2R7D

Crystal structure of ribonuclease II family protein from Deinococcus radiodurans, triclinic crystal form. NorthEast Structural Genomics target DrR63


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The Structure and Enzymatic Properties of a Novel RNase II Family Enzyme from Deinococcus radiodurans.

Schmier, B.J.Seetharaman, J.Deutscher, M.P.Hunt, J.F.Malhotra, A.

(2012) J Mol Biol 415: 547-559

  • DOI: 10.1016/j.jmb.2011.11.031
  • Primary Citation of Related Structures:  
    2R7F, 2R7D

  • PubMed Abstract: 
  • Exoribonucleases are vital in nearly all aspects of RNA metabolism, including RNA maturation, end-turnover, and degradation. RNase II and RNase R are paralogous members of the RNR superfamily of nonspecific, 3'→5', processive exoribonucleases. In Escherichia coli, RNase II plays a primary role in mRNA decay and has a preference for unstructured RNA ...

    Exoribonucleases are vital in nearly all aspects of RNA metabolism, including RNA maturation, end-turnover, and degradation. RNase II and RNase R are paralogous members of the RNR superfamily of nonspecific, 3'→5', processive exoribonucleases. In Escherichia coli, RNase II plays a primary role in mRNA decay and has a preference for unstructured RNA. RNase R, in contrast, is capable of digesting structured RNA and plays a role in the degradation of both mRNA and stable RNA. Deinococcus radiodurans, a radiation-resistant bacterium, contains two RNR family members. The shorter of these, DrR63, includes a sequence signature typical of RNase R, but we show here that this enzyme is an RNase II-type exonuclease and cannot degrade structured RNA. We also report the crystal structure of this protein, now termed DrII. The DrII structure reveals a truncated RNA binding region in which the N-terminal cold shock domains, typical of most RNR family nucleases, are replaced by an unusual winged helix-turn-helix domain, where the "wing" is contributed by the C-terminal S1 domain. Consistent with its truncated RNA binding region, DrII is able to remove 3' overhangs from RNA molecules closer to duplexes than do other RNase II-type enzymes. DrII also displays distinct sensitivity to pyrimidine-rich regions of single-stranded RNA and is able to process tRNA precursors with adenosine-rich 3' extensions in vitro. These data indicate that DrII is the RNase II of D. radiodurans and that its structure and catalytic properties are distinct from those of other related enzymes.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, PO Box 016129, Miami, FL 33101-6129, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease II family proteinA, B, C469Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: DR_0020
Find proteins for Q9RYD0 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Explore Q9RYD0 
Go to UniProtKB:  Q9RYD0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A], E [auth B], F [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, CL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.762α = 60.08
b = 92.205β = 89.57
c = 92.345γ = 71.11
Software Package:
Software NamePurpose
CNSrefinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-01-11
    Changes: Database references
  • Version 1.3: 2012-02-01
    Changes: Database references
  • Version 1.4: 2018-01-24
    Changes: Structure summary