6OZW

Crystal structure of the 65-kilodalton amino-terminal fragment of DNA topoisomerase I from Streptococcus mutans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 

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Literature

Crystal structure of the 65-kilodalton amino-terminal fragment of DNA topoisomerase I from the gram-positive model organism Streptococcus mutans.

Jones, J.A.Hevener, K.E.

(2019) Biochem Biophys Res Commun 516: 333-338

  • DOI: 10.1016/j.bbrc.2019.06.034
  • Primary Citation of Related Structures:  
    6OZW

  • PubMed Abstract: 
  • Herein we report the first structure of topoisomerase I determined from the gram-positive bacterium, S. mutans. Bacterial topoisomerase I is an ATP-independent type 1A topoisomerase that uses the inherent torsional strain within hyper-negatively supercoiled DNA as an energy source for its critical function of DNA relaxation ...

    Herein we report the first structure of topoisomerase I determined from the gram-positive bacterium, S. mutans. Bacterial topoisomerase I is an ATP-independent type 1A topoisomerase that uses the inherent torsional strain within hyper-negatively supercoiled DNA as an energy source for its critical function of DNA relaxation. Interest in the enzyme has gained momentum as it has proven to be essential in various bacterial organisms. In order to aid in further biochemical characterization, the apo 65-kDa amino-terminal fragment of DNA topoisomerase I from the gram-positive model organism Streptococcus mutans was crystalized and a three-dimensional structure was determined to 2.06 Å resolution via x-ray crystallography. The overall structure illustrates the four classic major domains that create the traditional topoisomerase I "lock" formation comprised of a sizable toroidal aperture atop what is considered to be a highly dynamic body. A catalytic tyrosine residue resides at the interface between two domains and is known to form a 5' phosphotyrosine DNA-enzyme intermediate during transient single-stranded cleavage required for enzymatic relaxation of hyper negative DNA supercoils. Surrounding the catalytic tyrosine residue is the remainder of the highly conserved active site. Within 5 Å from the catalytic center, only one dissimilar residue is observed between topoisomerase I from S. mutans and the gram-negative model organism E. coli. Immediately adjacent to the conserved active site, however, S. mutans topoisomerase I displays a somewhat unique nine residue loop extension not present in any bacterial topoisomerase I structures previously determined other than that of an extremophile.


    Organizational Affiliation

    Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, 38163, United States. Electronic address: khevener@uthsc.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA topoisomerase 1A595Streptococcus mutans UA159Mutation(s): 0 
Gene Names: topASMU_1002
EC: 5.6.2.2 (PDB Primary Data), 5.6.2.1 (UniProt)
UniProt
Find proteins for Q8DUD3 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159))
Explore Q8DUD3 
Go to UniProtKB:  Q8DUD3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download Ideal Coordinates CCD File 
H [auth A] , I [auth A] , J [auth A] , K [auth A] , L [auth A] , M [auth A] , N [auth A] , O [auth A] , 
H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  N [auth A],  O [auth A],  P [auth A],  Q [auth A],  R [auth A],  S [auth A],  T [auth A],  U [auth A]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.581α = 90
b = 98.366β = 90
c = 72.706γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP20 GM103408

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.2: 2020-01-15
    Changes: Database references