3ECP

Crystal Structure Of Tn5 Transposase Complexed With 5' Phosphorylated Transposon End DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Phosphate coordination and movement of DNA in the Tn5 synaptic complex: role of the (R)YREK motif

Klenchin, V.A., Czyz, A., Goryshin, I.Y., Gradman, R., Lovell, S., Rayment, I., Reznikoff, W.S.

(2008) Nucleic Acids Res 36: 5855-5862

  • DOI: 10.1093/nar/gkn577
  • Primary Citation of Related Structures:  
    3ECP

  • PubMed Abstract: 

    • Bacterial DNA transposition is an important model system for studying DNA recombination events such as HIV-1 DNA integration and RAG-1-mediated V(D)J recombination. This communication focuses on the role of protein-phosphate contacts in manipulating DNA structure as a requirement for transposition catalysis ...

    Bacterial DNA transposition is an important model system for studying DNA recombination events such as HIV-1 DNA integration and RAG-1-mediated V(D)J recombination. This communication focuses on the role of protein-phosphate contacts in manipulating DNA structure as a requirement for transposition catalysis. In particular, the participation of the nontransferred strand (NTS) 5' phosphate in Tn5 transposition strand transfer is analyzed. The 5' phosphate plays no direct catalytic role, nonetheless its presence stimulates strand transfer approximately 30-fold. X-ray crystallography indicates that transposase-DNA complexes formed with NTS 5' phosphorylated DNA have two properties that contrast with structures formed with complexes lacking the 5' phosphate or complexes generated from in-crystal hairpin cleavage. Transposase residues R210, Y319 and R322 of the (R)YREK motif coordinate the 5' phosphate rather than the subterminal NTS phosphate, and the 5' NTS end is moved away from the 3' transferred strand end. Mutation R210A impairs the 5' phosphate stimulation. It is posited that DNA phosphate coordination by R210, Y319 and R322 results in movement of the 5' NTS DNA away from the 3'-end thus allowing efficient target DNA binding. It is likely that this role for the newly identified RYR triad is utilized by other transposase-related proteins.

    Organizational Affiliation: 

    Department of Biochemistry, University of Wisconsin at Madison, 433 Babcock Drive, Madison, WI 53706, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tn5 transposaseA477Escherichia coliMutation(s): 3 
Gene Names: orf163, tnpA, tnp
EC: 3.1
UniProt
Find proteins for Q46731 (Escherichia coli)
Explore Q46731 
Go to UniProtKB:  Q46731
Entity Groups  
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UniProt GroupQ46731
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA transferred strandB 20N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA non-transferred strandC 20N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.508α = 90
b = 113.508β = 90
c = 228.775γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2008-09-01 
  • Released Date: 2008-10-21 
    • Deposition Author(s): Klenchin, V.A.

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-29
    Changes: Database references
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations