5Y9P

Staphylococcus aureus RNase HII

  • Classification: HYDROLASE
  • Organism(s): Staphylococcus aureus
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2017-08-26 Released: 2018-08-01 
  • Deposition Author(s): Hang, T., Wu, M., Zhang, X.
  • Funding Organization(s): Chinese Academy of Sciences, National Key Research and Development Program of China, Foundation for Innovative Research Groups of the National Natural Science Foundation of China, National Natural Science Foundation of China, Scientific Research Grant of Hefei Science Center of CAS, Anhui Provincial Natural Science Foundation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into a novel functional dimer of Staphylococcus aureus RNase HII

Hang, T.Zhang, X.Wu, M.Wang, C.Ling, S.Xu, L.Gong, Q.Tian, C.Zhang, X.Zang, J.

(2018) Biochem Biophys Res Commun 503: 1207-1213

  • DOI: 10.1016/j.bbrc.2018.07.026
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • RNase HII exists ubiquitously in organisms and functions as a monomer in prokaryotes. We determined the crystal structure of Staphylococcus aureus RNase HII (Sa-RNase HII), which displays a novel dimer conformation, with the active site of each monom ...

    RNase HII exists ubiquitously in organisms and functions as a monomer in prokaryotes. We determined the crystal structure of Staphylococcus aureus RNase HII (Sa-RNase HII), which displays a novel dimer conformation, with the active site of each monomer covered by the other one. Both small-angle X-ray scattering and gel-filtration analysis confirmed that Sa-RNase HII exists as a homodimer in solution. Enzymatic analysis revealed that the "self-inhibited" dimeric form is catalytically active. Furthermore, continuous-wave electron paramagnetic resonance experiments clarified that the Sa-RNase HII dimer undergoes a large conformational change upon substrate binding, but remains a dimer to catalyze the reaction. Our structural and biochemical studies identified a novel functional dimer of Sa-RNase HII with distinct regulation mechanism for its catalytic activity.


    Organizational Affiliation

    Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Jinzhai Road, Hefei, 230026, China; Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, 230027, China. Electronic address: zangjy@ustc.edu.cn.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease HII
A
266Staphylococcus aureusMutation(s): 0 
Gene Names: rnhBAYM28_06605AYM37_06605ERS072738_01674ERS074020_01342HMPREF3211_01288
EC: 3.1.26.4
Find proteins for Q2FZ38 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FZ38
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.83α = 90
b = 61.83β = 90
c = 163.26γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaNo. XDB 08010101
National Key Research and Development Program of ChinaChinaNos. 2016YFA0400903
Foundation for Innovative Research Groups of the National Natural Science Foundation of ChinaChinaNos. 31621002
National Natural Science Foundation of ChinaChinaNos. U1532109, 31370756, and 31361163002
Scientific Research Grant of Hefei Science Center of CASChinaNo. 2015SRG-HSC043, 2015HSC-UP019
Anhui Provincial Natural Science FoundationChinaNos. 1608085QC52
National Natural Science Foundation of ChinaChinaNos. 31400627

Revision History 

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-09-12
    Changes: Data collection, Database references