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- PDB-2y7h: Atomic model of the DNA-bound methylase complex from the Type I r... -

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Basic information

Entry
Database: PDB / ID: 2y7h
TitleAtomic model of the DNA-bound methylase complex from the Type I restriction-modification enzyme EcoKI (M2S1). Based on fitting into EM map 1534.
Components
  • 5'-D(*GP*TP*TP*CP*AP*AP*CP*GP*TP*CP*GP*AP*CP*GP *TP*GP*CP*AP*AP*C)-3'
  • 5'-D(*GP*TP*TP*GP*CP*AP*CP*GP*TP*CP*GP*AP*CP*GP *TP*TP*GP*AP*AP*C)-3'
  • TYPE I RESTRICTION ENZYME ECOKI M PROTEIN
  • TYPE-1 RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


type I site-specific deoxyribonuclease complex / N-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA restriction-modification system / methylation / DNA binding / cytosol
Similarity search - Function
N6 adenine-specific DNA methyltransferase, N-terminal domain / : / Type I restriction enzyme EcoKI-like, methylase subunit, N-terminal domain superfamily / : / HsdM N-terminal domain / Type I restriction modification DNA specificity domain superfamily / Type I restriction modification DNA specificity domain / Type I restriction modification DNA specificity domain / N-6 DNA Methylase / DNA methylase, adenine-specific ...N6 adenine-specific DNA methyltransferase, N-terminal domain / : / Type I restriction enzyme EcoKI-like, methylase subunit, N-terminal domain superfamily / : / HsdM N-terminal domain / Type I restriction modification DNA specificity domain superfamily / Type I restriction modification DNA specificity domain / Type I restriction modification DNA specificity domain / N-6 DNA Methylase / DNA methylase, adenine-specific / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / DNA / DNA (> 10) / Type I restriction enzyme EcoKI specificity subunit / Type I restriction enzyme EcoKI methylase subunit
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 18 Å
AuthorsKennaway, C.K. / Obarska-Kosinska, A. / White, J.H. / Tuszynska, I. / Cooper, L.P. / Bujnicki, J.M. / Trinick, J. / Dryden, D.T.F.
CitationJournal: Nucleic Acids Res / Year: 2009
Title: The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein.
Authors: Christopher K Kennaway / Agnieszka Obarska-Kosinska / John H White / Irina Tuszynska / Laurie P Cooper / Janusz M Bujnicki / John Trinick / David T F Dryden /
Abstract: Type-I DNA restriction-modification (R/M) systems are important agents in limiting the transmission of mobile genetic elements responsible for spreading bacterial resistance to antibiotics. EcoKI, a ...Type-I DNA restriction-modification (R/M) systems are important agents in limiting the transmission of mobile genetic elements responsible for spreading bacterial resistance to antibiotics. EcoKI, a Type I R/M enzyme from Escherichia coli, acts by methylation- and sequence-specific recognition, leading to either methylation of DNA or translocation and cutting at a random site, often hundreds of base pairs away. Consisting of one specificity subunit, two modification subunits, and two DNA translocase/endonuclease subunits, EcoKI is inhibited by the T7 phage antirestriction protein ocr, a DNA mimic. We present a 3D density map generated by negative-stain electron microscopy and single particle analysis of the central core of the restriction complex, the M.EcoKI M(2)S(1) methyltransferase, bound to ocr. We also present complete atomic models of M.EcoKI in complex with ocr and its cognate DNA giving a clear picture of the overall clamp-like operation of the enzyme. The model is consistent with a large body of experimental data on EcoKI published over 40 years.
History
DepositionJan 31, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Other / Refinement description / Version format compliance
Revision 1.2Aug 23, 2017Group: Data collection / Derived calculations / Category: em_image_scans / em_software / struct_conn
Item: _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.3Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.4May 8, 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 / em_3d_fitting_list / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-1534
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TYPE-1 RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN
B: TYPE I RESTRICTION ENZYME ECOKI M PROTEIN
C: TYPE I RESTRICTION ENZYME ECOKI M PROTEIN
D: 5'-D(*GP*TP*TP*CP*AP*AP*CP*GP*TP*CP*GP*AP*CP*GP *TP*GP*CP*AP*AP*C)-3'
E: 5'-D(*GP*TP*TP*GP*CP*AP*CP*GP*TP*CP*GP*AP*CP*GP *TP*TP*GP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,2917
Polymers182,4945
Non-polymers7972
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein TYPE-1 RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN / HSDS TYPE I DNA RESTRICTION SPECIFICITY SUBUNIT / S.ECOKI / TYPE I RESTRICTION ENZYME ECOKI ...HSDS TYPE I DNA RESTRICTION SPECIFICITY SUBUNIT / S.ECOKI / TYPE I RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN / S PROTEIN


Mass: 51468.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K
References: UniProt: P05719, type I site-specific deoxyribonuclease
#2: Protein TYPE I RESTRICTION ENZYME ECOKI M PROTEIN / HSDM TYPE I DNA RESTRICTION METHYLTRANSFERASE SUBUNIT / M.ECOKI


Mass: 59378.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K
References: UniProt: P08957, type I site-specific deoxyribonuclease, site-specific DNA-methyltransferase (adenine-specific)
#3: DNA chain 5'-D(*GP*TP*TP*CP*AP*AP*CP*GP*TP*CP*GP*AP*CP*GP *TP*GP*CP*AP*AP*C)-3'


Mass: 6118.968 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: FLIPPED OUT ADENINE / Source: (synth.) ESCHERICHIA COLI (E. coli)
#4: DNA chain 5'-D(*GP*TP*TP*GP*CP*AP*CP*GP*TP*CP*GP*AP*CP*GP *TP*TP*GP*AP*AP*C)-3'


Mass: 6149.978 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: FLIPPED OUT ADENINE BASE / Source: (synth.) ESCHERICHIA COLI (E. coli)
#5: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: M.ECOKI WITH DNA / Type: COMPLEX
Buffer solutionName: 20MM TRIS-CL, 100 MM NACL / pH: 4.7 / Details: 20MM TRIS-CL, 100 MM NACL
SpecimenConc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO
EM stainingType: NEGATIVE / Material: Uranyl Acetate
Specimen supportDetails: CARBON

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Electron microscopy imaging

MicroscopyModel: JEOL 1200EX / Date: Feb 1, 2008
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 80 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 40000 X / Calibrated magnification: 39500 X / Nominal defocus max: 870 nm / Nominal defocus min: 275 nm / Cs: 2 mm
Specimen holderTemperature: 294 K
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1Situsmodel fitting
2UCSF Chimeramodel fitting
3UROmodel fitting
4EMAN3D reconstruction
5IMAGIC3D reconstruction
6MRC IMAGE PROCESSING PACKAGE3D reconstruction
CTF correctionDetails: FILTERED AT FIRST ZERO
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionMethod: RANDOM SPHERES STARTING MODEL / Resolution: 18 Å / Num. of particles: 17807 / Nominal pixel size: 3.12 Å / Actual pixel size: 3.12 Å / Magnification calibration: TMV
Details: HSDM N-TERMINAL DOMAIN RETRACED FROM PDB ENTRY 2AR0. DISORDERED C-TERMINUS OF HSDM MODELLED INTO DENSITY.
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: METHOD--UROX REFINEMENT PROTOCOL--RIGID BODY
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11S7Z

1s7z

11S7Z1PDBexperimental model
21YF2

1yf2

11YF22PDBexperimental model
32AR0

2ar0

12AR03PDBexperimental model
RefinementHighest resolution: 18 Å
Refinement stepCycle: LAST / Highest resolution: 18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11972 820 54 0 12846

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