5XEX

Crystal structure of S.aureus PNPase catalytic domain

• PDB DOI:  https://doi.org/10.2210/pdb5XEX/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus aureus subsp. aureus NCTC 8325
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2017-04-06 Released: 2017-10-18 
• Deposition Author(s): Wang, X., Zhang, X., Zang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.249 
• R-Value Work: 0.223 
• R-Value Observed: 0.224 

Literature

Enolase binds to RnpA in competition with PNPase in Staphylococcus aureus

Wang, X., Wang, C., Wu, M., Tian, T., Cheng, T., Zhang, X., Zang, J.

(2017) FEBS Lett 591: 3523-3535

• PubMed: 28960276 
• DOI: https://doi.org/10.1002/1873-3468.12859
• Primary Citation of Related Structures:  
  5XEX


• PubMed Abstract: 
  

The RNA degradosome of the pathogen Staphylococcus aureus regulates the metabolism of RNA, the expression of virulence factors, and the formation of biofilms. It is composed of the RNases J1/J2, RNase Y, CshA, PNPase, Enolase, Pfk, and a newly identified component, RnpA. However, the function and new partners of RnpA in RNA degradosome remain unknown. Here, we identified PNPase and Enolase as two novel partners for RnpA. Further studies revealed that Enolase interacts with RnpA in competition with PNPase. Enzymatic assays showed that RnpA increases Enolase activity but has no effect on PNPase. These findings provide more information about the functional relationship between RnpA and RNA degradosome.

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Organizational Affiliation: 

Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 375.25 kDa 
• Atom Count: 24,313 
• Modelled Residue Count: 3,071 
• Deposited Residue Count: 3,354 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyribonucleotide nucleotidyltransferase	A, B, C, D, E, F	559	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0  Gene Names: pnp, pnpA, SAOUHSC_01251 EC: 2.7.7.8
UniProt
Find proteins for Q2FZ20 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FZ20  Go to UniProtKB:  Q2FZ20

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PPV	I [auth A], L [auth B], O [auth C], R [auth D], U [auth E], X [auth F]	PYROPHOSPHATE H4 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-N
PEG	G [auth A], J [auth B], M [auth C], P [auth D], S [auth E], V [auth F]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	H [auth A], K [auth B], N [auth C], Q [auth D], T [auth E], W [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.249 
• R-Value Work: 0.223 
• R-Value Observed: 0.224 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.699	α = 98.22
b = 93.773	β = 95.34
c = 130.242	γ = 120.01

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-10-18 
Deposition Author(s): Wang, X., Zhang, X., Zang, J.

Revision History  

• Version 1.0: 2017-10-18
  Type: Initial release
  
• Version 1.1: 2017-11-29
  Changes: Database references
• Version 1.2: 2018-02-07
  Changes: Database references