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- PDB-3otd: Crystal structure of human tRNAHis guanylyltransferase (Thg1)- Na... -

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Basic information

Entry
Database: PDB / ID: 3otd
TitleCrystal structure of human tRNAHis guanylyltransferase (Thg1)- NaI derivative
ComponentstRNA(His) guanylyltransferaseTRNA(His) guanylyltransferase
KeywordsTRANSFERASE / guanylyltransferase / polymerase-like palm domain / catalytic carboxylates
Function / homology
Function and homology information


stress-induced mitochondrial fusion / tRNAHis guanylyltransferase / tRNA guanylyltransferase activity / transferase complex / tRNA modification in the nucleus and cytosol / tRNA modification / mitochondrial fusion / tRNA processing / nucleotidyltransferase activity / guanyl-nucleotide exchange factor activity ...stress-induced mitochondrial fusion / tRNAHis guanylyltransferase / tRNA guanylyltransferase activity / transferase complex / tRNA modification in the nucleus and cytosol / tRNA modification / mitochondrial fusion / tRNA processing / nucleotidyltransferase activity / guanyl-nucleotide exchange factor activity / protein homotetramerization / response to oxidative stress / mitochondrial outer membrane / tRNA binding / GTP binding / magnesium ion binding / mitochondrion / ATP binding / identical protein binding / cytosol
Similarity search - Function
Thg1 C-terminal domain / Thg1 C terminal domain / tRNAHis guanylyltransferase Thg1 / tRNAHis guanylyltransferase catalytic domain / tRNAHis guanylyltransferase Thg1 superfamily / tRNAHis guanylyltransferase / tRNA(His) guanylyltransferase (Thg1) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Probable tRNA(His) guanylyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.28 Å
AuthorsHyde, S.J. / Eckenroth, B.E. / Doublie, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: tRNAHis guanylyltransferase (THG1), a unique 3'-5' nucleotidyl transferase, shares unexpected structural homology with canonical 5'-3' DNA polymerases.
Authors: Hyde, S.J. / Eckenroth, B.E. / Smith, B.A. / Eberley, W.A. / Heintz, N.H. / Jackman, J.E. / Doublie, S.
History
DepositionSep 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 9, 2014Group: Source and taxonomy
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_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

Downloads & links

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Assembly

Deposited unit
A: tRNA(His) guanylyltransferase
B: tRNA(His) guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,52712
Polymers63,2582
Non-polymers1,26910
Water1,928107
1
A: tRNA(His) guanylyltransferase
B: tRNA(His) guanylyltransferase
hetero molecules

A: tRNA(His) guanylyltransferase
B: tRNA(His) guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,05424
Polymers126,5164
Non-polymers2,53820
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area12640 Å2
ΔGint-76 kcal/mol
Surface area42300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.574, 140.574, 80.962
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain: (Details: chain A,B, using restrain)
DetailsThe biological unit is a tetramer generated from the dimer in the asymetric unit by the operation: Y, X, -Z+1

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Components

#1: Protein tRNA(His) guanylyltransferase / TRNA(His) guanylyltransferase / tRNA-histidine guanylyltransferase / Interphase cytoplasmic foci protein 45


Mass: 31628.938 Da / Num. of mol.: 2 / Fragment: UNP residues 30-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: KATO III / Gene: ICF45, THG1L / Plasmid: pME182-FL / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS
References: UniProt: Q9NWX6, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 3.16 Å3/Da / Density % sol: 61.09 %
Crystal growTemperature: 291 K / Method: hanging drop / pH: 7.5
Details: PEG 3350, MgSO4, pH 7.5, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 104 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 10, 2009 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.28→15 Å / Num. obs: 37206 / % possible obs: 99.9 % / Rmerge(I) obs: 0.087 / Χ2: 1.034 / Net I/σ(I): 9.6
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.28-2.360.80436351.031199.6
2.36-2.460.62836621.031100
2.46-2.570.51636621.0111100
2.57-2.70.35136771.031199.9
2.7-2.870.25636681.079199.9
2.87-3.090.17137021.0651100
3.09-3.40.10337300.9911100
3.4-3.880.06337411.0081100
3.88-4.860.04637731.073199.9
4.86-150.04139561.017199.9

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
CNSrefinement
PDB_EXTRACT3.1data extraction
SHELXDphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.28→15 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8192 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2584 3708 9.8 %
Rwork0.2361 --
obs-37084 98 %
Solvent computationBsol: 34.1007 Å2
Displacement parametersBiso max: 81.61 Å2 / Biso mean: 44.4873 Å2 / Biso min: 23.83 Å2
Baniso -1Baniso -2Baniso -3
1--4.796 Å20 Å20 Å2
2---4.796 Å20 Å2
3---9.591 Å2
Refinement stepCycle: LAST / Resolution: 2.28→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3998 0 10 107 4115
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.178
X-RAY DIFFRACTIONc_mcbond_it1.3091.5
X-RAY DIFFRACTIONc_scbond_it2.0982
X-RAY DIFFRACTIONc_mcangle_it2.1522
X-RAY DIFFRACTIONc_scangle_it3.212.5
Refine LS restraints NCSRms: 0.091 / Type: restrain / Weight: 50
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.28-2.290.3819100.25727181
2.29-2.30.3465710.3442654725
2.3-2.320.4009700.3471677747
2.32-2.330.4304750.3247661736
2.33-2.350.3723700.307676746
2.35-2.370.3097790.3011649728
2.37-2.390.3512750.2989704779
2.39-2.410.2774770.2878645722
2.41-2.420.3163810.277674755
2.42-2.440.2693910.2734636727
2.44-2.470.3346730.2906705778
2.47-2.490.3015720.2928648720
2.49-2.510.2737740.27671745
2.51-2.530.3279620.2756694756
2.53-2.560.3356900.2837662752
2.56-2.580.3245630.2889673736
2.58-2.610.3163720.2637663735
2.61-2.630.3028690.251672741
2.63-2.660.2915820.261678760
2.66-2.690.3086770.2744667744
2.69-2.720.2856820.2807670752
2.72-2.750.268630.2734690753
2.75-2.780.3272730.2685691764
2.78-2.820.3101710.2599656727
2.82-2.860.3045700.282684754
2.86-2.90.2901750.2521695770
2.9-2.940.3247690.2729651720
2.94-2.980.3172790.2874671750
2.98-3.030.3086800.2735671751
3.03-3.080.2877760.25676752
3.08-3.130.2365830.2463685768
3.13-3.180.2691780.2551662740
3.18-3.250.3059760.275701777
3.25-3.310.2546810.2628654735
3.31-3.380.267820.2534678760
3.38-3.460.2359640.2498687751
3.46-3.540.3306670.2627680747
3.54-3.640.2517790.2613697776
3.64-3.740.2406840.234655739
3.74-3.860.2361810.2403688769
3.86-40.2924890.2153659748
4-4.160.202820.2041688770
4.16-4.340.2223780.2004677755
4.34-4.560.167790.1729706785
4.56-4.840.1462550.1674713768
4.84-5.20.1933630.201706769
5.2-5.70.272830.2007699782
5.7-6.460.2515630.2305728791
6.46-7.940.2921890.2244721810
7.94-150.1636810.1636757838
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 DIFFRACTION5iod.paramiod.top

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