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- PDB-6bm7: Crystal structure of Trypanosoma brucei AdoMetDC/prozyme heterodi... -

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Basic information

Entry
Database: PDB / ID: 6bm7
TitleCrystal structure of Trypanosoma brucei AdoMetDC/prozyme heterodimer in complex with pyrimidineamine inhibitor UTSAM568
Components
  • (S-adenosylmethionine decarboxylase ...) x 2
  • Inactive S-adenosylmethionine decarboxylase prozyme
KeywordsLYASE/LYASE INHIBITOR / AdoMetDC / prozyme / decarboxylase / Trypanosoma / inhibitor / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


trypanothione biosynthetic process / positive regulation of spermidine biosynthetic process / spermine biosynthetic process / adenosylmethionine decarboxylase / adenosylmethionine decarboxylase activity / positive regulation of catalytic activity / spermidine biosynthetic process / S-adenosylmethionine metabolic process / catalytic complex / enzyme activator activity ...trypanothione biosynthetic process / positive regulation of spermidine biosynthetic process / spermine biosynthetic process / adenosylmethionine decarboxylase / adenosylmethionine decarboxylase activity / positive regulation of catalytic activity / spermidine biosynthetic process / S-adenosylmethionine metabolic process / catalytic complex / enzyme activator activity / protein heterodimerization activity / enzyme binding / cytosol
Similarity search - Function
S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase, conserved site / : / Adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase signature. / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase, core / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-DY7 / TRIETHYLENE GLYCOL / 1,4-DIAMINOBUTANE / Inactive S-adenosylmethionine decarboxylase prozyme / S-adenosylmethionine decarboxylase proenzyme
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsVolkov, O.A. / Chen, Z. / Phillips, M.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)2R37AI034432 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI090599 United States
CitationJournal: J. Med. Chem. / Year: 2018
Title: Species-Selective Pyrimidineamine Inhibitors of Trypanosoma brucei S-Adenosylmethionine Decarboxylase.
Authors: Volkov, O.A. / Brockway, A.J. / Wring, S.A. / Peel, M. / Chen, Z. / Phillips, M.A. / De Brabander, J.K.
History
DepositionNov 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.year / _pdbx_audit_support.funding_organization
Revision 1.2Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id
Revision 2.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-adenosylmethionine decarboxylase beta chain
B: S-adenosylmethionine decarboxylase alpha chain
C: S-adenosylmethionine decarboxylase beta chain
D: S-adenosylmethionine decarboxylase alpha chain
E: Inactive S-adenosylmethionine decarboxylase prozyme
F: Inactive S-adenosylmethionine decarboxylase prozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,23315
Polymers156,2806
Non-polymers1,9549
Water1267
1
A: S-adenosylmethionine decarboxylase beta chain
B: S-adenosylmethionine decarboxylase alpha chain
F: Inactive S-adenosylmethionine decarboxylase prozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0647
Polymers78,1403
Non-polymers9244
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12260 Å2
ΔGint-55 kcal/mol
Surface area25530 Å2
MethodPISA
2
C: S-adenosylmethionine decarboxylase beta chain
D: S-adenosylmethionine decarboxylase alpha chain
E: Inactive S-adenosylmethionine decarboxylase prozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1708
Polymers78,1403
Non-polymers1,0305
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12480 Å2
ΔGint-50 kcal/mol
Surface area26370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.090, 96.250, 98.840
Angle α, β, γ (deg.)90.000, 102.426, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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S-adenosylmethionine decarboxylase ... , 2 types, 4 molecules ACBD

#1: Protein S-adenosylmethionine decarboxylase beta chain


Mass: 9754.132 Da / Num. of mol.: 2 / Fragment: UNP residues 1-85
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb927.6.4410, Tb927.6.4460 / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q587A7, adenosylmethionine decarboxylase
#2: Protein S-adenosylmethionine decarboxylase alpha chain


Mass: 32041.992 Da / Num. of mol.: 2 / Fragment: UNP residues 87-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb927.6.4410, Tb927.6.4460 / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q587A7, adenosylmethionine decarboxylase

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Protein , 1 types, 2 molecules EF

#3: Protein Inactive S-adenosylmethionine decarboxylase prozyme / AdoMetDC prozyme


Mass: 36343.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A5HNV6

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Non-polymers , 6 types, 16 molecules

