Journal: J Mol Biol / Year: 2012 Title: Structural analysis of Chi1 Chitinase from Yen-Tc: the multisubunit insecticidal ABC toxin complex of Yersinia entomophaga. Authors: Jason N Busby / Michael J Landsberg / Robert M Simpson / Sandra A Jones / Ben Hankamer / Mark R H Hurst / J Shaun Lott / Abstract: Yersinia entomophaga MH96 is a native New Zealand soil bacterium that secretes a large ABC-type protein toxin complex, Yen-Tc, similar to those produced by nematode-associated bacteria such as ...Yersinia entomophaga MH96 is a native New Zealand soil bacterium that secretes a large ABC-type protein toxin complex, Yen-Tc, similar to those produced by nematode-associated bacteria such as Photorhabdus luminescens. Y. entomophaga displays an exceptionally virulent pathogenic phenotype in sensitive insect species, causing death within 72 h of infection. Because of this phenotype, there is intrinsic interest in the mechanism of action of Yen-Tc, and it also has the potential to function as a novel class of biopesticide. We have identified genes that encode chitinases as part of the toxin complex loci in Y. entomophaga MH96, P. luminescens, Photorhabdus asymbiotica and Xenorhabdus nematophila. Furthermore, we have shown that the secreted toxin complex from Y. entomophaga MH96 includes two chitinases as an integral part of the complex, a feature not described previously in other ABC toxins and possibly related to the severe disease caused by this bacterium. We present here the structure of the Y. entomophaga MH96 Chi1 chitinase, determined by X-ray crystallography to 1.74 Å resolution, and show that a ring of five symmetrically arranged lobes on the surface of the Yen-Tc toxin complex structure, as determined by single-particle electron microscopy, provides a good fit to the Chi1 monomer. We also confirm that the isolated chitinases display endochitinase activity, as does the complete toxin complex.
Resolution: 1.74→75.27 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.407 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.20989
5541
5 %
RANDOM
Rwork
0.16452
-
-
-
all
0.16678
104841
-
-
obs
0.16678
104841
96.88 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 22.089 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.21 Å2
-0.4 Å2
1.23 Å2
2-
-
-0.71 Å2
-0.42 Å2
3-
-
-
1.46 Å2
Refinement step
Cycle: LAST / Resolution: 1.74→75.27 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
7991
0
60
835
8886
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
8371
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.628
1.954
11376
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.695
5
1071
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.246
24.7
400
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.259
15
1350
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
11.403
15
41
X-RAY DIFFRACTION
r_chiral_restr
0.118
0.2
1228
X-RAY DIFFRACTION
r_gen_planes_refined
0.009
0.021
6475
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.473
1.5
5167
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
2.226
2
8321
X-RAY DIFFRACTION
r_scbond_it
3.402
3
3204
X-RAY DIFFRACTION
r_scangle_it
4.86
4.5
3033
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.743→1.788 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.298
393
-
Rwork
0.272
7684
-
obs
-
-
95.63 %
+
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