4X09

Structure of human RNase 6 in complex with sulphate anions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.722 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The first crystal structure of human RNase 6 reveals a novel substrate-binding and cleavage site arrangement.

Prats-Ejarque, G.Arranz-Trullen, J.Blanco, J.A.Pulido, D.Nogues, M.V.Moussaoui, M.Boix, E.

(2016) Biochem.J. 473: 1523-1536

  • DOI: 10.1042/BCJ20160245
  • Also Cited By: 6ENP, 5OAB

  • PubMed Abstract: 
  • Human RNase 6 is a cationic secreted protein that belongs to the RNase A superfamily. Its expression is induced in neutrophils and monocytes upon bacterial infection, suggesting a role in host defence. We present here the crystal structure of RNase 6 ...

    Human RNase 6 is a cationic secreted protein that belongs to the RNase A superfamily. Its expression is induced in neutrophils and monocytes upon bacterial infection, suggesting a role in host defence. We present here the crystal structure of RNase 6 obtained at 1.72 Å (1 Å=0.1 nm) resolution, which is the first report for the protein 3D structure and thereby setting the basis for functional studies. The structure shows an overall kidney-shaped globular fold shared with the other known family members. Three sulfate anions bound to RNase 6 were found, interacting with residues at the main active site (His(15), His(122) and Gln(14)) and cationic surface-exposed residues (His(36), His(39), Arg(66) and His(67)). Kinetic characterization, together with prediction of protein-nucleotide complexes by molecular dynamics, was applied to analyse the RNase 6 substrate nitrogenous base and phosphate selectivity. Our results reveal that, although RNase 6 is a moderate catalyst in comparison with the pancreatic RNase type, its structure includes lineage-specific features that facilitate its activity towards polymeric nucleotide substrates. In particular, enzyme interactions at the substrate 5' end can provide an endonuclease-type cleavage pattern. Interestingly, the RNase 6 crystal structure revealed a novel secondary active site conformed by the His(36)-His(39) dyad that facilitates the polynucleotide substrate catalysis.


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      Huang, Y.C.,Lin, Y.M.,Chang, T.W.,Wu, S.J.,Lee, Y.S.,Chang, M.D.,Chen, C.,Wu, S.H.,Liao, Y.D.
      (2007) J. Biol. Chem. 282: 4626


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, E-08193 Cerdanyola del Vallès, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease K6
A
128Homo sapiensMutation(s): 0 
Gene Names: RNASE6 (RNS6)
EC: 3.1.27.-
Find proteins for Q93091 (Homo sapiens)
Go to Gene View: RNASE6
Go to UniProtKB:  Q93091
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.722 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 27.733α = 90.00
b = 38.860β = 90.00
c = 97.965γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
Cootmodel building
PHENIXphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBFU2012-38965
Generalitat de CatalunyaSpain2009 SGR 795

Revision History 

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2016-06-08
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence