2AS0

Crystal Structure of PH1915 (APC 5817): A Hypothetical RNA Methyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of a novel SAM-dependent methyltransferase PH1915 from Pyrococcus horikoshii.

Sun, W.Xu, X.Pavlova, M.Edwards, A.M.Joachimiak, A.Savchenko, A.Christendat, D.

(2005) Protein Sci. 14: 3121-3128

  • DOI: 10.1110/ps.051821805

  • PubMed Abstract: 
  • The S-adenosyl-L-methionine (SAM)-dependent methyltransferases represent a diverse and biologically important class of enzymes. These enzymes utilize the ubiquitous methyl donor SAM as a cofactor to methylate proteins, small molecules, lipids, and nu ...

    The S-adenosyl-L-methionine (SAM)-dependent methyltransferases represent a diverse and biologically important class of enzymes. These enzymes utilize the ubiquitous methyl donor SAM as a cofactor to methylate proteins, small molecules, lipids, and nucleic acids. Here we present the crystal structure of PH1915 from Pyrococcus horikoshii OT3, a predicted SAM-dependent methyltransferase. This protein belongs to the Cluster of Orthologous Group 1092, and the presented crystal structure is the first representative structure of this protein family. Based on sequence and 3D structure analysis, we have made valuable functional insights that will facilitate further studies for characterizing this group of proteins. Specifically, we propose that PH1915 and its orthologs are rRNA- or tRNA-specific methyltransferases.


    Organizational Affiliation

    Department of Botany, University of Toronto, 25 Willcocks Street, Toronto, Ontario M5S 3B2, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
hypothetical protein PH1915
A, B
396Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Find proteins for O59578 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Go to UniProtKB:  O59578
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 70.513α = 90.00
b = 86.161β = 114.16
c = 76.693γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
SOLVEphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-09-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance