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- EMDB-3499: Substrate specificity in plant nitrilase helical assemblies is de... -

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Basic information

Entry
Database: EMDB / ID: EMD-3499
TitleSubstrate specificity in plant nitrilase helical assemblies is determined by their twist.
Map dataCapsella rubella NITRILASE 1
Sample
  • Complex: Capsella rubella NITRILASE 1 filament
    • Protein or peptide: NITRILASE 1
Biological speciesCapsella rubella (plant)
Methodhelical reconstruction / negative staining / Resolution: 20.0 Å
AuthorsWoodward JD / Trompetter I / Sewell BT / Piotrowski M
CitationJournal: Commun Biol / Year: 2018
Title: Substrate specificity of plant nitrilase complexes is affected by their helical twist.
Authors: Jeremy D Woodward / Inga Trompetter / B Trevor Sewell / Markus Piotrowski /
Abstract: Nitrilases are oligomeric, helix-forming enzymes from plants, fungi and bacteria that are involved in the metabolism of various natural and artificial nitriles. These biotechnologically important ...Nitrilases are oligomeric, helix-forming enzymes from plants, fungi and bacteria that are involved in the metabolism of various natural and artificial nitriles. These biotechnologically important enzymes are often specific for certain substrates, but directed attempts at modifying their substrate specificities by exchanging binding pocket residues have been largely unsuccessful. Thus, the basis for their selectivity is still unknown. Here we show, based on work with two highly similar nitrilases from the plant , that modifying nitrilase helical twist, either by exchanging an interface residue or by imposing a different twist, without altering any binding pocket residues, changes substrate preference. We reveal that helical twist and substrate size correlate and when binding pocket residues are exchanged between two nitrilases that show the same twist but different specificities, their specificities change. Based on these findings we propose that helical twist influences the overall size of the binding pocket.
History
DepositionNov 15, 2016-
Header (metadata) releaseDec 14, 2016-
Map releaseJan 17, 2018-
UpdateNov 21, 2018-
Current statusNov 21, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0414
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0414
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3499.png

Downloads & links

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Map

FileDownload / File: emd_3499.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCapsella rubella NITRILASE 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.22 Å/pix.
x 64 pix.
= 270.08 Å		4.22 Å/pix.
x 64 pix.
= 270.08 Å		4.22 Å/pix.
x 64 pix.
= 270.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.22 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0414 / Movie #1: 0.0414
Minimum - Maximum-0.050834656 - 0.1226951
Average (Standard dev.)0.004762911 (±0.020804184)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-32-32-32
Dimensions646464
Spacing646464
CellA=B=C: 270.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.224.224.22
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z270.080270.080270.080
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS-32-32-32
NC/NR/NS646464
D min/max/mean-0.0510.1230.005

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Supplemental data

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Sample components

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Entire : Capsella rubella NITRILASE 1 filament

EntireName: Capsella rubella NITRILASE 1 filament
Components
  • Complex: Capsella rubella NITRILASE 1 filament
    • Protein or peptide: NITRILASE 1

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Supramolecule #1: Capsella rubella NITRILASE 1 filament

SupramoleculeName: Capsella rubella NITRILASE 1 filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Capsella rubella (plant)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET21-b(+)
Molecular weightTheoretical: 26 kDa/nm

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Macromolecule #1: NITRILASE 1

MacromoleculeName: NITRILASE 1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: nitrilase
Source (natural)Organism: Capsella rubella (plant)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSSTVKNTAD PVDGVAPSSI VRVTIVQAST VYNNTPATLD KAEKYVVEAA SKGAKLVLFP EAFVGGYPRG FRFGLATGVH NEEGRDEFRK YHASAIKVPG PEVERLAELA GKTNVYLVMG AIEKDGYTLY CTALFFSPQG QFLGKHRKLM PTTLERCIWG QGDGSTIPVY ...String:
MSSTVKNTAD PVDGVAPSSI VRVTIVQAST VYNNTPATLD KAEKYVVEAA SKGAKLVLFP EAFVGGYPRG FRFGLATGVH NEEGRDEFRK YHASAIKVPG PEVERLAELA GKTNVYLVMG AIEKDGYTLY CTALFFSPQG QFLGKHRKLM PTTLERCIWG QGDGSTIPVY DTPIGKLGAA ICWENRMPLY RTALYAKGIE IYCAPTADGS KEWQSSMMHI ALEGGCFVLS ACQFCLRKDF PDHPDYLFTD WEDYKEDDAI VSQGGSVIIS PLGQVLAGPN FESEGLITAD LDLGDVARAK LYFDAVGHYS RPDVLHLTVN EHPKKTVTFM TKVEKAEDDS NK

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Experimental details

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Structure determination

Methodnegative staining
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
200.0 mMNaClsodium chloride
50.0 mMC4H11NO3TRIS-Hcl
StainingType: NEGATIVE / Material: Uranyl Acetate
Details: The protein was allowed to adhere for 30 s, blotted, washed three-times with distilled water and stained with uranyl acetate, blotted again and allowed to dry at room temperature.
GridModel: Grid-tech / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 20.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.02 kPa

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 31 / Average exposure time: 1.0 sec. / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 0.5 µm / Calibrated defocus min: 0.3 µm / Calibrated magnification: 50200 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.2 mm / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: PHILIPS ROTATION HOLDER
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 90
Applied symmetry - Helical parameters - Δz: 14.5 Å
Applied symmetry - Helical parameters - Δ&Phi: -68.5 °
Applied symmetry - Helical parameters - Axial symmetry: D2 (2x2 fold dihedral)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER (ver. 11) / Software - details: IHRSR / Number images used: 1068
Segment selectionNumber selected: 1079 / Software - Name: EMAN / Software - details: Boxer / Details: Picked using Eman Boxer in helix mode
Startup modelType of model: INSILICO MODEL
In silico model: Featureless cylinder approximating the diameter of the filament.
Final angle assignmentType: NOT APPLICABLE / Software - Name: SPIDER (ver. 11) / Software - details: IHRSR

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