PDBsum entry 1rr8

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protein dna_rna ligands links
Isomerase/DNA PDB id
Protein chain
494 a.a. *
Waters ×304
* Residue conservation analysis
PDB id:
Name: Isomerase/DNA
Title: Structural mechanisms of camptothecin resistance by mutations in human topoisomerase i
Structure: 5'- d( Ap Ap Ap Ap Ap Gp Ap Cp Tp T Gp Gp Ap Ap Ap Ap Ap Tp Tp Tp Tp T)-3'. Chain: a. Engineered: yes. 5'- d( Ap Ap Ap Ap Ap Tp Tp Tp Tp Tp Cp Cp Ap Ap Gp Tp Cp Tp Tp Tp Tp T)-3'. Chain: b.
Source: Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Gene: top1. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: sf9.
Biol. unit: Trimer (from PQS)
2.60Å     R-factor:   0.242     R-free:   0.294
Authors: J.E.Chrencik,B.L.Staker,A.B.Burgin,L.Stewart,M.R.Redinbo
Key ref:
J.E.Chrencik et al. (2004). Mechanisms of camptothecin resistance by human topoisomerase I mutations. J Mol Biol, 339, 773-784. PubMed id: 15165849 DOI: 10.1016/j.jmb.2004.03.077
08-Dec-03     Release date:   06-Jul-04    
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Protein chain
Pfam   ArchSchema ?
P11387  (TOP1_HUMAN) -  DNA topoisomerase 1
765 a.a.
494 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 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!
  Cellular component     chromosome   1 term 
  Biological process     DNA topological change   1 term 
  Biochemical function     DNA binding     3 terms  


DOI no: 10.1016/j.jmb.2004.03.077 J Mol Biol 339:773-784 (2004)
PubMed id: 15165849  
Mechanisms of camptothecin resistance by human topoisomerase I mutations.
J.E.Chrencik, B.L.Staker, A.B.Burgin, P.Pourquier, Y.Pommier, L.Stewart, M.R.Redinbo.
Human topoisomerase I relaxes superhelical tension associated with DNA replication, transcription and recombination by reversibly nicking one strand of duplex DNA and forming a covalent 3'-phosphotyrosine linkage. This enzyme is the sole target of the camptothecin family of anticancer compounds, which acts by stabilizing the covalent protein-DNA complex and enhancing apoptosis through blocking the advancement of replication forks. Mutations that impart resistance to camptothecin have been identified in several regions of human topoisomerase I. We present the crystal structures of two camptothecin-resistant forms of human topoisomerase I (Phe361Ser at 2.6A resolution and Asn722Ser at 2.3A resolution) in ternary complexes with DNA and topotecan (Hycamtin), a camptothecin analogue currently in widespread clinical use. While the alteration of Asn722 to Ser leads to the elimination of a water-mediated contact between the enzyme and topotecan, we were surprised to find that a well-ordered water molecule replaces the hydrophobic phenylalanine side-chain in the Phe361Ser structure. We further consider camptothecin-resistant mutations at seven additional sites in human topoisomerase I and present structural evidence explaining their possible impact on drug binding. These results advance our understanding of the mechanism of cell poisoning by camptothecin and suggest specific modifications to the drug that may improve efficacy.
  Selected figure(s)  
Figure 1.
Figure 1. (a) A 2.3 Å resolution crystal structure of human topoisomerase I in covalent complex with a 22 base-pair duplex DNA containing topotecan and an Asn722Ser mutation. The CAP region sits above the DNA and is composed of core sub-domains I and II. The CAT region sits below the DNA and consists of core sub-domain III and the C-terminal domain. The linker domain, which follows in primary sequence the CAP and connects the CAP and CAT regions of the enzyme, protrudes away from the body of the protein structure. CPT-resistant mutations discussed here (Table 1) are indicated in CPK and colored cyan. (b) Molecular surface of human topoisomerase I in the ternary complex of the enzyme, DNA and topotecan (TTC; magenta), viewed in roughly the same orientation as in (a) A channel vert, similar 16 Å in width at the interface of the CAP and CAT regions appears to allow TTC to gain access to the active site in the protein–DNA complex.
