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- PDB-2ibs: Crystal structure of the adenine-specific DNA methyltransferase M... -

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Basic information

Entry
Database: PDB / ID: 2ibs
TitleCrystal structure of the adenine-specific DNA methyltransferase M.TaqI complexed with the cofactor analog AETA and a 10 bp DNA containing 2-aminopurine at the target position
Components
  • 5'-D(*GP*AP*CP*AP*TP*CP*GP*(6MA)P*AP*C)-3'
  • 5'-D(*GP*TP*TP*CP*GP*(2PR)P*TP*GP*TP*C)-3'
  • Modification methylase TaqI
KeywordsTRANSFERASE/DNA / DNA / DNA methyltransferase / 2-aminopurine / base flipping / nucleotide flipping / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA restriction-modification system / DNA binding
Similarity search - Function
Type II restriction enzyme and methyltransferase RM.Eco57I-like / Eco57I restriction-modification methylase / N6 adenine-specific DNA methyltransferase, TaqI class, C-terminal / N6 adenine-specific DNA methyltransferase, TaqI class / Adenine-n6-DNA-methyltransferase Taqi, Chain A, domain 2 / Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2 / TaqI-like C-terminal specificity domain / TaqI-like C-terminal specificity domain / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site ...Type II restriction enzyme and methyltransferase RM.Eco57I-like / Eco57I restriction-modification methylase / N6 adenine-specific DNA methyltransferase, TaqI class, C-terminal / N6 adenine-specific DNA methyltransferase, TaqI class / Adenine-n6-DNA-methyltransferase Taqi, Chain A, domain 2 / Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2 / TaqI-like C-terminal specificity domain / TaqI-like C-terminal specificity domain / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-DEOXY-5'-[2-(AMINO)ETHYLTHIO]ADENOSINE / DNA / Type II methyltransferase M.TaqI
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPljevaljcic, G. / Lenz, T. / Scheidig, A.J. / Weinhold, E.
Citation
Journal: J.Am.Chem.Soc. / Year: 2007
Title: 2-Aminopurine Flipped into the Active Site of the Adenine-Specific DNA Methyltransferase M.TaqI: Crystal Structures and Time-Resolved Fluorescence
Authors: Lenz, T. / Bonnist, E.Y.M. / Pljevaljcic, G. / Neely, R.K. / Dryden, D.T.F. / Scheidig, A.J. / Jones, A.C. / Weinhold, E.
#1: Journal: Nat.Struct.Biol. / Year: 2001
Title: Structure of the N6-adenine DNA methyltransferase M.TaqI in complex with DNA and a cofactor analog
Authors: Goedecke, K. / Pignot, M. / Goody, R.S. / Scheidig, A.J. / Weinhold, E.
#2: Journal: J.Mol.Biol. / Year: 1997
Title: Differential binding of S-adenosylmethionine S-adenosylhomocysteine and Sinefungin to the adenine-specific DNA methyltransferase M.TaqI
Authors: Schluckebier, G. / Kozak, M. / Bleimling, N. / Weinhold, E. / Saenger, W.
History
DepositionSep 12, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*GP*TP*TP*CP*GP*(2PR)P*TP*GP*TP*C)-3'
C: 5'-D(*GP*AP*CP*AP*TP*CP*GP*(6MA)P*AP*C)-3'
E: 5'-D(*GP*TP*TP*CP*GP*(2PR)P*TP*GP*TP*C)-3'
F: 5'-D(*GP*AP*CP*AP*TP*CP*GP*(6MA)P*AP*C)-3'
A: Modification methylase TaqI
D: Modification methylase TaqI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,7218
Polymers108,0686
Non-polymers6532
Water13,673759
1
B: 5'-D(*GP*TP*TP*CP*GP*(2PR)P*TP*GP*TP*C)-3'
C: 5'-D(*GP*AP*CP*AP*TP*CP*GP*(6MA)P*AP*C)-3'
A: Modification methylase TaqI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3614
Polymers54,0343
Non-polymers3261
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-D(*GP*TP*TP*CP*GP*(2PR)P*TP*GP*TP*C)-3'
F: 5'-D(*GP*AP*CP*AP*TP*CP*GP*(6MA)P*AP*C)-3'
D: Modification methylase TaqI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3614
Polymers54,0343
Non-polymers3261
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.530, 69.160, 114.640
Angle α, β, γ (deg.)90.00, 92.18, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains two independent biological assemblies, each consisting of M.TaqI, DNA and cofactor analog AETA.

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Components

#1: DNA chain 5'-D(*GP*TP*TP*CP*GP*(2PR)P*TP*GP*TP*C)-3'


Mass: 3051.001 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Solid-phase DNA synthesis using commercially available phosphoramidites
#2: DNA chain 5'-D(*GP*AP*CP*AP*TP*CP*GP*(6MA)P*AP*C)-3'


Mass: 3052.046 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Solid-phase DNA synthesis using commercially available phosphoramidites
#3: Protein Modification methylase TaqI / Adenine-specific methyltransferase TaqI / M.TaqI


Mass: 47931.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Strain: YT1 / Gene: taqIM / Plasmid: PA1/MTAQ-A49A / Production host: Escherichia coli (E. coli) / Strain (production host): ER2267
References: UniProt: P14385, site-specific DNA-methyltransferase (adenine-specific)
#4: Chemical ChemComp-NEA / 5'-DEOXY-5'-[2-(AMINO)ETHYLTHIO]ADENOSINE


Mass: 326.375 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18N6O3S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 759 / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 3 microliters crystallization buffer (10mM Tris/HCl, 300mM NaCl, pH 7.3) containing the complex plus 1 microliter reservoir solution (100mM KCl, 100mM MgCl2, 6% isopropanol, 50mM sodium ...Details: 3 microliters crystallization buffer (10mM Tris/HCl, 300mM NaCl, pH 7.3) containing the complex plus 1 microliter reservoir solution (100mM KCl, 100mM MgCl2, 6% isopropanol, 50mM sodium cacodylate, pH 6.0), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Tris/HCl11
2NaClSodium chloride11
3KCl11
4MgCl211
5isopropanol11
6sodium cacodylate11
7H2O11
8Tris/HCl12
9NaClSodium chloride12
10KCl12
11MgCl212
12sodium cacodylate12
13H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 13, 2001 / Details: mirror
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.4→19.67 Å / Num. all: 36601 / Num. obs: 36299 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.69 % / Biso Wilson estimate: 25.27 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 9.33
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 4.63 / Num. unique all: 4175 / Rsym value: 0.334 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ProDCdata collection
MAR345data collection
XDSdata scaling
CNS1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G38
Resolution: 2.4→19.67 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.886 / SU B: 8.906 / SU ML: 0.212 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.856 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25193 1812 5 %RANDOM
Rwork0.19517 ---
obs0.19806 36299 99.62 %-
all-36438 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6384 810 44 759 7997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0227549
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9822.10810422
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9475786
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.93122.215298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.966151082
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1941554
X-RAY DIFFRACTIONr_chiral_restr0.0580.21101
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025520
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1450.23284
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.24853
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0780.2727
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1210.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0620.239
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2171.54072
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.38726358
X-RAY DIFFRACTIONr_scbond_it0.36634319
X-RAY DIFFRACTIONr_scangle_it0.6424.54063
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.403→2.465 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 127 -
Rwork0.229 2497 -
obs-2624 98.5 %

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