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- PDB-3epk: Crystallographic snapshots of eukaryotic dimethylallyltransferase... -

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Basic information

Entry
Database: PDB / ID: 3epk
TitleCrystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism
Components
  • tRNA
  • tRNA isopentenyltransferase
KeywordsTransferase/RNA / Transferase / Alternative initiation / ATP-binding / Cytoplasm / Mitochondrion / Nucleotide-binding / Nucleus / tRNA processing / Transferase-RNA COMPLEX
Function / homology
Function and homology information


tRNA dimethylallyltransferase / tRNA dimethylallyltransferase activity / AMP dimethylallyltransferase activity / tRNA modification / tRNA binding / nucleolus / mitochondrion / ATP binding / nucleus / metal ion binding / cytosol
Similarity search - Function
tRNA isopentenyltransferase, eukaryotes / Histone, subunit A - #140 / IPP transferase / Dimethylallyltransferase / IPP transferase / Classic Zinc Finger / Histone, subunit A / Double Stranded RNA Binding Domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...tRNA isopentenyltransferase, eukaryotes / Histone, subunit A - #140 / IPP transferase / Dimethylallyltransferase / IPP transferase / Classic Zinc Finger / Histone, subunit A / Double Stranded RNA Binding Domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DIMETHYLALLYL S-THIOLODIPHOSPHATE / PYROPHOSPHATE / RNA / RNA (> 10) / tRNA dimethylallyltransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsHuang, R.H. / Zhou, C.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: insight into tRNA recognition and reaction mechanism.
Authors: Zhou, C. / Huang, R.H.
History
DepositionSep 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 2, 2019Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Structure summary
Category: chem_comp / entity / struct_ref_seq
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 2.1Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA isopentenyltransferase
E: tRNA
B: tRNA isopentenyltransferase
F: tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,75722
Polymers140,8464
Non-polymers91118
Water4,252236
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: tRNA isopentenyltransferase
E: tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,92111
Polymers70,4232
Non-polymers4989
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-96 kcal/mol
Surface area27920 Å2
MethodPISA
3
B: tRNA isopentenyltransferase
F: tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,83711
Polymers70,4232
Non-polymers4149
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-98 kcal/mol
Surface area28470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.854, 209.844, 125.501
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain: (Details: chain A,B, using restrain)
NCS domain segments:

Dom-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 13 - 415 / Label seq-ID: 1 - 403

Component-IDAuth asym-IDLabel asym-ID
1AA
2BC

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Components

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Protein / RNA chain , 2 types, 4 molecules ABEF

#1: Protein tRNA isopentenyltransferase / Isopentenyl-diphosphate: tRNA isopentenyltransferase / IPP transferase / IPTase / IPPT


Mass: 48199.000 Da / Num. of mol.: 2 / Fragment: UNP residues 13-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MOD5 / Plasmid: pLM-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07884, EC: 2.5.1.8
#2: RNA chain tRNA


Mass: 22224.121 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: RNA was prepared by in vitro transcription with T7 RNA polymerase

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Non-polymers , 5 types, 254 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O6P2S
#6: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

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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: 3.78 Å3/Da / Density % sol: 67.49 %
Crystal growTemperature: 278 K / Method: vapor diffusion / pH: 6.5
Details: Pentaerythritol propoxylate 426, pH 6.5, vapor diffusion, temperature 278K, VAPOR DIFFUSION
Components of the solutionsName: Pentaerythritol propoxylate 426

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONAPS 21-ID-F10.97850.9785
SYNCHROTRONAPS 21-ID-G20.97850.9785
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDNov 12, 2007
MARMOSAIC 300 mm CCD2CCDNov 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 32701

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 3.2→50 Å / Occupancy max: 1.01 / Occupancy min: 1 / FOM work R set: 0.856 / σ(F): 1480
RfactorNum. reflection% reflection
Rfree0.24 2522 7.1 %
Rwork0.19 --
obs-31221 87.7 %
Solvent computationBsol: 29.081 Å2
Displacement parametersBiso max: 195.4 Å2 / Biso mean: 72.171 Å2 / Biso min: 7.73 Å2
Baniso -1Baniso -2Baniso -3
1--15.356 Å20 Å20 Å2
2--20.315 Å20 Å2
3----4.959 Å2
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6678 2944 39 236 9897
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.201
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_scbond_it1.6312
X-RAY DIFFRACTIONc_mcangle_it2.3422
X-RAY DIFFRACTIONc_scangle_it2.7192.5
Refine LS restraints NCSRms: 0.074 / Type: restrain / Weight: 100
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5pp.parpp.top

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