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- PDB-2np6: Crystal structure of the adenine-specific DNA methyltransferase M... -

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Basic information

Entry
Database: PDB / ID: 2np6
TitleCrystal structure of the adenine-specific DNA methyltransferase M.TaqI complexed with the cofactor analog AETA and a 10 bp DNA containing an abasic site analog 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*(3DR)P*TP*GP*TP*C)-3'
  • Modification methylase TaqI
KeywordsTRANSFERASE/DNA / DNA / DNA methyltransferase / abasic site analog / 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 / methylation / DNA binding
Similarity search - Function
Adenine-n6-DNA-methyltransferase Taqi, Chain A, domain 2 / N6 adenine-specific DNA methyltransferase, TaqI class / N6 adenine-specific DNA methyltransferase, TaqI class, C-terminal / Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2 / TaqI-like C-terminal specificity domain / TaqI-like C-terminal specificity domain / Type II restriction enzyme and methyltransferase RM.Eco57I-like / Eco57I restriction-modification methylase / : / N-6 Adenine-specific DNA methylases signature. ...Adenine-n6-DNA-methyltransferase Taqi, Chain A, domain 2 / N6 adenine-specific DNA methyltransferase, TaqI class / N6 adenine-specific DNA methyltransferase, TaqI class, C-terminal / Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2 / TaqI-like C-terminal specificity domain / TaqI-like C-terminal specificity domain / Type II restriction enzyme and methyltransferase RM.Eco57I-like / Eco57I restriction-modification methylase / : / 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
ISOPROPYL ALCOHOL / 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: 2.1 Å
AuthorsLenz, T. / Scheidig, A.J. / Weinhold, E.
Citation
Journal: To be Published
Title: Caught in the act II: Visualization of an intermediate in the DNA base-flipping pathway induced by the adenine-specific DNA methyltransferase M.TaqI
Authors: Lenz, T. / Scheidig, A.J. / 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
DepositionOct 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Aug 30, 2023Group: 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 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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
B: 5'-D(*GP*TP*TP*CP*GP*(3DR)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*(3DR)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)108,81913
Polymers107,8026
Non-polymers1,0177
Water9,476526
1
B: 5'-D(*GP*TP*TP*CP*GP*(3DR)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)54,3486
Polymers53,9013
Non-polymers4473
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-D(*GP*TP*TP*CP*GP*(3DR)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)54,4727
Polymers53,9013
Non-polymers5714
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.342, 68.817, 114.196
Angle α, β, γ (deg.)90.00, 92.22, 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

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DNA chain , 2 types, 4 molecules BECF

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


Mass: 2917.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Solid-phase DNA synthesis
#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

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Protein , 1 types, 2 molecules AD

#3: Protein Modification methylase TaqI / E.C.2.1.1.72 / 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)

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Non-polymers , 4 types, 533 molecules

#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O
#5: Chemical ChemComp-NEA / 5'-DEOXY-5'-[2-(AMINO)ETHYLTHIO]ADENOSINE


Mass: 326.375 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18N6O3S
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / 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: 2.14 Å3/Da / Density % sol: 42.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 3 microliters crystallization buffer (10 mM Tris/HCl, 300 mM NaCl, pH 7.3) containing the complex plus 1 microliter reservoir solution (100 mM KCl, 100 mM MgCl2, 6% isopropanol, 50 mM sodium ...Details: 3 microliters crystallization buffer (10 mM Tris/HCl, 300 mM NaCl, pH 7.3) containing the complex plus 1 microliter reservoir solution (100 mM KCl, 100 mM MgCl2, 6% isopropanol, 50 mM sodium cacodylate, pH 6.0), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1Tris/HCl11
2NaCl11
3H2O11
4KCl12
5MgCl212
6isopropanol12
7sodium cacodylate12
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 13, 2005 / Details: ID14-3 (mirror)
RadiationMonochromator: ID14-3 (mirror) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.1→19.76 Å / Num. all: 53925 / Num. obs: 53381 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 18.86 Å2 / Rmerge(I) obs: 0.165 / Rsym value: 0.165 / Net I/σ(I): 7.66
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.77 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 3.09 / Num. unique all: 7006 / Rsym value: 0.447 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ProDCdata collection
MAR345data collection
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G38

1g38


Resolution: 2.1→19.76 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.811 / SU B: 6.851 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.308 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28624 2668 5 %RANDOM
Rwork0.2283 ---
obs0.23119 53379 99.13 %-
all-53850 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.965 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20.2 Å2
2--0.13 Å20 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6389 790 68 526 7773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227548
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.342.10610407
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2915785
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.23522.174299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.146151081
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.611555
X-RAY DIFFRACTIONr_chiral_restr0.080.21099
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025503
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1880.23576
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24809
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2499
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.288
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4091.54064
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.71226360
X-RAY DIFFRACTIONr_scbond_it0.98334294
X-RAY DIFFRACTIONr_scangle_it1.5454.54047
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 196 -
Rwork0.256 3532 -
obs-3728 99.7 %

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