6P5R

Structure of T. brucei MERS1-GDP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of MERS1, the 5' processing enzyme of mitochondrial mRNAs in Trypanosoma brucei.

Schumacher, M.A.Zeng, W.Henderson, M.

(2019) Rna --: --

  • DOI: 10.1261/rna.072231.119
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Most mitochondrial mRNAs are transcribed as polycistronic precursors that are cleaved by endonucleases to produce mature mRNA transcripts. However, recent studies have shown that mitochondrial transcripts in the kinetoplastid protozoan, Trypanosoma b ...

    Most mitochondrial mRNAs are transcribed as polycistronic precursors that are cleaved by endonucleases to produce mature mRNA transcripts. However, recent studies have shown that mitochondrial transcripts in the kinetoplastid protozoan, Trypanosoma brucei, are transcribed individually. Also unlike most mitochondrial mRNAs, the 5' end of these transcripts harbor a triphosphate that is hydrolyzed. This modification is carried out by a putative Nudix hydrolase called MERS1. The Nudix motif in MERS1 is degenerate, lacking a conserved glutamic acid, thus it is unclear how it may bind its substrates and whether it contains a Nudix fold. To obtain insight into this unusual hydrolase we determined structures of apo, GTP-bound and RNA-bound T. brucei MERS1 to 2.35 Å, 2.45 Å and 2.60 Å respectively. The MERS1 structure has a unique fold that indeed contains a Nudix motif. The nucleotide bound structures combined with binding studies reveal that MERS1 shows preference for RNA sequences with a central guanine repeat which it binds in a single stranded conformation. The apo MERS1 structure indicates that a significant portion of its nucleotide-binding site folds upon substrate binding. Finally, a potential interaction region for a binding partner, MERS2, that activates MERS1 was identified. The MERS2-like peptide inserts a glutamate near the missing Nudix acidic residue in the RNA binding pocket, suggesting how the enzyme may be activated. Thus, the combined studies reveal insight into the structure and enzyme properties of MERS1 and its substrate binding activities.


    Organizational Affiliation

    Duke University School of Medicine maria.schumacher@duke.edu.,Duke University School of Medicine.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial edited mRNA stability factor 1
A
410Trypanosoma bruceiMutation(s): 0 
Gene Names: MERS1
Find proteins for B6SBM0 (Trypanosoma brucei)
Go to UniProtKB:  B6SBM0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.227 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 90.815α = 90.00
b = 114.453β = 90.00
c = 77.964γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
AutoSolphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-05-30 
  • Released Date: 2019-11-06 
  • Deposition Author(s): Schumacher, M.A.

Revision History 

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-20
    Type: Database references