5HJI

Crystal Structure of Pyrococcus abyssi Trm5a complexed with adenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structures of the bifunctional tRNA methyltransferase Trm5a

Wang, C.Jia, Q.Chen, R.Wei, Y.Li, J.Ma, J.Xie, W.

(2016) Sci Rep 6: 33553-33553

  • DOI: 10.1038/srep33553
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • tRNA methyltransferase Trm5 catalyses the transfer of a methyl group from S-adenosyl-L-methionine to G37 in eukaryotes and archaea. The N1-methylated guanosine is the product of the initial step of the wyosine hypermodification, which is essential fo ...

    tRNA methyltransferase Trm5 catalyses the transfer of a methyl group from S-adenosyl-L-methionine to G37 in eukaryotes and archaea. The N1-methylated guanosine is the product of the initial step of the wyosine hypermodification, which is essential for the maintenance of the reading frame during translation. As a unique member of this enzyme family, Trm5a from Pyrococcus abyssi (PaTrm5a) catalyses not only the methylation of N1, but also the further methylation of C7 on 4-demethylwyosine at position 37 to produce isowyosine, but the mechanism for the double methylation is poorly understood. Here we report four crystal structures of PaTrm5a ranging from 1.7- to 2.3-Å, in the apo form or in complex with various SAM analogues. These structures reveal that Asp243 specifically recognises the base moiety of SAM at the active site. Interestingly, the protein in our structures all displays an extended conformation, quite different from the well-folded conformation of Trm5b from Methanocaldococcus jannaschii reported previously, despite their similar overall architectures. To rule out the possibilities of crystallisation artefacts, we conducted the fluorescence resonance energy transfer (FRET) experiments. The FRET data suggested that PaTrm5a adopts a naturally extended conformation in solution, and therefore the open conformation is a genuine state of PaTrm5a.


    Organizational Affiliation

    State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong 510275, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
tRNA (guanine(37)-N1)-methyltransferase Trm5a
A
352Pyrococcus abyssi (strain GE5 / Orsay)Mutation(s): 0 
Gene Names: taw22 (trm5a)
EC: 2.1.1.-, 2.1.1.228
Find proteins for Q9V2G1 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V2G1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADN
Query on ADN

Download SDF File 
Download CCD File 
A
ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.727α = 90.00
b = 54.718β = 90.00
c = 128.948γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
CrysalisProdata reduction
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Guangdong Innovative Research TeamChina2011Y038
Science and Technology Program of GuangzhouChina201504010025
Fundamental Research Funds for the Central UniversitiesChina15lgjc02

Revision History 

  • Version 1.0: 2016-10-12
    Type: Initial release