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PDBsum entry 1i7d

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protein dna_rna ligands metals links
Isomerase/DNA PDB id
1i7d
Jmol
Contents
Protein chain
620 a.a. *
DNA/RNA
Ligands
SO4
Metals
_CL
Waters ×332
* Residue conservation analysis
PDB id:
1i7d
Name: Isomerase/DNA
Title: Noncovalent complex of e.Coli DNA topoisomerase iii with an 8-base single-stranded DNA oligonucleotide
Structure: 5'-d( Cp Gp Cp Ap Ap Cp Tp T)-3'. Chain: b. Engineered: yes. DNA topoisomerase iii. Chain: a. Engineered: yes. Mutation: yes
Source: Synthetic: yes. Escherichia coli. Organism_taxid: 562. Strain: hms-83. Gene: topb. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PQS)
Resolution:
2.05Å     R-factor:   0.233     R-free:   0.260
Authors: A.Changela,R.J.Digate,A.Mondragon
Key ref:
A.Changela et al. (2001). Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule. Nature, 411, 1077-1081. PubMed id: 11429611 DOI: 10.1038/35082615
Date:
08-Mar-01     Release date:   29-Jun-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P14294  (TOP3_ECOLI) -  DNA topoisomerase 3
Seq:
Struc:
 
Seq:
Struc:
653 a.a.
620 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.5.99.1.2  - 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     chromosome separation   3 terms 
  Biochemical function     nucleotide binding     8 terms  

 

 
DOI no: 10.1038/35082615 Nature 411:1077-1081 (2001)
PubMed id: 11429611  
 
 
Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule.
A.Changela, R.J.DiGate, A.Mondragón.
 
  ABSTRACT  
 
A variety of cellular processes, including DNA replication, transcription, and chromosome condensation, require enzymes that can regulate the ensuing topological changes occurring in DNA. Such enzymes-DNA topoisomerases-alter DNA topology by catalysing the cleavage of single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA), the passage of DNA through the resulting break, and the rejoining of the broken phosphodiester backbone. DNA topoisomerase III from Escherichia coli belongs to the type IA family of DNA topoisomerases, which transiently cleave ssDNA via formation of a covalent 5' phosphotyrosine intermediate. Here we report the crystal structure, at 2.05 A resolution, of an inactive mutant of E. coli DNA topoisomerase III in a non-covalent complex with an 8-base ssDNA molecule. The enzyme undergoes a conformational change that allows the oligonucleotide to bind within a groove leading to the active site. We note that the ssDNA molecule adopts a conformation like that of B-DNA while bound to the enzyme. The position of the DNA within the realigned active site provides insight into the role of several highly conserved residues during catalysis. These findings confirm various aspects of the type IA topoisomerase mechanism while suggesting functional implications for other topoisomerases and proteins that perform DNA rearrangements.
 
  Selected figure(s)  
 