#4: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#5: Chemical ChemComp-DY7 / 2-amino-4-[(3,5-dibromophenyl)amino]-6-methylpyrimidin-1-ium


Mass: 359.040 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H11Br2N4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12N2
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.63 % / Description: plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1 uL 4 mg/mL protein in crystallization buffer (50 mM Bis-Tris propane, pH 7.2, 50 mM sodium chloride, 4 mM TCEP, 2 mM putrescine, 0.5 mM N4-(3,5-dibromophenyl)-6-methylpyrimidine-2,4- ...Details: 1 uL 4 mg/mL protein in crystallization buffer (50 mM Bis-Tris propane, pH 7.2, 50 mM sodium chloride, 4 mM TCEP, 2 mM putrescine, 0.5 mM N4-(3,5-dibromophenyl)-6-methylpyrimidine-2,4-diamine [UTSAM568], 1% DMSO) + 1 uL reservoir solution (17% PEG6000, 100 mM Bis-Tris propane, pH 7.0) + 0.5 uL unliganded protein microseeds obtained using Seed-Bead method in stabilization solution (100 mM Bis-Tris propane, pH 8.9, 50 mM HEPES, pH 7.2, 19% PEG6000, 50 mM sodium chloride, 4 mM TCEP, 2 mM putrescine)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.91905 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91905 Å / Relative weight: 1
ReflectionResolution: 2.98→50 Å / Num. obs: 30294 / % possible obs: 99.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 49.2238648407 Å2 / Rpim(I) all: 0.074 / Rrim(I) all: 0.194 / Net I/σ(I): 10
Reflection shellResolution: 3→3.05 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1.87 / Num. unique obs: 1466 / CC1/2: 0.712 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5TVM

5tvm


Resolution: 2.98→48.2623233532 Å / SU ML: 0.341675147008 / Cross valid method: FREE R-VALUE / σ(F): 1.33789805147 / Phase error: 26.3118648791
RfactorNum. reflection% reflection
Rfree0.254857270037 2520 4.97591027565 %
Rwork0.199589623624 --
obs0.202335356515 50644 84.6026628356 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 58.4151476361 Å2
Refinement stepCycle: LAST / Resolution: 2.98→48.2623233532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10193 0 117 7 10317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031458482905210561
X-RAY DIFFRACTIONf_angle_d0.55860276821614309
X-RAY DIFFRACTIONf_chiral_restr0.04462526152161549
X-RAY DIFFRACTIONf_plane_restr0.003649429093241830
X-RAY DIFFRACTIONf_dihedral_angle_d13.41709118146214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9756-3.03280.428230715028610.2763892266931225X-RAY DIFFRACTION39.1595615104
3.0328-3.09470.303772707357890.2685202732261751X-RAY DIFFRACTION54.3414057885
3.0947-3.1620.300163757996990.2664519101491818X-RAY DIFFRACTION58.7316176471
3.162-3.23550.3253588588951050.2787895367342011X-RAY DIFFRACTION62.7893175074
3.2355-3.31640.2752857113481110.2441493348312234X-RAY DIFFRACTION69.8956780924
3.3164-3.4060.2951636275061270.2186628429422399X-RAY DIFFRACTION77.1297709924
3.406-3.50620.2911592644881370.2067780211332630X-RAY DIFFRACTION84.0777879064
3.5062-3.61940.287510967451500.2011432822922872X-RAY DIFFRACTION89.5142180095
3.6194-3.74870.2363369930231530.1948582828652916X-RAY DIFFRACTION94.2567567568
3.7487-3.89870.239487612621610.2012759391253132X-RAY DIFFRACTION97.5703703704
3.8987-4.07610.2861846472481670.1972770987053181X-RAY DIFFRACTION99.6725215838
4.0761-4.29080.2442840631411680.1812474342283135X-RAY DIFFRACTION99.8790444512
4.2908-4.55950.2347563989761670.1644102376583148X-RAY DIFFRACTION99.7592536864
4.5595-4.91120.2376770170251620.163179719553117X-RAY DIFFRACTION99.0634441088
4.9112-5.40480.212003289521680.1770145522043163X-RAY DIFFRACTION99.88005997
5.4048-6.18560.2536044390821640.1906799523643164X-RAY DIFFRACTION99.7901049475
6.1856-7.78780.2456763692071660.2177584627873132X-RAY DIFFRACTION99.4571773221
7.7878-48.26860.2362324834951650.2060920463053096X-RAY DIFFRACTION97.6932294787

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