1EG2

CRYSTAL STRUCTURE OF RHODOBACTER SPHEROIDES (N6 ADENOSINE) METHYLTRANSFERASE (M.RSRI)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of RsrI methyltransferase, a member of the N6-adenine beta class of DNA methyltransferases.

Scavetta, R.D.Thomas, C.B.Walsh, M.A.Szegedi, S.Joachimiak, A.Gumport, R.I.Churchill, M.E.

(2000) Nucleic Acids Res. 28: 3950-3961

  • DOI: 10.1093/nar/28.20.3950

  • PubMed Abstract: 
  • DNA methylation is important in cellular, developmental and disease processes, as well as in bacterial restriction-modification systems. Methylation of DNA at the amino groups of cytosine and adenine is a common mode of protection against restriction ...

    DNA methylation is important in cellular, developmental and disease processes, as well as in bacterial restriction-modification systems. Methylation of DNA at the amino groups of cytosine and adenine is a common mode of protection against restriction endonucleases afforded by the bacterial methyltransferases. The first structure of an N:6-adenine methyltransferase belonging to the beta class of bacterial methyltransferases is described here. The structure of M. RSR:I from Rhodobacter sphaeroides, which methylates the second adenine of the GAATTC sequence, was determined to 1.75 A resolution using X-ray crystallography. Like other methyltransferases, the enzyme contains the methylase fold and has well-defined substrate binding pockets. The catalytic core most closely resembles the PVU:II methyltransferase, a cytosine amino methyltransferase of the same beta group. The larger nucleotide binding pocket observed in M. RSR:I is expected because it methylates adenine. However, the most striking difference between the RSR:I methyltransferase and the other bacterial enzymes is the structure of the putative DNA target recognition domain, which is formed in part by two helices on an extended arm of the protein on the face of the enzyme opposite the active site. This observation suggests that a dramatic conformational change or oligomerization may take place during DNA binding and methylation.


    Organizational Affiliation

    Department of Pharmacology, University of Colorado Health Sciences Center, 4200 East Ninth Avenue, Denver, CO 80262, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MODIFICATION METHYLASE RSRI
A
319Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: rsrIM
EC: 2.1.1.72
Find proteins for P14751 (Rhodobacter sphaeroides)
Go to UniProtKB:  P14751
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MTA
Query on MTA

Download SDF File 
Download CCD File 
A
5'-DEOXY-5'-METHYLTHIOADENOSINE
C11 H15 N5 O3 S
WUUGFSXJNOTRMR-IOSLPCCCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.214 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 70.420α = 90.00
b = 130.253β = 90.00
c = 67.284γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SHARPphasing
MARMADdata reduction
XTALdata collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-10-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description