2EI9

Crystal structure of R1Bm endonuclease domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Characterization of the sequence specificity of the R1Bm endonuclease domain by structural and biochemical studies.

Maita, N.Aoyagi, H.Osanai, M.Shirakawa, M.Fujiwara, H.

(2007) Nucleic Acids Res. 35: 3918-3927

  • DOI: 10.1093/nar/gkm397

  • PubMed Abstract: 
  • R1Bm is a long interspersed element (LINE) inserted into a specific sequence within 28S rDNA of the silkworm genome. Of two open reading frames (ORFs) of R1Bm, ORF2 encodes a reverse transcriptase (RT) and an endonuclease (EN) domain which digests sp ...

    R1Bm is a long interspersed element (LINE) inserted into a specific sequence within 28S rDNA of the silkworm genome. Of two open reading frames (ORFs) of R1Bm, ORF2 encodes a reverse transcriptase (RT) and an endonuclease (EN) domain which digests specifically both top and bottom strand of the target sequence in 28S rDNA. To elucidate the sequence specificity of EN domain of R1Bm (R1Bm EN), we examined the cleavage tendency for the target sequences, and found that 5'-A(G/C)(A/T)!(A/G)T-3' is the consensus sequence (! = cleavage site). We also determined the crystal structure of R1Bm EN at 2.0 A resolution. Its structure was basically similar to AP endonuclease family, but had a special beta-hairpin at the edge of the DNA binding surface, which is a common feature among EN of LINEs. Point-mutations on the DNA binding surface of R1Bm EN significantly decreased the cleavage activities, but did not affect the sequence recognition in most residues. However, two mutants Y98A and N180A had altered cleavage patterns, suggesting an important role of these residues (Y98 and N180) for the sequence recognition of R1Bm EN. In addition, Y98A mutant showed another cleavage pattern, that implies de novo design of novel sequence-specific EN.


    Organizational Affiliation

    Graduate School of Systems Life Sciences, Kyushu University, Fukuoka 812-8582, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Non-LTR retrotransposon R1Bmks ORF2 protein
A
240Bombyx moriMutation(s): 0 
EC: 2.7.7.49
Find proteins for Q7M4J4 (Bombyx mori)
Go to UniProtKB:  Q7M4J4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACY
Query on ACY

Download SDF File 
Download CCD File 
A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.195 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 141.303α = 90.00
b = 141.303β = 90.00
c = 37.508γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALAdata scaling
CNSrefinement
MOSFLMdata reduction
ADSCdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance