biosynthesis in plants follow a secretory protein synthesis pathway. Together, our findings provide insights for the use of the pseudocyclic α-amylase inhibitors as useful leads for the development of orally active peptidyl bioactives, as well as an alternative scaffold for cyclic peptides for engineering metabolically stable human α-amylase inhibitors.


  • Organizational Affiliation
    • School of Biological Sciences, Nanyang Technological University, Singapore.

Macromolecule Content 

  • Total Structure Weight: 3.26 kDa 
  • Atom Count: 264 
  • Modeled Residue Count: 30 
  • Deposited Residue Count: 30 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
WRIGHTIDE R130Wrightia religiosaMutation(s): 0 
UniProt
Find proteins for V5W9K8 (Wrightia religiosa)
Explore V5W9K8 
Go to UniProtKB:  V5W9K8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV5W9K8
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free:  0.159 (Depositor), 0.161 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.158 (DCC) 
  • R-Value Observed: 0.158 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 16.194α = 90
b = 29.133β = 90
c = 47.701γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2014-07-23
    Changes: Database references
  • Version 1.2: 2014-07-30
    Changes: Database references
  • Version 1.3: 2014-10-15
    Changes: Database references
  • Version 1.4: 2015-03-18
    Changes: Database references
  • Version 1.5: 2023-12-20
    Changes: Data collection, Database references, Other, Refinement description
  • Version 1.6: 2024-10-16
    Changes: Structure summary