2DPM

DPNM DNA ADENINE METHYLTRANSFERASE FROM STREPTOCCOCUS PNEUMONIAE COMPLEXED WITH S-ADENOSYLMETHIONINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal structure of the DpnM DNA adenine methyltransferase from the DpnII restriction system of streptococcus pneumoniae bound to S-adenosylmethionine.

Tran, P.H.Korszun, Z.R.Cerritelli, S.Springhorn, S.S.Lacks, S.A.

(1998) Structure 6: 1563-1575


  • PubMed Abstract: 
  • . Methyltransferases (Mtases) catalyze the transfer of methyl groups from S-adenosylmethionine (AdoMet) to a variety of small molecular and macromolecular substrates. These enzymes contain a characteristic alpha/beta structural fold. Four groups of D ...

    . Methyltransferases (Mtases) catalyze the transfer of methyl groups from S-adenosylmethionine (AdoMet) to a variety of small molecular and macromolecular substrates. These enzymes contain a characteristic alpha/beta structural fold. Four groups of DNA Mtases have been defined and representative structures have been determined for three groups. DpnM is a DNA Mtase that acts on adenine N6 in the sequence GATC; the enzyme represents group alpha DNA Mtases, for which no structures are known.


    Related Citations: 
    • Nucleotide Sequence of the Dpn II DNA Methylase Gene of Streptococcus Pneumoniae and its Relationship to the dam Gene of Escherichia Coli
      Mannarelli, B.M.,Balganesh, T.S.,Greenberg, B.,Springhorn, S.S.,Lacks, S.A.
      (1985) Proc.Natl.Acad.Sci.USA 82: 4468
    • Crystallization of the DpnM Methylase from the DpnII Restriction System of Streptococcus Pneumoniae
      Cerritelli, S.,White, S.W.,Lacks, S.A.
      (1989) J.Mol.Biol. 207: 841
    • Genetic Basis of the Complementary DpnI and DpnII Restriction Systems of S.pneumoniae: An Intercellular Cassette Mechanism
      Lacks, S.A.,Mannarelli, B.M.,Springhorn, S.S.,Greenberg, B.
      (1986) Cell 46: 993
    • Proteins Encoded by the DpnII Restriction Gene Cassette. Two Methylases and an Endonuclease
      de la Campa, A.G.,Kale, P.,Springhorn, S.S.,Lacks, S.A.
      (1987) J.Mol.Biol. 196: 457


    Organizational Affiliation

    Department of Biology, Brookhaven National Laboratory, Upton, NY 11973,USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (ADENINE-SPECIFIC METHYLTRANSFERASE DPNII 1)
A
284Streptococcus pneumoniaeGene Names: dpnM
EC: 2.1.1.72
Find proteins for P04043 (Streptococcus pneumoniae)
Go to UniProtKB:  P04043
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HG
Query on HG

Download SDF File 
Download CCD File 
A
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
SAM
Query on SAM

Download SDF File 
Download CCD File 
A
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.238 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.600α = 90.00
b = 68.100β = 90.00
c = 85.200γ = 90.00
Software Package:
Software NamePurpose
PHASESphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-12-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2014-11-12
    Type: Structure summary
  • Version 1.4: 2017-10-04
    Type: Refinement description