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- PDB-6fdf: Crystal structure of S. pombe Dnmt2 methyltransferase -

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Basic information

Entry
Database: PDB / ID: 6fdf
TitleCrystal structure of S. pombe Dnmt2 methyltransferase
ComponentstRNA (cytosine(38)-C(5))-methyltransferase
KeywordsTRANSFERASE / Dnmt2 / Methyltransferase / S-adenosylhomocysteine / tRNA
Function / homology
Function and homology information


tRNA (cytidine) methyltransferase activity / tRNA (cytosine38-C5)-methyltransferase / tRNA C5-cytosine methylation / tRNA (cytidine-5-)-methyltransferase activity / tRNA binding / nucleus / cytosol
Similarity search - Function
DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / tRNA (cytosine(38)-C(5))-methyltransferase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.697 Å
AuthorsJohannsson, S. / Neumann, P. / Ficner, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSPP1784 Germany
CitationJournal: Sci Rep / Year: 2018
Title: Structural insights into the stimulation of S. pombe Dnmt2 catalytic efficiency by the tRNA nucleoside queuosine.
Authors: Johannsson, S. / Neumann, P. / Wulf, A. / Welp, L.M. / Gerber, H.D. / Krull, M. / Diederichsen, U. / Urlaub, H. / Ficner, R.
History
DepositionDec 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: tRNA (cytosine(38)-C(5))-methyltransferase
B: tRNA (cytosine(38)-C(5))-methyltransferase
C: tRNA (cytosine(38)-C(5))-methyltransferase
D: tRNA (cytosine(38)-C(5))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,75319
Polymers153,2034
Non-polymers2,55115
Water14,988832
1
A: tRNA (cytosine(38)-C(5))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0536
Polymers38,3011
Non-polymers7535
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: tRNA (cytosine(38)-C(5))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9615
Polymers38,3011
Non-polymers6614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: tRNA (cytosine(38)-C(5))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8694
Polymers38,3011
Non-polymers5693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: tRNA (cytosine(38)-C(5))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8694
Polymers38,3011
Non-polymers5693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.817, 114.781, 113.759
Angle α, β, γ (deg.)90.000, 131.050, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
tRNA (cytosine(38)-C(5))-methyltransferase / DNA (cytosine-5)-methyltransferase-like protein 2 / Dnmt2 / M.SpomI / SpIM.SpoI


Mass: 38300.660 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: pmt1, SPBC19C2.02 / Production host: Escherichia coli (E. coli)
References: UniProt: P40999, tRNA (cytosine38-C5)-methyltransferase
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 832 / 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: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 50 mM MES pH 6.5 1 % w/v PEG 4000 4 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.697→40.795 Å / Num. obs: 162497 / % possible obs: 99 % / Redundancy: 3.492 % / Biso Wilson estimate: 33.42 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03 / Rrim(I) all: 0.035 / Χ2: 1.051 / Net I/σ(I): 20.63
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.83.5740.5092.69255330.8130.59899.3
1.8-1.93.5050.2684.86204180.9310.31799.4
1.9-23.3290.1488.18165900.9750.17699.1
2-2.53.5420.05918.68485820.9960.06999.2
2.5-33.5590.03233.28215440.9980.03899
3-43.3270.02443.18170270.9990.02998.3
4-53.5370.02255.3560930.9980.02698.7
5-63.3870.02255.5127350.9980.02698.3
6-103.2930.02552.7729040.9970.0397.4
10-203.3480.03151.897180.9940.03895.2
20-302.8570.03942.92700.990.04988.6
30-40.7952.1880.02932.9160.9960.03941

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.697→40.795 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.57
RfactorNum. reflection% reflection
Rfree0.1948 2099 1.29 %
Rwork0.1739 --
obs0.1742 162497 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 107.23 Å2 / Biso mean: 44.8102 Å2 / Biso min: 20.61 Å2
Refinement stepCycle: final / Resolution: 1.697→40.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10266 0 170 832 11268
Biso mean--51.43 49.64 -
Num. residues----1269
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.697-1.73650.27721320.2706101051023794
1.7365-1.77990.25561420.24941080110943100
1.7799-1.8280.27381390.2381063210771100
1.828-1.88180.28971410.22841078710928100
1.8818-1.94260.2391400.2051106871082799
1.9426-2.0120.22911400.198107191085999
2.012-2.09250.22281410.19241074410885100
2.0925-2.18780.21231400.19391074110881100
2.1878-2.30310.23991410.19181072410865100
2.3031-2.44740.19341410.184107571089899
2.4474-2.63630.23181390.1854106891082899
2.6363-2.90160.21971410.1795107521089399
2.9016-3.32120.19041410.1759107391088099
3.3212-4.18380.15741400.1505106971083799
4.1838-40.80690.17211410.1564108241096599
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.20450.16771.65520.75180.01871.57470.02060.1172-0.1506-0.0480.0544-0.01040.0967-0.0624-0.07990.3035-0.01570.02120.2513-0.04390.2395-41.793415.549197.3639
21.9955-0.309-0.99390.9843-0.12653.33830.05940.06530.0717-0.02450.0106-0.0398-0.00430.1284-0.06960.1837-0.0238-0.00220.1651-0.0210.2228-48.177543.655982.1556
31.5383-0.6967-0.80952.60731.03152.45310.0748-0.0510.14970.07420.0551-0.2427-0.29150.138-0.12470.2501-0.0346-0.02210.223-0.0290.2202-62.373113.052945.2919
43.1573-1.24971.66952.0932-0.79292.3324-0.1019-0.09980.03170.07260.0540.0483-0.1806-0.20.04330.2548-0.03050.01510.265-0.01740.2228-78.4336-16.362555.6275
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 6 through 335)A6 - 335
2X-RAY DIFFRACTION2(chain 'B' and resid 5 through 335)B5 - 335
3X-RAY DIFFRACTION3(chain 'C' and resid 6 through 335)C6 - 335
4X-RAY DIFFRACTION4(chain 'D' and resid 6 through 335)D6 - 335

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