2LYD

The solution structure of the Dm DCP1 EVH1 domain in complex with the XRN1 DBM peptide

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 21 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

A direct interaction between DCP1 and XRN1 couples mRNA decapping to 5' exonucleolytic degradation.

Braun, J.E., Truffault, V., Boland, A., Huntzinger, E., Chang, C.T., Haas, G., Weichenrieder, O., Coles, M., Izaurralde, E.

(2012) Nat Struct Mol Biol 19: 1324-1331

  • DOI: 10.1038/nsmb.2413
  • Primary Citation of Related Structures:  
    2LYD

  • PubMed Abstract: 

    • The removal of the mRNA 5' cap structure by the decapping enzyme DCP2 leads to rapid 5'→3' mRNA degradation by XRN1, suggesting that the two processes are coordinated, but the coupling mechanism is unknown. DCP2 associates with the decapping activators EDC4 and DCP1 ...

    The removal of the mRNA 5' cap structure by the decapping enzyme DCP2 leads to rapid 5'→3' mRNA degradation by XRN1, suggesting that the two processes are coordinated, but the coupling mechanism is unknown. DCP2 associates with the decapping activators EDC4 and DCP1. Here we show that XRN1 directly interacts with EDC4 and DCP1 in human and Drosophila melanogaster cells, respectively. In D. melanogaster cells, this interaction is mediated by the DCP1 EVH1 domain and a DCP1-binding motif (DBM) in the XRN1 C-terminal region. The NMR structure of the DCP1 EVH1 domain bound to the DBM reveals that the peptide docks at a conserved aromatic cleft, which is used by EVH1 domains to recognize proline-rich ligands. Our findings reveal a role for XRN1 in decapping and provide a molecular basis for the coupling of decapping to 5'→3' mRNA degradation.

    Organizational Affiliation: 

    Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Decapping protein 1A134Drosophila melanogasterMutation(s): 0 
Gene Names: 
UniProt
Find proteins for Q9W1H5 (Drosophila melanogaster)
Explore Q9W1H5 
Go to UniProtKB:  Q9W1H5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9W1H5
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Pacman proteinB38Drosophila melanogasterMutation(s): 0 
Gene Names: 
EC: 3.1.13
UniProt
Find proteins for E1JJR3 (Drosophila melanogaster)
Explore E1JJR3 
Go to UniProtKB:  E1JJR3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1JJR3
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 21 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 2LYD Olderado

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2012-09-17 
  • Released Date: 2012-10-17 
    • Deposition Author(s): Truffault, V.

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2012-10-31
    Changes: Database references
  • Version 1.2: 2012-11-28
    Changes: Database references
  • Version 1.3: 2012-12-19
    Changes: Database references