4RUL

Crystal structure of full-length E.Coli topoisomerase I in complex with ssDNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for suppression of hypernegative DNA supercoiling by E. coli topoisomerase I.

Tan, K.Zhou, Q.Cheng, B.Zhang, Z.Joachimiak, A.Tse-Dinh, Y.C.

(2015) Nucleic Acids Res. 43: 11031-11046

  • DOI: 10.1093/nar/gkv1073

  • PubMed Abstract: 
  • Escherichia coli topoisomerase I has an essential function in preventing hypernegative supercoiling of DNA. A full length structure of E. coli topoisomerase I reported here shows how the C-terminal domains bind single-stranded DNA (ssDNA) to recogniz ...

    Escherichia coli topoisomerase I has an essential function in preventing hypernegative supercoiling of DNA. A full length structure of E. coli topoisomerase I reported here shows how the C-terminal domains bind single-stranded DNA (ssDNA) to recognize the accumulation of negative supercoils in duplex DNA. These C-terminal domains of E. coli topoisomerase I are known to interact with RNA polymerase, and two flexible linkers within the C-terminal domains may assist in the movement of the ssDNA for the rapid removal of transcription driven negative supercoils. The structure has also unveiled for the first time how the 4-Cys zinc ribbon domain and zinc ribbon-like domain bind ssDNA with primarily π-stacking interactions. This novel structure, in combination with new biochemical data, provides important insights into the mechanism of genome regulation by type IA topoisomerases that is essential for life, as well as the structures of homologous type IA TOP3α and TOP3β from higher eukaryotes that also have multiple 4-Cys zinc ribbon domains required for their physiological functions.


    Organizational Affiliation

    Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439, USA ktan@anl.gov.,Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA.,Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA Biomolecular Sciences Institute, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA ytsedinh@fiu.edu.,Department of Biochemistry and Molecular Biology, Basic Science Building, New York Medical College, Valhalla, NY 10595, USA.,Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA topoisomerase 1
A
867Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: topA (supX)
EC: 5.6.2.1
Find proteins for P06612 (Escherichia coli (strain K12))
Go to UniProtKB:  P06612
Entity ID: 2
MoleculeChainsLengthOrganism
single strand DNAB29synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 85.613α = 90.00
b = 80.295β = 91.26
c = 97.475γ = 90.00
Software Package:
Software NamePurpose
SBC-Collectdata collection
PHENIXrefinement
HKL-3000phasing
HKL-3000data reduction
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-11-04
    Type: Initial release
  • Version 1.1: 2016-01-06
    Type: Database references