2GAI | pdb_00002gai

Structure of Full Length Topoisomerase I from Thermotoga maritima in triclinic crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.232 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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Literature

Crystal Structure of Full Length Topoisomerase I from Thermotoga maritima

Hansen, G.Harrenga, A.Wieland, B.Schomburg, D.Reinemer, P.

(2006) J Mol Biology 358: 1328-1340

  • DOI: https://doi.org/10.1016/j.jmb.2006.03.012
  • Primary Citation Related Structures: 
    2GAI, 2GAJ

  • PubMed Abstract: 

    DNA topoisomerases are a family of enzymes altering the topology of DNA by concerted breakage and rejoining of the phosphodiester backbone of DNA. Bacterial and archeal type IA topoisomerases, including topoisomerase I, topoisomerase III, and reverse gyrase, are crucial in regulation of DNA supercoiling and maintenance of genetic stability. The crystal structure of full length topoisomerase I from Thermotoga maritima was determined at 1.7A resolution and represents an intact and fully active bacterial topoisomerase I. It reveals the torus-like structure of the conserved transesterification core domain comprising domains I-IV and a tightly associated C-terminal zinc ribbon domain (domain V) packing against domain IV of the core domain. The previously established zinc-independence of the functional activity of T.maritima topoisomerase I is further supported by its crystal structure as no zinc ion is bound to domain V. However, the structural integrity is preserved by the formation of two disulfide bridges between the four Zn-binding cysteine residues. A functional role of domain V in DNA binding and recognition is suggested and discussed in the light of the structure and previous biochemical findings. In addition, implications for bacterial topoisomerases I are provided.


  • Organizational Affiliation
    • Bayer HealthCare AG, Pharma R and D Europe, Enabling Technologies, D-42096 Wuppertal, Germany.

Macromolecule Content 

  • Total Structure Weight: 145.61 kDa 
  • Atom Count: 10,600 
  • Modeled Residue Count: 1,162 
  • Deposited Residue Count: 1,266 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA topoisomerase I
A, B
633Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: topA
EC: 5.99.1.2 (PDB Primary Data), 5.6.2.1 (UniProt)
UniProt
Find proteins for P46799 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore P46799 
Go to UniProtKB:  P46799
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46799
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.232 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.118α = 83.4
b = 95.421β = 86.15
c = 96.508γ = 84.87
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2006-04-25 
  • Deposition Author(s): Hansen, G.

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-25
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary