Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 20.26 kDa 
• Atom Count: 1512 
• Modelled Residue Count: 157 
• Deposited Residue Count: 164 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

4S2Y

Structure of E. coli RppH bound to RNA and three magnesium ions

• PDB DOI: 10.2210/pdb4S2Y/pdb
• NDB: NA3355

• Classification: hydrolase/RNA
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-01-23 Released: 2015-02-11 
• Deposition Author(s): Vasilyev, N., Serganov, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.199 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 

Literature

Structures of RNA Complexes with the Escherichia coli RNA Pyrophosphohydrolase RppH Unveil the Basis for Specific 5'-End-dependent mRNA Decay.

Vasilyev, N., Serganov, A.

(2015) J Biol Chem 290: 9487-9499

• PubMed: 25657011 
• DOI: 10.1074/jbc.M114.634824
• Primary Citation of Related Structures:  
  4S2V, 4S2W, 4S2X, 4S2Y


• PubMed Abstract: 
  

5'-End-dependent RNA degradation impacts virulence, stress responses, and DNA repair in bacteria by controlling the decay of hundreds of mRNAs. The RNA pyrophosphohydrolase RppH, a member of the Nudix hydrolase superfamily, triggers this degradation pathway by removing pyrophosphate from the triphosphorylated RNA 5' terminus. Here, we report the x-ray structures of Escherichia coli RppH (EcRppH) in apo- and RNA-bound forms. These structures show distinct conformations of EcRppH·RNA complexes on the catalytic pathway and suggest a common catalytic mechanism for Nudix hydrolases. EcRppH interacts with RNA by a bipartite mechanism involving specific recognition of the 5'-terminal triphosphate and the second nucleotide, thus enabling discrimination against mononucleotides as substrates. The structures also reveal the molecular basis for the preference of the enzyme for RNA substrates bearing guanine in the second position by identifying a protein cleft in which guanine interacts with EcRppH side chains via cation-π contacts and hydrogen bonds. These interactions explain the modest specificity of EcRppH at the 5' terminus and distinguish the enzyme from the highly selective RppH present in Bacillus subtilis. The divergent means by which RNA is recognized by these two functionally and structurally analogous enzymes have important implications for mRNA decay and the regulation of protein biosynthesis in bacteria.

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Organizational Affiliation: 

From the Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016 [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA pyrophosphohydrolase	A	161	Escherichia coli K-12	Mutation(s): 2  Gene Names: rppH, nudH, ygdP, b2830, JW2798 EC: 3.6.1
UniProt
Find proteins for P0A776 (Escherichia coli (strain K12)) Explore P0A776  Go to UniProtKB:  P0A776

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*(APC)*GP*U)-3')	B	3	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A], D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.199 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.631	α = 90
b = 36.484	β = 102.3
c = 58.073	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHENIX	model building
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-01-23 
• Released Date: 2015-02-11 
Deposition Author(s): Vasilyev, N., Serganov, A.

Revision History  

• Version 1.0: 2015-02-11
  Type: Initial release
  
• Version 1.1: 2015-02-25
  Changes: Database references
• Version 1.2: 2015-05-06
  Changes: Database references