Figure 2.
Figure 2: Comparison of the bound ssDNA structure to B-DNA. a, Stereo view showing the superposition of the bound ssDNA molecule onto one strand of an ideal B-DNA model. Superposition of the two molecules using the six nucleotides at the 3' end of the oligonucleotide gives an r.m.s.d. value of 1.7 for all atoms. The bound ssDNA is depicted with grey bonds and coloured by atom, while the complementary strands of the B-DNA model are shown in green and blue. b, Stereo view of the modelling of B-DNA into the ssDNA binding groove. A hybrid B-DNA molecule was generated with the bound ssDNA molecule (coloured by atom) and a complementary strand from the B-DNA model (shown in blue). The faded regions of the complementary strand represent areas of the modelled DNA strand that would collide with the protein and prevent binding within the cleft.
Figure 4.
Figure 4: Active site and catalytic mechanism. a, Stereo view showing the E. coli DNA topoisomerase III active site in the presence and absence of DNA. Residues from the apo structure are shown in blue, while residues of the enzyme -DNA complex are coloured red. Secondary structural elements of domains I and III of the apo enzyme are depicted in light and dark shades of grey, respectively. Elements corresponding to domains I and III of the complex are coloured green and purple, respectively. b, A stereo view showing the active-site region formed at the interface of domains I and III in the presence of ssDNA. The bonds in the oligonucleotide are coloured yellow, and protein elements are coloured by domain as in Fig. 1a. Hydrogen bonding and electrostatic interactions are depicted by black dotted lines. A red dotted line highlights the orientation of Phe 328 towards the phosphate group of the putative scissile bond (green). c, Schematic diagram illustrating a possible mechanism of DNA cleavage used by type IA topoisomerases. A nearby group acting as a general base (B:) abstracts the proton from the tyrosine thus activating it for nucleophilic attack. In E. coli DNA topoisomerase III, Tyr 328 forms a covalent linkage with the 5' phosphate of the scissile bond while the pentavalent transition state is stabilized by Arg 330 and Lys 8. Cleavage of the ssDNA is facilitated by Glu 7 which acts as a general acid catalyst by donating a proton to the leaving 3'-oxygen atom of the scissile bond.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2001, 411, 1077-1081) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21219465 M.Babu, N.Beloglazova, R.Flick, C.Graham, T.Skarina, B.Nocek, A.Gagarinova, O.Pogoutse, G.Brown, A.Binkowski, S.Phanse, A.Joachimiak, E.V.Koonin, A.Savchenko, A.Emili, J.Greenblatt, A.M.Edwards, and A.F.Yakunin (2011).
A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair.
  Mol Microbiol, 79, 484-502.
PDB codes: 3nkd 3nke
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.  
21120860 T.Zeng, J.Li, and J.Liu (2011).
Distinct interfacial biclique patterns between ssDNA-binding proteins and those with dsDNAs.
  Proteins, 79, 598-610.  
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
21482796 Z.Zhang, B.Cheng, and Y.C.Tse-Dinh (2011).
Crystal structure of a covalent intermediate in DNA cleavage and rejoining by Escherichia coli DNA topoisomerase I.
  Proc Natl Acad Sci U S A, 108, 6939-6944.  
20686482 B.D.Bax, P.F.Chan, D.S.Eggleston, A.Fosberry, D.R.Gentry, F.Gorrec, I.Giordano, M.M.Hann, A.Hennessy, M.Hibbs, J.Huang, E.Jones, J.Jones, K.K.Brown, C.J.Lewis, E.W.May, M.R.Saunders, O.Singh, C.E.Spitzfaden, C.Shen, A.Shillings, A.J.Theobald, A.Wohlkonig, N.D.Pearson, and M.N.Gwynn (2010).
Type IIA topoisomerase inhibition by a new class of antibacterial agents.
  Nature, 466, 935-940.
PDB codes: 2xco 2xcq 2xcr 2xcs 2xct
20485342 B.H.Schmidt, A.B.Burgin, J.E.Deweese, N.Osheroff, and J.M.Berger (2010).
A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases.
  Nature, 465, 641-644.
PDB codes: 3l4j 3l4k
21087076 W.Yang (2010).
Topoisomerases and site-specific recombinases: similarities in structure and mechanism.
  Crit Rev Biochem Mol Biol, 45, 520-534.  
19222228 J.E.Deweese, A.M.Burch, A.B.Burgin, and N.Osheroff (2009).
Use of divalent metal ions in the dna cleavage reaction of human type II topoisomerases.
  Biochemistry, 48, 1862-1869.  
19106140 N.M.Baker, R.Rajan, and A.Mondragón (2009).
Structural studies of type I topoisomerases.
  Nucleic Acids Res, 37, 693-701.  
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.  
