4PY5

Thermovibrio ammonificans RNase H3 in complex with 19-mer RNA/DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

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This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure of RNase H3-substrate complex reveals parallel evolution of RNA/DNA hybrid recognition.

Figiel, M., Nowotny, M.

(2014) Nucleic Acids Res 42: 9285-9294

  • DOI: 10.1093/nar/gku615
  • Primary Citation of Related Structures:  
    4PY5

  • PubMed Abstract: 

    • RNases H participate in the replication and maintenance of genomic DNA. RNase H1 cleaves the RNA strand of RNA/DNA hybrids, and RNase H2 in addition hydrolyzes the RNA residue of RNA-DNA junctions. RNase H3 is structurally closely related to RNases H2, but its biochemical properties are similar to type 1 enzymes ...

    RNases H participate in the replication and maintenance of genomic DNA. RNase H1 cleaves the RNA strand of RNA/DNA hybrids, and RNase H2 in addition hydrolyzes the RNA residue of RNA-DNA junctions. RNase H3 is structurally closely related to RNases H2, but its biochemical properties are similar to type 1 enzymes. Its unique N-terminal substrate-binding domain (N-domain) is related to TATA-binding protein. Here, we report the first crystal structure of RNase H3 in complex with its RNA/DNA substrate. Just like RNases H1, type 3 enzyme recognizes the 2'-OH groups of the RNA strand and detects the DNA strand by binding a phosphate group and inducing B-form conformation. Moreover, the N-domain recognizes RNA and DNA in a manner that is highly similar to the hybrid-binding domain of RNases H1. Our structure demonstrates a remarkable example of parallel evolution of the elements used in the specific recognition of RNA and DNA.

    Organizational Affiliation: 

    Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland mnowotny@iimcb.gov.pl.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RibonucleaseA271Thermovibrio ammonificans HB-1Mutation(s): 1 
Gene Names: Theam_0945
EC: 3.1.26 (PDB Primary Data), 3.1.26.4 (UniProt)
UniProt
Find proteins for E8T217 (Thermovibrio ammonificans (strain DSM 15698 / JCM 12110 / HB-1))
Explore E8T217 
Go to UniProtKB:  E8T217
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE8T217
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-R(*GP*AP*GP*UP*GP*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3'B 19N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*GP*CP*AP*CP*TP*C)-3'C 19N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.449α = 90
b = 67.661β = 90
c = 107.514γ = 90
Software Package:
Software NamePurpose
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2014-08-27
    Changes: Database references
  • Version 1.2: 2014-10-29
    Changes: Structure summary