6K5P

Structure of mosquito-larvicidal Binary toxin receptor, Cqm1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.805 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of BinAB toxin receptor (Cqm1) protein and molecular dynamics simulations reveal the role of unique Ca(II) ion.

Sharma, M.Kumar, V.

(2019) Int.J.Biol.Macromol. --: --

  • DOI: 10.1016/j.ijbiomac.2019.08.126

  • PubMed Abstract: 
  • Glycoside hydrolase 13 (GH13) family represents a large and diverse enzyme family. Cqm1, an amylomaltase of Culex mosquito, belongs to the GH13 family and subfamily 17 (GH13_17). The protein acts as the receptor for mosquito-larvicidal BinAB toxin th ...

    Glycoside hydrolase 13 (GH13) family represents a large and diverse enzyme family. Cqm1, an amylomaltase of Culex mosquito, belongs to the GH13 family and subfamily 17 (GH13_17). The protein acts as the receptor for mosquito-larvicidal BinAB toxin that is used world-wide for control of the mosquito population. The protein was crystallized in the presence of a mixture of divalent metal ions. Cqm1 crystal structure was solved using the MRSAD method using Cd(II) anomalous at 1.9 Å wavelength and the structure was refined against 1.8 Å synchrotron data. One tightly bound Ca(II) ion in each of the monomer was observed and this site is suggested here to be unique to the GH13_17 family. Molecular dynamics simulations provide clues for the functional role of Ca(II) ion shown earlier to be essential for enzymatic activity. An optimized substrate (maltotriose) bound structure of the complex was constructed based on which 'retaining-type' mechanism can be predicted reliably. It reveals large conformational change in aromatic residues situated at active-site entrance. A Cd(II) ion was observed overlapping with the substrate-binding site. Kinetics data suggests non-competitive inhibition of Cqm1 by Cd(II). This is the first structure from the GH13_17 family and provides template for constructing reliable models for other members.


    Related Citations: 
    • Receptor protein of Lysinibacillus sphaericus mosquito-larvicidal toxin displays amylomaltase activity.
      Sharma, M.,Gupta, G.D.,Kumar, V.
      (2018) Insect Biochem. Mol. Biol. 93: 37
    • Mosquito-larvicidal binary toxin receptor protein (Cqm1): crystallization and X-ray crystallographic analysis.
      Sharma, M.,Lakshmi, A.,Gupta, G.D.,Kumar, V.
      (2018) Acta Crystallogr F Struct Biol Commun 74: 571


    Organizational Affiliation

    Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai 400085, India. Electronic address: vinay@barc.gov.in.,Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai 400085, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Binary toxin receptor protein
A, B, C, D
561N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

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Download CCD File 
A, B, C, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CO
Query on CO

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Download CCD File 
C, D
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

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Download CCD File 
A, B, C, D
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.805 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.181α = 90.00
b = 191.486β = 90.00
c = 205.332γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
AutoPROCdata scaling
PHENIXrefinement
DMphasing
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-05-30 
  • Released Date: 2019-09-11 
  • Deposition Author(s): Kumar, V., Sharma, M.

Revision History 

  • Version 1.0: 2019-09-11
    Type: Initial release