18096618 B.Cheng, E.P.Sorokin, and Y.C.Tse-Dinh (2008).
Mutation adjacent to the active site tyrosine can enhance DNA cleavage and cell killing by the TOPRIM Gly to Ser mutant of bacterial topoisomerase I.
  Nucleic Acids Res, 36, 1017-1025.  
18186484 B.Xiong, D.L.Burk, J.Shen, X.Luo, H.Liu, J.Shen, and A.M.Berghuis (2008).
The type IA topoisomerase catalytic cycle: A normal mode analysis and molecular dynamics simulation.
  Proteins, 71, 1984-1994.  
18653531 J.E.Deweese, A.B.Burgin, and N.Osheroff (2008).
Human topoisomerase IIalpha uses a two-metal-ion mechanism for DNA cleavage.
  Nucleic Acids Res, 36, 4883-4893.  
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
17157875 A.F.Monzingo, A.Ozburn, S.Xia, R.J.Meyer, and J.D.Robertus (2007).
The structure of the minimal relaxase domain of MobA at 2.1 A resolution.
  J Mol Biol, 366, 165-178.
PDB code: 2ns6
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.  
18097402 K.C.Dong, and J.M.Berger (2007).
Structural basis for gate-DNA recognition and bending by type IIA topoisomerases.
  Nature, 450, 1201-1205.
PDB code: 2rgr
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
16582104 D.Strahs, C.X.Zhu, B.Cheng, J.Chen, and Y.C.Tse-Dinh (2006).
Experimental and computational investigations of Ser10 and Lys13 in the binding and cleavage of DNA substrates by Escherichia coli DNA topoisomerase I.
  Nucleic Acids Res, 34, 1785-1797.  
16629677 L.Chen, and L.Huang (2006).
Oligonucleotide cleavage and rejoining by topoisomerase III from the hyperthermophilic archaeon Sulfolobus solfataricus: temperature dependence and strand annealing-promoted DNA religation.
  Mol Microbiol, 60, 783-794.  
16650908 P.Forterre (2006).
DNA topoisomerase V: a new fold of mysterious origin.
  Trends Biotechnol, 24, 245-247.  
15537633 J.L.Plank, S.H.Chu, J.R.Pohlhaus, T.Wilson-Sali, and T.S.Hsieh (2005).
Drosophila melanogaster topoisomerase IIIalpha preferentially relaxes a positively or negatively supercoiled bubble substrate and is essential during development.
  J Biol Chem, 280, 3564-3573.  
16314322 L.Sari, and I.Andricioaei (2005).
Rotation of DNA around intact strand in human topoisomerase I implies distinct mechanisms for positive and negative supercoil relaxation.
  Nucleic Acids Res, 33, 6621-6634.  
14725760 A.C.Rodríguez, and D.Stock (2004).
Studying topoisomerases in the fourth dimension.
  Structure, 12, 7-9.  
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.  
15215234 B.Cheng, J.Feng, V.Mulay, S.Gadgil, and Y.C.Tse-Dinh (2004).
Site-directed mutagenesis of residues involved in G Strand DNA binding by Escherichia coli DNA topoisomerase I.
  J Biol Chem, 279, 39207-39213.  
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.  
15247343 M.Kampmann, and D.Stock (2004).
Reverse gyrase has heat-protective DNA chaperone activity independent of supercoiling.
  Nucleic Acids Res, 32, 3537-3545.  
15016354 P.Auffinger, L.Bielecki, and E.Westhof (2004).
Anion binding to nucleic acids.
  Structure, 12, 379-388.  
12581655 A.Changela, K.Perry, B.Taneja, and A.Mondragón (2003).
DNA manipulators: caught in the act.
  Curr Opin Struct Biol, 13, 15-22.  
14625590 A.Guasch, M.Lucas, G.Moncalián, M.Cabezas, R.Pérez-Luque, F.X.Gomis-Rüth, F.de la Cruz, and M.Coll (2003).
Recognition and processing of the origin of transfer DNA by conjugative relaxase TrwC.
  Nat Struct Biol, 10, 1002-1010.
PDB codes: 1omh 1osb 1qx0
12912928 D.L.Theobald, and S.C.Schultz (2003).
Nucleotide shuffling and ssDNA recognition in Oxytricha nova telomere end-binding protein complexes.
  EMBO J, 22, 4314-4324.
PDB codes: 1pa6 1ph1 1ph2 1ph3 1ph4 1ph5 1ph6 1ph7 1ph8 1ph9 1phj
12191478 A.B.Hickman, D.R.Ronning, R.M.Kotin, and F.Dyda (2002).
Structural unity among viral origin binding proteins: crystal structure of the nuclease domain of adeno-associated virus Rep.
  Mol Cell, 10, 327-337.
PDB code: 1m55
11823434 A.C.Rodríguez, and D.Stock (2002).
Crystal structure of reverse gyrase: insights into the positive supercoiling of DNA.
  EMBO J, 21, 418-426.
PDB codes: 1gku 1gl9
12007989 J.J.Champoux (2002).
A first view of the structure of a type IA topoisomerase with bound DNA.
  Trends Pharmacol Sci, 23, 199-201.  
11809772 K.Perry, and A.Mondragón (2002).
Biochemical characterization of an invariant histidine involved in Escherichia coli DNA topoisomerase I catalysis.
  J Biol Chem, 277, 13237-13245.  
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.