Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 90.66 kDa 
• Atom Count: 6782 
• Modelled Residue Count: 792 
• Deposited Residue Count: 792 
• Unique protein chains: 1

2AS0

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

• PDB DOI: 10.2210/pdb2AS0/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-08-22 Released: 2005-09-20 
• Deposition Author(s): Sun, W., Xu, X., Pavlova, M., Edwards, A.M., Joachimiak, A., Savchenko, A., Christendat, D., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.239 
• R-Value Work: 0.207 
• R-Value Observed: 0.207 

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

• PubMed: 16260766 
• DOI: 10.1110/ps.051821805
• Primary Citation of Related Structures:  
  2AS0


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein PH1915	A, B	396	Pyrococcus horikoshii	Mutation(s): 14  Gene Names: PH1915 EC: 2.1.1
UniProt
Find proteins for O59578 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59578  Go to UniProtKB:  O59578

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.239 
• R-Value Work: 0.207 
• R-Value Observed: 0.207 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.513	α = 90
b = 86.161	β = 114.16
c = 76.693	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-08-22 
• Released Date: 2005-09-20 
Deposition Author(s): Sun, W., Xu, X., Pavlova, M., Edwards, A.M., Joachimiak, A., Savchenko, A., Christendat, D., Midwest Center for Structural Genomics (MCSG)

Revision History  

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