3V9W

Crystal structure of RNase T in complex with a preferred ssDNA (TTA) with two Mg in the active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

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, 3VA3

  • 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 products for next-step processing ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease TA, B, C, D235Escherichia coli K-12Mutation(s): 1 
Gene Names: rntb1652JW1644
EC: 3.1.13
UniProt
Find proteins for P30014 (Escherichia coli (strain K12))
Explore P30014 
Go to UniProtKB:  P30014
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30014
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*CP*TP*TP*A)-3')E, F, G, H 5N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.34α = 90
b = 46.34β = 90
c = 315.354γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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