1MW8

Crystal Structure of a Complex between H365R mutant of 67 kDA N-terminal fragment of E. coli DNA Topoisomerase I and 5'-ACTTCGGGATG-3'

• PDB DOI: https://doi.org/10.2210/pdb1MW8/pdb
• NAKB: 1MW8

• Classification: ISOMERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-09-27 Released: 2003-10-14 
• Deposition Author(s): Perry, K., Mondragon, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.273 
• R-Value Work: 0.223 
• R-Value Observed: 0.226 

Starting Model: experimental

Literature

Structure of a Complex between E. coli DNA Topoisomerase I and Single-Stranded DNA.

Perry, K., Mondragon, A.

(2003) Structure 11: 1349-1358

• PubMed: 14604525 
• DOI: https://doi.org/10.1016/j.str.2003.09.013
• Primary Citation of Related Structures:  
  1MW8, 1MW9


• PubMed Abstract: 
  

  In order to gain insights into the mechaism of ssDNA binding and recognition by Escherichia coli DNA topoisomerase I, the structure of the 67 kDa N-terminal fragment of topoisomerase I was solved in complex with ssDNA. The structure reveals a new conformational stage in the multistep catalytic cycle of type IA topoisomerases. In the structure, the ssDNA binding groove leading to the active site is occupied, but the active site is not fully formed. Large conformational changes are not seen; instead, a single helix parallel to the ssDNA binding groove shifts to clamp the ssDNA. The structure helps clarify the temporal sequence of conformational events, starting from an initial empty enzyme and proceeding to a ssDNA-occupied and catalytically competent active site.

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Organizational Affiliation: 

Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 71.12 kDa 
• Atom Count: 5,346 
• Modelled Residue Count: 568 
• Deposited Residue Count: 603 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA Topoisomerase I	B [auth X]	592	Escherichia coli	Mutation(s): 1  Gene Names: TopA EC: 5.99.1.2 (PDB Primary Data), 5.6.2.1 (UniProt)
UniProt
Find proteins for P06612 (Escherichia coli (strain K12)) Explore P06612  Go to UniProtKB:  P06612

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*AP*CP*TP*TP*CP*GP*GP*GP*AP*TP*G)-3'	A [auth Y]	11	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TMP	H [auth X]	THYMIDINE-5'-PHOSPHATE C10 H15 N2 O8 P GYOZYWVXFNDGLU-XLPZGREQSA-N
SO4	C [auth X], D [auth X], E [auth X], F [auth X], G [auth X]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.273 
• R-Value Work: 0.223 
• R-Value Observed: 0.226 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.392	α = 90
b = 79.148	β = 90
c = 141.798	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
CNS	refinement
MAR345	data collection
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-10-14 
Deposition Author(s): Perry, K., Mondragon, A.

Revision History  

• Version 1.0: 2003-10-14
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.5: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.6: 2024-02-14
  Changes: Data collection
• Version 1.7: 2024-04-03
  Changes: Refinement description