5YGU

Crystal structure of Escherichia coli (strain K12) mRNA Decapping Complex RppH-DapF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

DapF stabilizes the substrate-favoring conformation of RppH to stimulate its RNA-pyrophosphohydrolase activity in Escherichia coli.

Wang, Q.Zhang, D.Guan, Z.Li, D.Pei, K.Liu, J.Zou, T.Yin, P.

(2018) Nucleic Acids Res 46: 6880-6892

  • DOI: 10.1093/nar/gky528
  • Primary Citation of Related Structures:  
    5YGU

  • PubMed Abstract: 
  • mRNA decay is an important strategy by which bacteria can rapidly adapt to their ever-changing surroundings. The 5'-terminus state of mRNA determines the velocity of decay of many types of RNA. In Escherichia coli, RNA pyrophosphohydrolase (RppH) is responsible for the removal of the 5'-terminal triphosphate from hundreds of mRNAs and triggers its rapid degradation by ribonucleases ...

    mRNA decay is an important strategy by which bacteria can rapidly adapt to their ever-changing surroundings. The 5'-terminus state of mRNA determines the velocity of decay of many types of RNA. In Escherichia coli, RNA pyrophosphohydrolase (RppH) is responsible for the removal of the 5'-terminal triphosphate from hundreds of mRNAs and triggers its rapid degradation by ribonucleases. A diaminopimelate epimerase, DapF, can directly interact with RppH and stimulate its hydrolysis activity in vivo and in vitro. However, the molecular mechanism remains to be elucidated. Here, we determined the complex structure of DapF-RppH as a heterotetramer in a 2:2 molar ratio. DapF-bound RppH exhibits an RNA-favorable conformation similar to the RNA-bound state, suggesting that association with DapF promotes and stabilizes RppH in a conformation that facilitates substrate RNA binding and thus stimulates the activity of RppH. To our knowledge, this is the first published structure of an RNA-pyrophosphohydrolysis complex in bacteria. Our study provides a framework for further investigation of the potential regulators involved in the RNA-pyrophosphohydrolysis process in prokaryotes.


    Organizational Affiliation

    National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Diaminopimelate epimeraseA274Escherichia coli K-12Mutation(s): 0 
Gene Names: dapFb3809JW5592
EC: 5.1.1.7
UniProt
Find proteins for P0A6K1 (Escherichia coli (strain K12))
Explore P0A6K1 
Go to UniProtKB:  P0A6K1
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RNA pyrophosphohydrolaseB168Escherichia coli K-12Mutation(s): 1 
Gene Names: rppHnudHygdPb2830JW2798
EC: 3.6.1
UniProt
Find proteins for P0A776 (Escherichia coli (strain K12))
Explore P0A776 
Go to UniProtKB:  P0A776
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.418α = 90
b = 86.418β = 90
c = 173.093γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2018-07-18
    Changes: Data collection, Database references
  • Version 1.2: 2018-08-08
    Changes: Data collection, Database references