PDBsum entry 2csd

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Isomerase PDB id
Protein chains
516 a.a.
PDB id:
Name: Isomerase
Title: Crystal structure of topoisomerase v (61 kda fragment)
Structure: Topoisomerase v. Chain: a, b. Fragment: n-term 61 kda fragment. Synonym: top61. Engineered: yes
Source: Methanopyrus kandleri. Organism_taxid: 2320. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
2.90Å     R-factor:   0.240     R-free:   0.308
Authors: B.Taneja,A.Patel,A.Slesarev,A.Mondragon
Key ref:
B.Taneja et al. (2006). Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerases. EMBO J, 25, 398-408. PubMed id: 16395333 DOI: 10.1038/sj.emboj.7600922
21-May-05     Release date:   31-Jan-06    
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Protein chains
Pfam   ArchSchema ?
Q977W1  (Q977W1_9EURY) -  Topoisomerase V
984 a.a.
516 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA repair   1 term 
  Biochemical function     DNA binding     1 term  


DOI no: 10.1038/sj.emboj.7600922 EMBO J 25:398-408 (2006)
PubMed id: 16395333  
Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerases.
B.Taneja, A.Patel, A.Slesarev, A.Mondragón.
Topoisomerases are involved in controlling and maintaining the topology of DNA and are present in all kingdoms of life. Unlike all other types of topoisomerases, similar type IB enzymes have only been identified in bacteria and eukarya. The only putative type IB topoisomerase in archaea is represented by Methanopyrus kandleri topoisomerase V. Despite several common functional characteristics, topoisomerase V shows no sequence similarity to other members of the same type. The structure of the 61 kDa N-terminal fragment of topoisomerase V reveals no structural similarity to other topoisomerases. Furthermore, the structure of the active site region is different, suggesting no conservation in the cleavage and religation mechanism. Additionally, the active site is buried, indicating the need of a conformational change for activity. The presence of a topoisomerase in archaea with a unique structure suggests the evolution of a separate mechanism to alter DNA.
  Selected figure(s)  
Figure 2.
Figure 2 The multiHhH domain is flexible, while the topoisomerase domain is rigid. Schematic diagram showing the superposition of the two monomers in the asymmetric unit of crystal Form I. The active site residues are shown in yellow. In (A) only the multiHhH domains were used for the superposition, while in (B) the topoisomerase domains were used for the superposition. The figure illustrates the variability in the multiHhH domains (Supplementary data). For clarity, in each monomer the topoisomerase domain and the multiHhH domain are shown in different shades of the same color.
Figure 4.
Figure 4 Model for a topoisomerase domain-DNA complex. (A) Electrostatic surface representation of the topoisomerase domain. The diagram shows that the topoisomerase has a large positively charged groove in one face of the protein centered around the active site. The insets correspond to 90 views of the molecule and show that there are no additional large positively charged regions in the protein. The electrostatic potential was calculated with the program APBS (Baker et al, 2001), with a dielectric constant of 80 for the solvent and 20 for the protein. The surface is colored with a blue to red gradient from +5 to -5 K[b]T/e. (B) The diagram shows a model of the topoisomerase domain in complex with B-DNA. The coloring scheme is the same as in Figure 1. To create the model, the linker helix and the multiHhH domain were removed. DNA was docked using the HTH motif of human Pax6-paired domain-DNA complex (Xu et al, 1999), but replacing the DNA with a canonical, straight B-DNA model. No attempts were made to prevent steric clashes. In the model, the active site tyrosine is ideally placed to interact with the phosphodiester backbone and the other putative active site residues are also in the vicinity of DNA. The model suggests a potential way for topo-61 to interact with DNA, making extensive interactions.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2006, 25, 398-408) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22108601 S.M.Vos, E.M.Tretter, B.H.Schmidt, and J.M.Berger (2011).
All tangled up: how cells direct, manage and exploit topoisomerase function.
  Nat Rev Mol Cell Biol, 12, 827-841.  
20637419 R.Rajan, B.Taneja, and A.Mondragón (2010).
Structures of minimal catalytic fragments of topoisomerase V reveals conformational changes relevant for DNA binding.
  Structure, 18, 829-838.
PDB codes: 3m6k 3m6z 3m7d 3m7g
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.  
18755053 A.J.Schoeffler, and J.M.Berger (2008).
DNA topoisomerases: harnessing and constraining energy to govern chromosome topology.
  Q Rev Biophys, 41, 41.  
19105819 C.Brochier-Armanet, S.Gribaldo, and P.Forterre (2008).
A DNA topoisomerase IB in Thaumarchaeota testifies for the presence of this enzyme in the last common ancestor of Archaea and Eucarya.
  Biol Direct, 3, 54.  
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
17982461 A.Dong, X.Xu, A.M.Edwards, C.Chang, M.Chruszcz, M.Cuff, M.Cymborowski, R.Di Leo, O.Egorova, E.Evdokimova, E.Filippova, J.Gu, J.Guthrie, A.Ignatchenko, A.Joachimiak, N.Klostermann, Y.Kim, Y.Korniyenko, W.Minor, Q.Que, A.Savchenko, T.Skarina, K.Tan, A.Yakunin, A.Yee, V.Yim, R.Zhang, H.Zheng, M.Akutsu, C.Arrowsmith, G.V.Avvakumov, A.Bochkarev, L.G.Dahlgren, S.Dhe-Paganon, S.Dimov, L.Dombrovski, P.Finerty, S.Flodin, A.Flores, S.Gräslund, M.Hammerström, M.D.Herman, B.S.Hong, R.Hui, I.Johansson, Y.Liu, M.Nilsson, L.Nedyalkova, P.Nordlund, T.Nyman, J.Min, H.Ouyang, H.W.Park, C.Qi, W.Rabeh, L.Shen, Y.Shen, D.Sukumard, W.Tempel, Y.Tong, L.Tresagues, M.Vedadi, J.R.Walker, J.Weigelt, M.Welin, H.Wu, T.Xiao, H.Zeng, and H.Zhu (2007).
In situ proteolysis for protein crystallization and structure determination.
  Nat Methods, 4, 1019-1021.
PDB codes: 2p35 2pz9 2qni 2r8b 2r8w 2r9q 2ra5 2rc3
17804808 B.Taneja, B.Schnurr, A.Slesarev, J.F.Marko, and A.Mondragón (2007).
Topoisomerase V relaxes supercoiled DNA by a constrained swiveling mechanism.
  Proc Natl Acad Sci U S A, 104, 14670-14675.  
  17277459 Y.Bai, T.C.Auperin, and L.Tong (2007).
The use of in situ proteolysis in the crystallization of murine CstF-77.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 135-138.  
  17012808 C.R.Mandel, D.Gebauer, H.Zhang, and L.Tong (2006).
A serendipitous discovery that in situ proteolysis is essential for the crystallization of yeast CPSF-100 (Ydh1p).
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1041-1045.  
16650908 P.Forterre (2006).
DNA topoisomerase V: a new fold of mysterious origin.
  Trends Biotechnol, 24, 245-247.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.