6D13

Crystal structure of E.coli RppH-DapF complex

• PDB DOI:  https://doi.org/10.2210/pdb6D13/pdb

• Classification: isomerase/hydrolase
• Organism(s): Escherichia coli S88
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-04-11 Released: 2018-05-23 
• Deposition Author(s): Gao, A., Serganov, A.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI), Department of Energy (DOE, United States)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.06 Å
• R-Value Free: 0.264 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 

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

• PubMed: 29733359 
• DOI: https://doi.org/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. 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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 52.62 kDa 
• Atom Count: 3,461 
• Modelled Residue Count: 433 
• Deposited Residue Count: 452 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminopimelate epimerase	A	275	Escherichia coli S88	Mutation(s): 0  Gene Names: dapF, ECS88_4235 EC: 5.1.1.7
UniProt
Find proteins for P0A6K1 (Escherichia coli (strain K12)) Explore P0A6K1  Go to UniProtKB:  P0A6K1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA pyrophosphohydrolase	B	177	Escherichia coli S88	Mutation(s): 0  Gene Names: rppH, nudH, ECS88_3125 EC: 3.6.1
UniProt
Find proteins for P0A776 (Escherichia coli (strain K12)) Explore P0A776  Go to UniProtKB:  P0A776

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], N [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
CL	K [auth A], L [auth A], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.06 Å
• R-Value Free: 0.264 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.81	α = 90
b = 85.81	β = 90
c = 177.374	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

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

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	R01GM112940
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	P41 GM103403
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	S10 RR029205
Department of Energy (DOE, United States)	United States	DE-AC02-06CH11357
Department of Energy (DOE, United States)	United States	KP1605010
Department of Energy (DOE, United States)	United States	KC0401040
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	P41GM111244
Department of Energy (DOE, United States)	United States	DE-SC0012704
Department of Energy (DOE, United States)	United States	DE-SC0012704
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	R01GM035769
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	R01AI108889

Revision History  

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