6MV7

Crystal structure of RNAse 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

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This is version 2.1 of the entry. See complete history


Literature

Insights into Structural and Dynamical Changes Experienced by Human RNase 6 upon Ligand Binding.

Narayanan, C.Bernard, D.N.Letourneau, M.Gagnon, J.Gagne, D.Bafna, K.Calmettes, C.Couture, J.F.Agarwal, P.K.Doucet, N.

(2020) Biochemistry 59: 755-765

  • DOI: 10.1021/acs.biochem.9b00888
  • Primary Citation of Related Structures:  
    6MV6, 6MV7

  • PubMed Abstract: 
  • Ribonuclease 6 (RNase 6) is one of eight catalytically active human pancreatic-type RNases that belong to a superfamily of rapidly evolving enzymes. Like some of its human homologues, RNase 6 exhibits host defense properties such as antiviral and antibacterial activities ...

    Ribonuclease 6 (RNase 6) is one of eight catalytically active human pancreatic-type RNases that belong to a superfamily of rapidly evolving enzymes. Like some of its human homologues, RNase 6 exhibits host defense properties such as antiviral and antibacterial activities. Recently solved crystal structures of this enzyme in its nucleotide-free form show the conservation of the prototypical kidney-shaped fold preserved among vertebrate RNases, in addition to revealing the presence of a unique secondary active site. In this study, we determine the structural and conformational properties experienced by RNase 6 upon binding to substrate and product analogues. We present the first crystal structures of RNase 6 bound to a nucleotide ligand (adenosine 5'-monophosphate), in addition to RNase 6 bound to phosphate ions. While the enzyme preserves B 2 subsite ligand preferences, our results show a lack of typical B 2 subsite interactions normally observed in homologous ligand-bound RNases. A comparison of the dynamical properties of RNase 6 in its apo-, substrate-, and product-bound states highlight the unique dynamical properties experienced on time scales ranging from nano- to milliseconds. Overall, our results confirm the specific evolutionary adaptation of RNase 6 relative to its unique catalytic and biological activities.


    Organizational Affiliation

    PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications , Université Laval , 1045 Avenue de la Médecine , Quebec , Quebec G1V 0A6 , Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease K6A128Homo sapiensMutation(s): 0 
Gene Names: RNASE6RNS6
EC: 3.1.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q93091 (Homo sapiens)
Explore Q93091 
Go to UniProtKB:  Q93091
PHAROS:  Q93091
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP (Subject of Investigation/LOI)
Query on AMP

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.65α = 90
b = 38.83β = 90
c = 97.92γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 2.0: 2020-01-15
    Type: Coordinate replacement
    Reason: Polymer geometry
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Refinement description, Structure summary
  • Version 2.1: 2020-05-27
    Changes: Database references