2DPM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.238 
  • R-Value Observed: 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

  • DOI: 10.1016/s0969-2126(98)00154-3
  • Primary Citation of Related Structures:  
    2DPM

  • 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 DNA Mtases have been defined and representative structures have been determined for three groups ...

    . 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: 
    • 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
    • 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
    • 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
    • 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 U S A 82: 4468

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (ADENINE-SPECIFIC METHYLTRANSFERASE DPNII 1)A284Streptococcus pneumoniaeMutation(s): 0 
Gene Names: dpnM
EC: 2.1.1.72
UniProt
Find proteins for P04043 (Streptococcus pneumoniae)
Explore P04043 
Go to UniProtKB:  P04043
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04043
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download Ideal Coordinates CCD File 
C [auth A]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
HG
Query on HG

Download Ideal Coordinates CCD File 
B [auth A]MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.238 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.6α = 90
b = 68.1β = 90
c = 85.2γ = 90
Software Package:
Software NamePurpose
PHASESphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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