4XBO

Crystal structure of full length E.coli TrmJ in complex with SAH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

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Literature

tRNA recognition by a bacterial tRNA Xm32 modification enzyme from the SPOUT methyltransferase superfamily

Liu, R.J.Long, T.Zhou, M.Zhou, X.L.Wang, E.D.

(2015) Nucleic Acids Res 43: 7489-7503

  • DOI: 10.1093/nar/gkv745
  • Primary Citation of Related Structures:  
    4XBO

  • PubMed Abstract: 
  • TrmJ proteins from the SPOUT methyltransferase superfamily are tRNA Xm32 modification enzymes that occur in bacteria and archaea. Unlike archaeal TrmJ, bacterial TrmJ require full-length tRNA molecules as substrates. It remains unknown how bacterial TrmJs recognize substrate tRNAs and specifically catalyze a 2'-O modification at ribose 32 ...

    TrmJ proteins from the SPOUT methyltransferase superfamily are tRNA Xm32 modification enzymes that occur in bacteria and archaea. Unlike archaeal TrmJ, bacterial TrmJ require full-length tRNA molecules as substrates. It remains unknown how bacterial TrmJs recognize substrate tRNAs and specifically catalyze a 2'-O modification at ribose 32. Herein, we demonstrate that all six Escherichia coli (Ec) tRNAs with 2'-O-methylated nucleosides at position 32 are substrates of EcTrmJ, and we show that the elbow region of tRNA, but not the amino acid acceptor stem, is needed for the methylation reaction. Our crystallographic study reveals that full-length EcTrmJ forms an unusual dimer in the asymmetric unit, with both the catalytic SPOUT domain and C-terminal extension forming separate dimeric associations. Based on these findings, we used electrophoretic mobility shift assay, isothermal titration calorimetry and enzymatic methods to identify amino acids within EcTrmJ that are involved in tRNA binding. We found that tRNA recognition by EcTrmJ involves the cooperative influences of conserved residues from both the SPOUT and extensional domains, and that this process is regulated by the flexible hinge region that connects these two domains.


    Organizational Affiliation

    State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China University of Chinese Academy of Sciences, Beijing 100039, China School of Life Science and Technology, ShanghaiTech University, 319 Yue Yang Road, Shanghai 200031, China edwang@sibs.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJA, B254Escherichia coli K-12Mutation(s): 0 
Gene Names: trmJyfhQb2532JW2516
EC: 2.1.1.200
UniProt
Find proteins for P0AE01 (Escherichia coli (strain K12))
Explore P0AE01 
Go to UniProtKB:  P0AE01
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.863α = 90
b = 136.571β = 90
c = 99.612γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31130064
National Natural Science Foundation of ChinaChina31270775

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-23
    Type: Initial release
  • Version 1.1: 2017-10-18
    Changes: Author supporting evidence, Database references, Derived calculations