3AY0

Crystal structure of Methanocaldococcus jannaschii Trm5 in complex with adenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Differentiating analogous tRNA methyltransferases by fragments of the methyl donor.

Lahoud, G.Goto-Ito, S.Yoshida, K.Ito, T.Yokoyama, S.Hou, Y.M.

(2011) Rna 17: 1236-1246

  • DOI: 10.1261/rna.2706011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacterial TrmD and eukaryotic-archaeal Trm5 form a pair of analogous tRNA methyltransferase that catalyze methyl transfer from S-adenosyl methionine (AdoMet) to N(1) of G37, using catalytic motifs that share no sequence or structural homology. Here w ...

    Bacterial TrmD and eukaryotic-archaeal Trm5 form a pair of analogous tRNA methyltransferase that catalyze methyl transfer from S-adenosyl methionine (AdoMet) to N(1) of G37, using catalytic motifs that share no sequence or structural homology. Here we show that natural and synthetic analogs of AdoMet are unable to distinguish TrmD from Trm5. Instead, fragments of AdoMet, adenosine and methionine, are selectively inhibitory of TrmD rather than Trm5. Detailed structural information of the two enzymes in complex with adenosine reveals how Trm5 escapes targeting by adopting an altered structure, whereas TrmD is trapped by targeting due to its rigid structure that stably accommodates the fragment. Free energy analysis exposes energetic disparities between the two enzymes in how they approach the binding of AdoMet versus fragments and provides insights into the design of inhibitors selective for TrmD.


    Organizational Affiliation

    Thomas Jefferson University, Department of Biochemistry and Molecular Biology, Philadelphia, Pennsylvania 19107, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein MJ0883
A, B
336Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Mutation(s): 0 
Gene Names: trm5b
EC: 2.1.1.228
Find proteins for Q58293 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  Q58293
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ADN
Query on ADN

Download SDF File 
Download CCD File 
A, B
ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ADNKd: 910000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 61.490α = 90.00
b = 67.127β = 93.75
c = 92.239γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction
CNSrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-17
    Type: Initial release