5XEX

Crystal structure of S.aureus PNPase catalytic domain

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 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 

    Hefei National Laboratory for Physical Sciences at Microscale CAS Center for Excellence in Biomacromolecules, Collaborative Innovation Center of Chemistry for Life Sciences, and School of Life Sciences, University of Science and Technology of China, Hefei, China.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyribonucleotide nucleotidyltransferase
A, B, C, D, E
A, B, C, D, E, F
559Staphylococcus aureus subsp. aureus NCTC 8325Mutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FZ20
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PPV
Query on PPV
Download Ideal Coordinates CCD File 
I [auth A]
L [auth B]
O [auth C]
R [auth D]
U [auth E]
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
Query on PEG
Download Ideal Coordinates CCD File 
G [auth A]
J [auth B]
M [auth C]
P [auth D]
S [auth E]
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
Query on GOL
Download Ideal Coordinates CCD File 
H [auth A]
K [auth B]
N [auth C]
Q [auth D]
T [auth E]
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 = 93.699α = 98.22
b = 93.773β = 95.34
c = 130.242γ = 120.01
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description