4TX4

Crystal Structure of a Single-Domain Cysteine Protease Inhibitor from Cowpea (Vigna unguiculata)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Expression in Escherichia coli of cysteine protease inhibitors from cowpea (Vigna unguiculata): The crystal structure of a single-domain cystatin gives insights on its thermal and pH stability.

Monteiro Junior, J.E.Valadares, N.F.Pereira, H.D.Dyszy, F.H.da Costa Filho, A.J.Uchoa, A.F.de Oliveira, A.S.da Silveira Carvalho, C.P.Grangeiro, T.B.

(2017) Int. J. Biol. Macromol. 102: 29-41

  • DOI: 10.1016/j.ijbiomac.2017.04.008

  • PubMed Abstract: 
  • Two cysteine proteinase inhibitors from cowpea, VuCys1 and VuCys2, were produced in E. coli ArcticExpress (DE3). The recombinant products strongly inhibited papain and chymopapain as well as the midgut proteases from Callosobruchus maculatus larvae, ...

    Two cysteine proteinase inhibitors from cowpea, VuCys1 and VuCys2, were produced in E. coli ArcticExpress (DE3). The recombinant products strongly inhibited papain and chymopapain as well as the midgut proteases from Callosobruchus maculatus larvae, a bruchid that uses cysteine proteases as major digestive enzymes. Heat treatment at 100°C for up to 60min or incubation at various pH values caused little reduction in the papain inhibitory activity of both inhibitors. Moreover, minor conformational variations, as probed by circular dichroism spectroscopy, were observed after VuCys1 and VuCys2 were subjected to these treatments. The crystal structure of VuCys1 was determined at a resolution of 1.95Å, revealing a domain-swapped dimer in the asymmetric unit. However, the two lobes of the domain-swapped dimer are positioned closer to each other in VuCys1 in comparison to other similar cystatin structures. Moreover, some polar residues from opposite lobes recruit water molecules, forming a hydrogen bond network that mediates contacts between the lobes, thus generating an extended open interface. Due to the closer distance between the lobes, a small hydrophobic core is also formed, further stabilizing the folded domain-swapped dimer. These structural features might account for the extraordinary thermal and pH stability of VuCys1.


    Organizational Affiliation

    Departamento de Biologia, Centro de Ciências, Universidade Federal do Ceará (UFC), Fortaleza, CE, Brazil. Electronic address: tbgrangeiro@gmail.com.,Departamento de Bioquímica, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil.,Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Brazil.,Laboratório de Biofísica Molecular, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, Brazil.,Instituto de Física de São Carlos, Universidade de São Paulo, Brazil.,Departamento de Bioquímica e Biologia Molecular, Centro de Ciências, UFC, Fortaleza, CE, Brazil.,Departamento de Biologia, Centro de Ciências, Universidade Federal do Ceará (UFC), Fortaleza, CE, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cysteine proteinase inhibitor
B, A
83Vigna unguiculataMutation(s): 0 
Find proteins for Q06445 (Vigna unguiculata)
Go to UniProtKB:  Q06445
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 41.830α = 90.00
b = 64.640β = 90.00
c = 87.113γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing
XSCALEdata scaling
d*TREKdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil--
Sao Paulo Research Foundation (FAPESP)Brazil--

Revision History 

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2017-05-31
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence
  • Version 1.3: 2019-04-17
    Type: Author supporting evidence, Data collection
  • Version 1.4: 2020-01-01
    Type: Author supporting evidence