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 

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This is version 1.4 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: https://doi.org/10.1093/nar/28.20.3950
  • Primary Citation of Related Structures:  
    1EG2

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MODIFICATION METHYLASE RSRI319Cereibacter sphaeroidesMutation(s): 0 
EC: 2.1.1.72
UniProt
Find proteins for P14751 (Cereibacter sphaeroides)
Explore P14751 
Go to UniProtKB:  P14751
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14751
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MTA
Query on MTA

Download Ideal Coordinates CCD File 
B [auth A]5'-DEOXY-5'-METHYLTHIOADENOSINE
C11 H15 N5 O3 S
WUUGFSXJNOTRMR-IOSLPCCCSA-N
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 = 70.42α = 90
b = 130.253β = 90
c = 67.284γ = 90
Software Package:
Software NamePurpose
XTALdata collection
SCALEPACKdata scaling
SOLVEphasing
SHARPphasing
CNSrefinement
MARMADdata reduction
DENZOdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2000-10-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references, Derived calculations