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- PDB-6dft: Trypanosoma brucei deoxyhypusine synthase -

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Basic information

Entry
Database: PDB / ID: 6dft
TitleTrypanosoma brucei deoxyhypusine synthase
Components
  • Deoxyhypusine synthase
  • Deoxyhypusine synthase regulatory subunit
KeywordsTRANSFERASE / heterotetramer / Rossman fold / pseudoenzyme / NAD+
Function / homology
Function and homology information


peptidyl-lysine modification to peptidyl-hypusine / deoxyhypusine synthase / deoxyhypusine synthase activity / spermidine metabolic process / regulation of cytoplasmic translation / positive regulation of catalytic activity / protein heterotetramerization / catalytic complex / enzyme activator activity / enzyme binding ...peptidyl-lysine modification to peptidyl-hypusine / deoxyhypusine synthase / deoxyhypusine synthase activity / spermidine metabolic process / regulation of cytoplasmic translation / positive regulation of catalytic activity / protein heterotetramerization / catalytic complex / enzyme activator activity / enzyme binding / protein homodimerization activity / membrane / cytoplasm
Similarity search - Function
Deoxyhypusine Synthase / Deoxyhypusine synthase / Deoxyhypusine synthase / Deoxyhypusine synthase superfamily / Deoxyhypusine synthase / DHS-like NAD/FAD-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Deoxyhypusine synthase / Deoxyhypusine synthase regulatory subunit
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
Model detailsActive enzyme is a heterotetramer, composed of a heterodimer of the catalytic and pseudoenzyme monomers.
AuthorsTomchick, D.R. / Phillips, M.A. / Afanador, G.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37AI034432 United States
Citation
Journal: Structure / Year: 2018
Title: Trypanosomatid Deoxyhypusine Synthase Activity Is Dependent on Shared Active-Site Complementation between Pseudoenzyme Paralogs.
Authors: Afanador, G.A. / Tomchick, D.R. / Phillips, M.A.
#1: Journal: J Biol Chem / Year: 2013
Title: Allosteric Activation of Trypanosomatid Deoxyhypusine Synthase by a Catalytically Dead Paralog
Authors: Suong, N. / Jones, D.C. / Wyllie, S. / Fairlamb, A.H. / Phillips, M.A.
History
DepositionMay 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxyhypusine synthase
B: Deoxyhypusine synthase regulatory subunit
C: Deoxyhypusine synthase
D: Deoxyhypusine synthase regulatory subunit
E: Deoxyhypusine synthase
F: Deoxyhypusine synthase regulatory subunit
G: Deoxyhypusine synthase
H: Deoxyhypusine synthase regulatory subunit
I: Deoxyhypusine synthase
J: Deoxyhypusine synthase regulatory subunit
K: Deoxyhypusine synthase
L: Deoxyhypusine synthase regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)533,85725
Polymers525,87312
Non-polymers7,98413
Water00
1
A: Deoxyhypusine synthase
B: Deoxyhypusine synthase regulatory subunit
C: Deoxyhypusine synthase
D: Deoxyhypusine synthase regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,9689
Polymers175,2914
Non-polymers2,6775
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27260 Å2
ΔGint-153 kcal/mol
Surface area44290 Å2
MethodPISA
2
E: Deoxyhypusine synthase
F: Deoxyhypusine synthase regulatory subunit
G: Deoxyhypusine synthase
H: Deoxyhypusine synthase regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,9458
Polymers175,2914
Non-polymers2,6544
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26880 Å2
ΔGint-141 kcal/mol
Surface area44590 Å2
MethodPISA
3
I: Deoxyhypusine synthase
J: Deoxyhypusine synthase regulatory subunit
K: Deoxyhypusine synthase
L: Deoxyhypusine synthase regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,9458
Polymers175,2914
Non-polymers2,6544
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27180 Å2
ΔGint-135 kcal/mol
Surface area43870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.358, 242.162, 266.303
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Deoxyhypusine synthase


Mass: 50226.137 Da / Num. of mol.: 6 / Fragment: catalytic monomer
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: DHSc / Plasmid: pETDuet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q38BX0, deoxyhypusine synthase
#2: Protein
Deoxyhypusine synthase regulatory subunit / Inactive deoxyhypusine synthase


Mass: 37419.312 Da / Num. of mol.: 6 / Fragment: pseudoenzyme monomer
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: DHSp / Plasmid: pETDuet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q4GZD1, deoxyhypusine synthase
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.66 % / Description: THIN PLATE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES, 10 mM TCEP, 2 mM NAD+, 8% PEG 6000, 20% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 20, 2017 / Details: monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 52848 / % possible obs: 97.2 % / Redundancy: 4.1 % / Biso Wilson estimate: 64.48 Å2 / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.101 / Rrim(I) all: 0.214 / Χ2: 0.87 / Net I/σ(I): 4.1 / Num. measured all: 214291
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.5-3.563.40.79625560.650.4550.9240.62594.4
3.56-3.633.50.67924920.6630.3840.7860.62594.3
3.63-3.693.50.66625540.6980.3790.7720.93695.9
3.69-3.773.50.57825640.7080.3260.6680.84495.2
3.77-3.853.60.48925450.8030.2760.5660.70896
3.85-3.943.60.49125600.8840.2770.5671.21795.9
3.94-4.043.50.39925970.8470.2310.4640.86495.3
4.04-4.153.40.32825200.8460.1950.3840.85595.4
4.15-4.274.10.30326830.9030.1620.3460.90498.1
4.27-4.414.20.26925990.9110.1420.3060.99297.7
4.41-4.574.30.23926770.9270.1270.2721.03498.7
4.57-4.754.40.22226390.9340.1180.2531.04898.6
4.75-4.974.40.20627190.9390.1090.2351.00798.9
4.97-5.234.50.18926480.9470.0990.2140.95398.7
5.23-5.554.10.1826520.9450.0990.2070.86297.3
5.55-5.984.80.1727070.9650.0860.1910.7899.3
5.98-6.584.80.15127260.9670.0750.1690.74398.8
6.58-7.534.60.12227360.9760.0620.1380.77499
7.53-9.484.40.09427700.9840.0480.1060.83797.6
9.48-504.40.08129040.9840.0420.0920.74997.6

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RQD

1rqd


Resolution: 3.5→48.752 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.62
RfactorNum. reflection% reflectionSelection details
Rfree0.2623 1956 3.98 %RANDOM
Rwork0.2224 ---
obs0.224 49148 91.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.42 Å2 / Biso mean: 57.1506 Å2 / Biso min: 23.31 Å2
Refinement stepCycle: final / Resolution: 3.5→48.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31800 0 529 0 32329
Biso mean--46.97 --
Num. residues----4144
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5001-3.58760.3374720.30171790186249
3.5876-3.68460.34731130.28292719283276
3.6846-3.7930.33341320.26593248338089
3.793-3.91540.35071390.27883350348993
3.9154-4.05520.30291430.25213429357294
4.0552-4.21750.26561440.22373458360295
4.2175-4.40930.26221470.21123559370698
4.4093-4.64160.22021520.19553625377798
4.6416-4.93220.22821490.19573614376399
4.9322-5.31260.23321490.19453592374198
5.3126-5.84640.26611520.21513639379198
5.8464-6.69060.26561530.23013662381599
6.6906-8.42230.26071530.20823674382798
8.4223-48.75720.20711580.20063833399197

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