6D1V

Crystal structure of E. coli RppH-DapF complex, monomer bound to RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and kinetic insights into stimulation of RppH-dependent RNA degradation by the metabolic enzyme DapF.

Gao, A.Vasilyev, N.Luciano, D.J.Levenson-Palmer, R.Richards, J.Marsiglia, W.M.Traaseth, N.J.Belasco, J.G.Serganov, A.

(2018) Nucleic Acids Res 46: 6841-6856

  • DOI: 10.1093/nar/gky327
  • Primary Citation of Related Structures:  
    6D13, 6D1Q, 6D1V

  • PubMed Abstract: 
  • Vitally important for controlling gene expression in eukaryotes and prokaryotes, the deprotection of mRNA 5' termini is governed by enzymes whose activity is modulated by interactions with ancillary factors. In Escherichia coli, 5'-end-dependent mRNA degradation begins with the generation of monophosphorylated 5' termini by the RNA pyrophosphohydrolase RppH, which can be stimulated by DapF, a diaminopimelate epimerase involved in amino acid and cell wall biosynthesis ...

    Vitally important for controlling gene expression in eukaryotes and prokaryotes, the deprotection of mRNA 5' termini is governed by enzymes whose activity is modulated by interactions with ancillary factors. In Escherichia coli, 5'-end-dependent mRNA degradation begins with the generation of monophosphorylated 5' termini by the RNA pyrophosphohydrolase RppH, which can be stimulated by DapF, a diaminopimelate epimerase involved in amino acid and cell wall biosynthesis. We have determined crystal structures of RppH-DapF complexes and measured rates of RNA deprotection. These studies show that DapF potentiates RppH activity in two ways, depending on the nature of the substrate. Its stimulatory effect on the reactivity of diphosphorylated RNAs, the predominant natural substrates of RppH, requires a substrate long enough to reach DapF in the complex, while the enhanced reactivity of triphosphorylated RNAs appears to involve DapF-induced changes in RppH itself and likewise increases with substrate length. This study provides a basis for understanding the intricate relationship between cellular metabolism and mRNA decay and reveals striking parallels with the stimulation of decapping activity in eukaryotes.


    Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Diaminopimelate epimeraseA275Escherichia coli K-12Mutation(s): 0 
Gene Names: dapF
EC: 5.1.1.7
UniProt
Find proteins for A7ZU14 (Escherichia coli O139:H28 (strain E24377A / ETEC))
Explore A7ZU14 
Go to UniProtKB:  A7ZU14
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7ZU14
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RNA pyrophosphohydrolaseB160Escherichia coli K-12Mutation(s): 0 
Gene Names: rppHnudHygdPb2830JW2798
EC: 3.6.1
UniProt
Find proteins for A7ZQT6 (Escherichia coli O139:H28 (strain E24377A / ETEC))
Explore A7ZQT6 
Go to UniProtKB:  A7ZQT6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7ZQT6
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
RNA (5'-D(*(APC))-R(P*GP*U)-3')C 3Escherichia coli
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A],
N [auth B],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
N [auth B],
O [auth B],
P [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A],
Q [auth B],
R [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
K [auth B],
L [auth B],
M [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.644α = 90
b = 191.986β = 90
c = 51.207γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-04-12 
  • Released Date: 2018-05-23 
  • Deposition Author(s): Gao, A., Serganov, A.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesP41 GM103403
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesS10 RR029205
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357
Department of Energy (DOE, United States)United StatesKP1605010
Department of Energy (DOE, United States)United StatesKC0401040
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesP41GM111244
Department of Energy (DOE, United States)United StatesDE-SC0012704
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR01GM112940
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR01GM035769
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR01AI108889
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesF99CA212474

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2018-08-08
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence