Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 52.59 kDa 
• Atom Count: 2726 
• Modelled Residue Count: 307 
• Deposited Residue Count: 462 
• Unique protein chains: 1

1Q67

Crystal structure of Dcp1p

• PDB DOI: 10.2210/pdb1Q67/pdb

• Classification: TRANSCRIPTION
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-08-12 Released: 2004-03-02 
• Deposition Author(s): She, M., Decker, C.J., Liu, Y., Chen, N., Parker, R., Song, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.268 
• R-Value Work: 0.227 
• R-Value Observed: 0.227 

Literature

Crystal structure of Dcp1p and its functional implications in mRNA decapping

She, M., Decker, C.J., Sundramurthy, K., Liu, Y., Chen, N., Parker, R., Song, H.

(2004) Nat Struct Mol Biol 11: 249-256

• PubMed: 14758354 
• DOI: 10.1038/nsmb730
• Primary Citation of Related Structures:  
  1Q67


• PubMed Abstract: 
  

A major pathway of eukaryotic mRNA turnover begins with deadenylation, followed by decapping and 5'-->3' exonucleolytic degradation. A critical step in this pathway is decapping, which is carried out by an enzyme composed of Dcp1p and Dcp2p. The crystal structure of Dcp1p shows that it markedly resembles the EVH1 family of protein domains. Comparison of the proline-rich sequence (PRS)-binding sites in this family of proteins with Dcp1p indicates that it belongs to a novel class of EVH1 domains. Mapping of the sequence conservation on the molecular surface of Dcp1p reveals two prominent sites. One of these is required for the function of the Dcp1p-Dcp2p complex, and the other, corresponding to the PRS-binding site of EVH1 domains, is probably a binding site for decapping regulatory proteins. Moreover, a conserved hydrophobic patch is shown to be critical for decapping.

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Related Citations: 

• An essential component of the decapping enzyme required for normal rates of mRNA turnover
  Beelman, C.A., Stevens, A., Caponigro, G., LaGrandeur, T.E., Hatfield, L., Fortner, D.M., Parker, R.
  (1996) Nature 382: 642

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Organizational Affiliation: 

Laboratory of Macromolecular Structure, Institute of Molecular and Cell Biology, 30 Medical Drive, Singapore 117609.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Decapping protein involved in mRNA degradation-Dcp1p	A, B	231	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: DCP1
UniProt
Find proteins for Q12517 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12517  Go to UniProtKB:  Q12517

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.268 
• R-Value Work: 0.227 
• R-Value Observed: 0.227 
• Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.55	α = 90
b = 123.55	β = 90
c = 77.9	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-08-12 
• Released Date: 2004-03-02 
Deposition Author(s): She, M., Decker, C.J., Liu, Y., Chen, N., Parker, R., Song, H.

Revision History  

• Version 1.0: 2004-03-02
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance