4X09

Structure of human RNase 6 in complex with sulphate anions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

Starting Model: experimental
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This is version 1.4 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: https://doi.org/10.1042/BCJ20160245
  • Primary Citation of Related Structures:  
    4X09

  • 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 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.


  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease K6128Homo sapiensMutation(s): 0 
Gene Names: RNASE6RNS6
EC: 3.1.27.5 (PDB Primary Data), 3.1.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q93091 (Homo sapiens)
Explore Q93091 
Go to UniProtKB:  Q93091
PHAROS:  Q93091
GTEx:  ENSG00000169413 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93091
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.733α = 90
b = 38.86β = 90
c = 97.965γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHENIXphasing
Aimlessdata scaling
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2016-06-08
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary