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PDBsum entry 1gku

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protein links
Topoisomerase PDB id
1gku
Jmol
Contents
Protein chain
1011 a.a. *
Waters ×157
* Residue conservation analysis
PDB id:
1gku
Name: Topoisomerase
Title: Reverse gyrase from archaeoglobus fulgidus
Structure: Reverse gyrase. Chain: b. Synonym: top-rg. Engineered: yes. Mutation: yes
Source: Archaeoglobus fulgidus. Organism_taxid: 224325. Strain: vc-16. Atcc: 49558. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: german collection of microorganisms (dsmz)
Resolution:
2.70Å     R-factor:   0.226     R-free:   0.295
Authors: A.C.Rodriguez,D.Stock
Key ref:
A.C.Rodríguez and D.Stock (2002). Crystal structure of reverse gyrase: insights into the positive supercoiling of DNA. EMBO J, 21, 418-426. PubMed id: 11823434 DOI: 10.1093/emboj/21.3.418
Date:
21-Aug-01     Release date:   11-Feb-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O29238  (RGYR_ARCFU) -  Reverse gyrase
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1054 a.a.
1011 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 21 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 2: E.C.3.6.4.12  - Dna helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate
ATP
+ H(2)O
= ADP
+ phosphate
   Enzyme class 3: E.C.5.99.1.3  - Dna topoisomerase (ATP-hydrolyzing).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP-dependent breakage, passage and rejoining of double-stranded DNA.
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     chromosome   1 term 
  Biological process     DNA topological change   3 terms 
  Biochemical function     nucleotide binding     13 terms  

 

 
    reference    
 
 
DOI no: 10.1093/emboj/21.3.418 EMBO J 21:418-426 (2002)
PubMed id: 11823434  
 
 
Crystal structure of reverse gyrase: insights into the positive supercoiling of DNA.
A.C.Rodríguez, D.Stock.
 
  ABSTRACT  
 
Reverse gyrase is the only topoisomerase known to positively supercoil DNA. The protein appears to be unique to hyperthermophiles, where its activity is believed to protect the genome from denaturation. The 120 kDa enzyme is the only member of the type I topoisomerase family that requires ATP, which is bound and hydrolysed by a helicase-like domain. We have determined the crystal structure of reverse gyrase from Archaeoglobus fulgidus in the presence and absence of nucleotide cofactor. The structure provides the first view of an intact supercoiling enzyme, explains mechanistic differences from other type I topoisomerases and suggests a model for how the two domains of the protein cooperate to positively supercoil DNA. Coordinates have been deposited in the Protein Data Bank under accession codes 1GKU and 1GL9.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Overall structure of reverse gyrase. (A) Stereo view of the molecule. The catalytic Tyr809 of the C-terminal domain is shown in red as a space-filled model, and helicase motif I (residues 78–85) in red ball-and-stick representation. The colouring of the subdomains of reverse gyrase is the same for all figures except Figures 4B and 5. (B) Side view of the molecule shown with a translucent space-filling envelope. Asterisks indicate four structural elements postulated to contact DNA: dark blue, a putative metal-binding site at the extreme N-terminus; light blue, a -hairpin (residues 201–217); green, the 'latch' subdomain H3 (residues 352–427); yellow, a Zn-finger motif (residues 584–601). The conformation of the Zn-finger as shown is uncertain due to poor electron density, and has not been included in the refined model. Maximum dimensions of the molecule are 130 70 50 Å. (C) End-on view of the molecule, with the N-terminal domain towards the front.
Figure 3.
Figure 3 The C-terminal domain of reverse gyrase and its interaction with the N-terminal domain. (A) Superposition of the C-terminal domain with the 67-kDa catalytic fragment of E.coli topoisomerase I (Lima et al., 1994), shown in grey. The position of domains II and III of topoisomerase I correspond to the 'closed' form of the enzyme. A box encloses the region featured in (B). (B) Stereo view of reverse gyrase superimposed with domains II and III of topoisomerase I in the putative 'open' form (Feinberg et al., 1999). The catalytic Tyr in both enzymes is indicated in red space-filling representation. The arrow indicates the putative movement of reverse gyrase subdomains T2 and T3 during strand passage. This movement would be prevented by subdomain H3 in its current position.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2002, 21, 418-426) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21051354 A.Ganguly, Y.Del Toro Duany, M.G.Rudolph, and D.Klostermeier (2011).
The latch modulates nucleotide and DNA binding to the helicase-like domain of Thermotoga maritima reverse gyrase and is required for positive DNA supercoiling.
  Nucleic Acids Res, 39, 1789-1800.
PDB code: 3oiy
21318561 J.Li, J.Liu, J.Zhou, and H.Xiang (2011).
Functional evaluation of four putative DNA-binding regions in Thermoanaerobacter tengcongensis reverse gyrase.
  Extremophiles, 15, 281-291.  
19560425 G.Dhar, J.K.Heiss, and R.C.Johnson (2009).
Mechanical constraints on Hin subunit rotation imposed by the Fis/enhancer system and DNA supercoiling during site-specific recombination.
  Mol Cell, 34, 746-759.  
19747077 M.Hilbert, A.R.Karow, and D.Klostermeier (2009).
The mechanism of ATP-dependent RNA unwinding by DEAD box proteins.
  Biol Chem, 390, 1237-1250.  
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.  
19150358 R.D.Shereda, N.J.Reiter, S.E.Butcher, and J.L.Keck (2009).
Identification of the SSB binding site on E. coli RecQ reveals a conserved surface for binding SSB's C terminus.
  J Mol Biol, 386, 612-625.  
19657341 W.K.Chu, and I.D.Hickson (2009).
RecQ helicases: multifunctional genome caretakers.
  Nat Rev Cancer, 9, 644-654.  
18755053 A.J.Schoeffler, and J.M.Berger (2008).
DNA topoisomerases: harnessing and constraining energy to govern chromosome topology.
  Q Rev Biophys, 41, 41.  
18614606 A.Valenti, G.Perugino, A.D'Amaro, A.Cacace, A.Napoli, M.Rossi, and M.Ciaramella (2008).
Dissection of reverse gyrase activities: insight into the evolution of a thermostable molecular machine.
  Nucleic Acids Res, 36, 4587-4597.  
18614530 C.B.de la Tour, L.Amrani, R.Cossard, K.C.Neuman, M.C.Serre, and M.Duguet (2008).
Mutational Analysis of the Helicase-like Domain of Thermotoga maritima Reverse Gyrase.
  J Biol Chem, 283, 27395-27402.  
18777006 F.Garnier, and M.Nadal (2008).
Transcriptional analysis of the two reverse gyrase encoding genes of Sulfolobus solfataricus P2 in relation to the growth phases and temperature conditions.
  Extremophiles, 12, 799-809.  
17984075 S.A.Harris, C.A.Laughton, and T.B.Liverpool (2008).
Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations.
  Nucleic Acids Res, 36, 21-29.  
18796525 Y.del Toro Duany, S.P.Jungblut, A.S.Schmidt, and D.Klostermeier (2008).
The reverse gyrase helicase-like domain is a nucleotide-dependent switch that is attenuated by the topoisomerase domain.
  Nucleic Acids Res, 36, 5882-5895.  
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
17044059 E.A.Weathers, M.E.Paulaitis, T.B.Woolf, and J.H.Hoh (2007).
Insights into protein structure and function from disorder-complexity space.
  Proteins, 66, 16-28.  
16617150 A.Valenti, A.Napoli, M.C.Ferrara, M.Nadal, M.Rossi, and M.Ciaramella (2006).
Selective degradation of reverse gyrase and DNA fragmentation induced by alkylating agent in the archaeon Sulfolobus solfataricus.
  Nucleic Acids Res, 34, 2098-2108.  
16395333 B.Taneja, A.Patel, A.Slesarev, and A.Mondragón (2006).
Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerases.
  EMBO J, 25, 398-408.
PDB codes: 2csb 2csd
16608853 J.L.Plank, and T.S.Hsieh (2006).
A novel, topologically constrained DNA molecule containing a double Holliday junction: design, synthesis, and initial biochemical characterization.
  J Biol Chem, 281, 17510-17516.  
16999829 T.Bankhead, K.Kobryn, and G.Chaconas (2006).
Unexpected twist: harnessing the energy in positive supercoils to control telomere resolution.
  Mol Microbiol, 62, 895-905.  
16407212 T.S.Hsieh, and J.L.Plank (2006).
Reverse gyrase functions as a DNA renaturase: annealing of complementary single-stranded circles and positive supercoiling of a bubble substrate.
  J Biol Chem, 281, 5640-5647.  
16188892 A.K.McClendon, A.C.Rodriguez, and N.Osheroff (2005).
Human topoisomerase IIalpha rapidly relaxes positively supercoiled DNA: implications for enzyme action ahead of replication forks.
  J Biol Chem, 280, 39337-39345.  
15673717 A.Napoli, A.Valenti, V.Salerno, M.Nadal, F.Garnier, M.Rossi, and M.Ciaramella (2005).
Functional interaction of reverse gyrase with single-strand binding protein of the archaeon Sulfolobus.
  Nucleic Acids Res, 33, 564-576.  
16077031 F.Allemand, N.Mathy, D.Brechemier-Baey, and C.Condon (2005).
The 5S rRNA maturase, ribonuclease M5, is a Toprim domain family member.
  Nucleic Acids Res, 33, 4368-4376.  
15840833 P.K.Shah, P.Aloy, P.Bork, and R.B.Russell (2005).
Structural similarity to bridge sequence space: finding new families on the bridges.
  Protein Sci, 14, 1305-1314.  
15788400 T.S.Hsieh, and C.Capp (2005).
Nucleotide- and stoichiometry-dependent DNA supercoiling by reverse gyrase.
  J Biol Chem, 280, 20467-20475.  
15190074 A.Napoli, A.Valenti, V.Salerno, M.Nadal, F.Garnier, M.Rossi, and M.Ciaramella (2004).
Reverse gyrase recruitment to DNA after UV light irradiation in Sulfolobus solfataricus.
  J Biol Chem, 279, 33192-33198.  
14711811 B.Cheng, J.Feng, S.Gadgil, and Y.C.Tse-Dinh (2004).
Flexibility at Gly-194 is required for DNA cleavage and relaxation activity of Escherichia coli DNA topoisomerase I.
  J Biol Chem, 279, 8648-8654.  
15139806 K.D.Corbett, and J.M.Berger (2004).
Structure, molecular mechanisms, and evolutionary relationships in DNA topoisomerases.
  Annu Rev Biophys Biomol Struct, 33, 95.  
15576038 M.D.Tibbetts, E.N.Shiozaki, L.Gu, E.R.McDonald, W.S.El-Deiry, and Y.Shi (2004).
Crystal structure of a FYVE-type zinc finger domain from the caspase regulator CARP2.
  Structure, 12, 2257-2263.
PDB code: 1y02
15247343 M.Kampmann, and D.Stock (2004).
Reverse gyrase has heat-protective DNA chaperone activity independent of supercoiling.
  Nucleic Acids Res, 32, 3537-3545.  
12581655 A.Changela, K.Perry, B.Taneja, and A.Mondragón (2003).
DNA manipulators: caught in the act.
  Curr Opin Struct Biol, 13, 15-22.  
12515582 B.G.Mirkin, T.I.Fenner, M.Y.Galperin, and E.V.Koonin (2003).
Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes.
  BMC Evol Biol, 3, 2.  
14527289 B.Grabowski, and Z.Kelman (2003).
Archeal DNA replication: eukaryal proteins in a bacterial context.
  Annu Rev Microbiol, 57, 487-516.  
14517231 D.A.Bernstein, M.C.Zittel, and J.L.Keck (2003).
High-resolution structure of the E.coli RecQ helicase catalytic core.
  EMBO J, 22, 4910-4921.
PDB codes: 1oyw 1oyy
12683966 K.S.Makarova, Y.I.Wolf, and E.V.Koonin (2003).
Potential genomic determinants of hyperthermophily.
  Trends Genet, 19, 172-176.  
12048189 A.C.Rodriguez (2002).
Studies of a positive supercoiling machine. Nucleotide hydrolysis and a multifunctional "latch" in the mechanism of reverse gyrase.
  J Biol Chem, 277, 29865-29873.  
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 code is shown on the right.