2FCA

The structure of BsTrmB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase.

Zegers, I.Gigot, D.van Vliet, F.Tricot, C.Aymerich, S.Bujnicki, J.M.Kosinski, J.Droogmans, L.

(2006) Nucleic Acids Res 34: 1925-1934

  • DOI: 10.1093/nar/gkl116
  • Primary Citation of Related Structures:  
    2FCA

  • PubMed Abstract: 
  • The structure of Bacillus subtilis TrmB (BsTrmB), the tRNA (m7G46) methyltransferase, was determined at a resolution of 2.1 A. This is the first structure of a member of the TrmB family to be determined by X-ray crystallography. It reveals a unique variant of the Rossmann-fold methyltransferase (RFM) structure, with the N-terminal helix folded on the opposite site of the catalytic domain ...

    The structure of Bacillus subtilis TrmB (BsTrmB), the tRNA (m7G46) methyltransferase, was determined at a resolution of 2.1 A. This is the first structure of a member of the TrmB family to be determined by X-ray crystallography. It reveals a unique variant of the Rossmann-fold methyltransferase (RFM) structure, with the N-terminal helix folded on the opposite site of the catalytic domain. The architecture of the active site and a computational docking model of BsTrmB in complex with the methyl group donor S-adenosyl-L-methionine and the tRNA substrate provide an explanation for results from mutagenesis studies of an orthologous enzyme from Escherichia coli (EcTrmB). However, unlike EcTrmB, BsTrmB is shown here to be dimeric both in the crystal and in solution. The dimer interface has a hydrophobic core and buries a potassium ion and five water molecules. The evolutionary analysis of the putative interface residues in the TrmB family suggests that homodimerization may be a specific feature of TrmBs from Bacilli, which may represent an early stage of evolution to an obligatory dimer.


    Organizational Affiliation

    Laboratorium Ultrastructuur, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
tRNA (guanine-N(7)-)-methyltransferaseA, B213Bacillus subtilisMutation(s): 0 
Gene Names: trmB
EC: 2.1.1.33
UniProt
Find proteins for O34522 (Bacillus subtilis (strain 168))
Explore O34522 
Go to UniProtKB:  O34522
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34522
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.233 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.83α = 90
b = 178.83β = 90
c = 41.95γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-15
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description