5CM2

Structure of Y. lipolytica Trm9-Trm112 complex, a methyltransferase modifying U34 in the anticodon loop of some tRNAs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Insights into molecular plasticity in protein complexes from Trm9-Trm112 tRNA modifying enzyme crystal structure.

Letoquart, J.van Tran, N.Caroline, V.Aleksandrov, A.Lazar, N.van Tilbeurgh, H.Liger, D.Graille, M.

(2015) Nucleic Acids Res 43: 10989-11002

  • DOI: 10.1093/nar/gkv1009
  • Primary Citation of Related Structures:  
    5CM2

  • PubMed Abstract: 
  • Most of the factors involved in translation (tRNA, rRNA and proteins) are subject to post-transcriptional and post-translational modifications, which participate in the fine-tuning and tight control of ribosome and protein synthesis processes. In eukaryotes, Trm112 acts as an obligate activating platform for at least four methyltransferases (MTase) involved in the modification of 18S rRNA (Bud23), tRNA (Trm9 and Trm11) and translation termination factor eRF1 (Mtq2) ...

    Most of the factors involved in translation (tRNA, rRNA and proteins) are subject to post-transcriptional and post-translational modifications, which participate in the fine-tuning and tight control of ribosome and protein synthesis processes. In eukaryotes, Trm112 acts as an obligate activating platform for at least four methyltransferases (MTase) involved in the modification of 18S rRNA (Bud23), tRNA (Trm9 and Trm11) and translation termination factor eRF1 (Mtq2). Trm112 is then at a nexus between ribosome synthesis and function. Here, we present a structure-function analysis of the Trm9-Trm112 complex, which is involved in the 5-methoxycarbonylmethyluridine (mcm(5)U) modification of the tRNA anticodon wobble position and hence promotes translational fidelity. We also compare the known crystal structures of various Trm112-MTase complexes, highlighting the structural plasticity allowing Trm112 to interact through a very similar mode with its MTase partners, although those share less than 20% sequence identity.


    Organizational Affiliation

    Laboratoire de Biochimie, CNRS, UMR 7654, Ecole Polytechnique, F-91128 Palaiseau Cedex, France Fonction et Architecture des Assemblages Macromoléculaires, Département B3S, Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, UMR 9198, CEA, Université Paris Sud, F-91405 Orsay Cedex, France marc.graille@polytechnique.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRNA METHYLTRANSFERASEA [auth Z]205Yarrowia lipolytica CLIB122Mutation(s): 0 
Gene Names: YALI0_D12837g
UniProt
Find proteins for Q6C999 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q6C999 
Go to UniProtKB:  Q6C999
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6C999
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TRNA METHYLTRANSFERASE ACTIVATOR SUBUNITB [auth M]130Yarrowia lipolytica CLIB122Mutation(s): 0 
Gene Names: YALI0_E24761g
UniProt
Find proteins for Q6C4P5 (Yarrowia lipolytica (strain CLIB 122 / E 150))
Explore Q6C4P5 
Go to UniProtKB:  Q6C4P5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6C4P5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth M]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: I 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.2α = 90
b = 176.2β = 90
c = 176.2γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2015-12-23
    Changes: Database references
  • Version 1.2: 2021-03-17
    Changes: Structure summary