3VA3

Crystal structure of RNase T in complex with a duplex DNA product (stem loop DNA with 2 nucleotide 3' overhang)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.714 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.263 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

How an exonuclease decides where to stop in trimming of nucleic acids: crystal structures of RNase T-product complexes

Hsiao, Y.-Y.Duh, Y.Chen, Y.P.Wang, Y.T.Yuan, H.S.

(2012) Nucleic Acids Res. 40: 8144-8154

  • DOI: 10.1093/nar/gks548
  • Primary Citation of Related Structures:  3V9S, 3V9U, 3V9W, 3V9X, 3V9Z, 3VA0

  • PubMed Abstract: 
  • Exonucleases are key enzymes in the maintenance of genome stability, processing of immature RNA precursors and degradation of unnecessary nucleic acids. However, it remains unclear how exonucleases digest nucleic acids to generate correct end product ...

    Exonucleases are key enzymes in the maintenance of genome stability, processing of immature RNA precursors and degradation of unnecessary nucleic acids. However, it remains unclear how exonucleases digest nucleic acids to generate correct end products for next-step processing. Here we show how the exonuclease RNase T stops its trimming precisely. The crystal structures of RNase T in complex with a stem-loop DNA, a GG dinucleotide and single-stranded DNA with different 3'-end sequences demonstrate why a duplex with a short 3'-overhang, a dinucleotide and a ssDNA with a 3'-end C cannot be further digested by RNase T. Several hydrophobic residues in RNase T change their conformation upon substrate binding and induce an active or inactive conformation in the active site that construct a precise machine to determine which substrate should be digested based on its sequence, length and structure. These studies thus provide mechanistic insights into how RNase T prevents over digestion of its various substrates, and the results can be extrapolated to the thousands of members of the DEDDh family of exonucleases.


    Organizational Affiliation

    Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan, ROC.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease T
A, B
235Escherichia coli (strain K12)Gene Names: rnt
EC: 3.1.13.-
Find proteins for P30014 (Escherichia coli (strain K12))
Go to UniProtKB:  P30014
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*TP*T)-3')C,D18N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CO
Query on CO

Download SDF File 
Download CCD File 
A, B
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.714 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.263 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 100.266α = 90.00
b = 112.684β = 90.00
c = 57.793γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-11
    Type: Initial release
  • Version 1.1: 2013-06-26
    Type: Database references