6F5Z

Complex between the Haloferax volcanii Trm112 methyltransferase activator and the Hvo_0019 putative methyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Evolutionary insights into Trm112-methyltransferase holoenzymes involved in translation between archaea and eukaryotes.

van Tran, N.Muller, L.Ross, R.L.Lestini, R.Letoquart, J.Ulryck, N.Limbach, P.A.de Crecy-Lagard, V.Cianferani, S.Graille, M.

(2018) Nucleic Acids Res 46: 8483-8499

  • DOI: https://doi.org/10.1093/nar/gky638
  • Primary Citation of Related Structures:  
    6F5Z

  • PubMed Abstract: 

    Protein synthesis is a complex and highly coordinated process requiring many different protein factors as well as various types of nucleic acids. All translation machinery components require multiple maturation events to be functional. These include post-transcriptional and post-translational modification steps and methylations are the most frequent among these events. In eukaryotes, Trm112, a small protein (COG2835) conserved in all three domains of life, interacts and activates four methyltransferases (Bud23, Trm9, Trm11 and Mtq2) that target different components of the translation machinery (rRNA, tRNAs, release factors). To clarify the function of Trm112 in archaea, we have characterized functionally and structurally its interaction network using Haloferax volcanii as model system. This led us to unravel that methyltransferases are also privileged Trm112 partners in archaea and that this Trm112 network is much more complex than anticipated from eukaryotic studies. Interestingly, among the identified enzymes, some are functionally orthologous to eukaryotic Trm112 partners, emphasizing again the similarity between eukaryotic and archaeal translation machineries. Other partners display some similarities with bacterial methyltransferases, suggesting that Trm112 is a general partner for methyltransferases in all living organisms.


  • Organizational Affiliation

    Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, F-91128 Palaiseau cedex, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
24-sterol C-methyltransferase
A, B
231Haloferax volcanii DS2Mutation(s): 0 
Gene Names: C498_18333
UniProt
Find proteins for D4GYL4 (Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2))
Explore D4GYL4 
Go to UniProtKB:  D4GYL4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD4GYL4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
UPF0434 family protein
C, D
61Haloferax volcanii DS2Mutation(s): 0 
Gene Names: HVO_1131
UniProt
Find proteins for D4GW82 (Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2))
Explore D4GW82 
Go to UniProtKB:  D4GW82
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD4GW82
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.61α = 90
b = 82.29β = 90
c = 88.03γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
RESOLVEphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-14-CE09-0016-02

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-11
    Type: Initial release
  • Version 1.1: 2018-07-25
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-03
    Changes: Data collection, Database references