PDBsum entry 2gaj

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Isomerase PDB id
Protein chains
581 a.a. *
Waters ×877
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Structure of full length topoisomerase i from thermotoga mar monoclinic crystal form
Structure: DNA topoisomerase i. Chain: a, b. Synonym: omega-protein, relaxing enzyme, untwisting enzyme, swivelase. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 243274. Strain: msb8. Gene: topa. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
1.95Å     R-factor:   0.197     R-free:   0.246
Authors: G.Hansen
Key ref:
G.Hansen et al. (2006). Crystal structure of full length topoisomerase I from Thermotoga maritima. J Mol Biol, 358, 1328-1340. PubMed id: 16600296 DOI: 10.1016/j.jmb.2006.03.012
09-Mar-06     Release date:   25-Apr-06    
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Protein chains
Pfam   ArchSchema ?
P46799  (TOP1_THEMA) -  DNA topoisomerase 1
633 a.a.
581 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Dna topoisomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA topological change   1 term 
  Biochemical function     isomerase activity     6 terms  


DOI no: 10.1016/j.jmb.2006.03.012 J Mol Biol 358:1328-1340 (2006)
PubMed id: 16600296  
Crystal structure of full length topoisomerase I from Thermotoga maritima.
G.Hansen, A.Harrenga, B.Wieland, D.Schomburg, P.Reinemer.
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.
  Selected figure(s)  
Figure 1.
Figure 1. Overall structure of topoisomerase I from T. maritima. Domains are colour-coded: domain I (yellow), II (green), III (red), IV (blue) and V (purple). For simplification in domains I–IV only β-strands of more than two residues length are indicated. (a) Topology cartoon of the structure. Cysteine residues 559, 561, 578 and 580 in domain V are indicated by circles. (b) Stereo representation of the molecule. To enable easy orientation secondary structure elements are labelled according to the E. coli topoisomerase I scheme.^4 Helices are represented by letters A–R and β-sheets by numbers 1–20.
Figure 5.
Figure 5. Schematic representation of single-stranded DNA binding to T. maritima topoisomerase I. Molecular surface of the molecule showing the DNA binding region of the protein. The individual domains are coloured as in Figure 1. The broken line marks the postulated elongated interaction surface path for single-stranded DNA. The DNA occupies the binding cleft in vicinity of the active site, travels across the interface of domains I and IV and interacts with the positively charged surface of domain V.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 358, 1328-1340) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19106140 N.M.Baker, R.Rajan, and A.Mondragón (2009).
Structural studies of type I topoisomerases.
  Nucleic Acids Res, 37, 693-701.  
19208647 P.Forterre, and D.Gadelle (2009).
Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms.
  Nucleic Acids Res, 37, 679-692.  
19688808 Z.Liu, R.Meng, Y.Zu, Q.Li, and L.Yao (2009).
Imaging and studying human topoisomerase I on mica surfaces in air and in liquid by atomic force microscopy.
  Scanning, 31, 160-166.  
18755053 A.J.Schoeffler, and J.M.Berger (2008).
DNA topoisomerases: harnessing and constraining energy to govern chromosome topology.
  Q Rev Biophys, 41, 41.  
17331537 A.Changela, R.J.DiGate, and A.Mondragón (2007).
Structural studies of E. coli topoisomerase III-DNA complexes reveal a novel type IA topoisomerase-DNA conformational intermediate.
  J Mol Biol, 368, 105-118.
PDB codes: 2o19 2o54 2o59 2o5c 2o5e
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