Figure 2.
Figure 2. (a) Electron density (2|F[obs]|−|F[calc]|, 2.3 Å resolution, contoured at 1σ) showing the Asn722Ser mutation in the structure of the mutant human topoisomerase I–DNA–TTC ternary complex. (b) Electron density (2|F[obs]|−|F[calc]|, 2.6 Å resolution, contoured at 1σ) showing the Phe361Ser mutation in the structure of the mutant human topoisomerase I–DNA–TTC ternary complex. (c) Stereo view of the electron density for topotecan as observed in the 2.3 Å resolution crystal structure of the Asn722Ser mutant human topoisomerase I in ternary complex with DNA and the drug (2|F[obs]|−|F[calc]|, contoured at 1σ).
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 339, 773-784) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22173432 Y.Pommier, and C.Marchand (2012).
Interfacial inhibitors: targeting macromolecular complexes.
  Nat Rev Drug Discov, 11, 25-36.  
21069656 C.Samorì, G.L.Beretta, G.Varchi, A.Guerrini, S.Di Micco, S.Basili, G.Bifulco, R.Riccio, S.Moro, E.Bombardelli, F.Zunino, and G.Fontana (2010).
Structure-activity relationship study of 16 a-thiocamptothecins: an integrated in vitro and in silico approach.
  ChemMedChem, 5, 2006-2015.  
20534341 Y.Pommier, E.Leo, H.Zhang, and C.Marchand (2010).
DNA topoisomerases and their poisoning by anticancer and antibacterial drugs.
  Chem Biol, 17, 421-433.  
19332675 A.Roy, S.BoseDasgupta, A.Ganguly, P.Jaisankar, and H.K.Majumder (2009).
Topoisomerase I gene mutations at F270 in the large subunit and N184 in the small subunit contribute to the resistance mechanism of the unicellular parasite Leishmania donovani towards 3,3'-diindolylmethane.
  Antimicrob Agents Chemother, 53, 2589-2598.  
19377506 J.L.Nitiss (2009).
Targeting DNA topoisomerase II in cancer chemotherapy.
  Nat Rev Cancer, 9, 338-350.  
19783447 M.A.Cinelli, B.Cordero, T.S.Dexheimer, Y.Pommier, and M.Cushman (2009).
Synthesis and biological evaluation of 14-(aminoalkyl-aminomethyl)aromathecins as topoisomerase I inhibitors: investigating the hypothesis of shared structure-activity relationships.
  Bioorg Med Chem, 17, 7145-7155.  
19106140 N.M.Baker, R.Rajan, and A.Mondragón (2009).
Structural studies of type I topoisomerases.
  Nucleic Acids Res, 37, 693-701.  
19767617 P.Fiorani, C.Tesauro, G.Mancini, G.Chillemi, I.D'Annessa, G.Graziani, L.Tentori, A.Muzi, and A.Desideri (2009).
Evidence of the crucial role of the linker domain on the catalytic activity of human topoisomerase I by experimental and simulative characterization of the Lys681Ala mutant.
  Nucleic Acids Res, 37, 6849-6858.  
19383846 Y.Pommier, and M.Cushman (2009).
The indenoisoquinoline noncamptothecin topoisomerase I inhibitors: update and perspectives.
  Mol Cancer Ther, 8, 1008-1014.  
18755053 A.J.Schoeffler, and J.M.Berger (2008).
DNA topoisomerases: harnessing and constraining energy to govern chromosome topology.
  Q Rev Biophys, 41, 41.  
18772225 C.Losasso, E.Cretaio, P.Fiorani, I.D'Annessa, G.Chillemi, and P.Benedetti (2008).
A single mutation in the 729 residue modulates human DNA topoisomerase IB DNA binding and drug resistance.
  Nucleic Acids Res, 36, 5635-5644.  
18292117 D.A.Koster, F.Czerwinski, L.Halby, A.Crut, P.Vekhoff, K.Palle, P.B.Arimondo, and N.H.Dekker (2008).
Single-molecule observations of topotecan-mediated TopIB activity at a unique DNA sequence.
  Nucleic Acids Res, 36, 2301-2310.  
18765473 G.Chillemi, I.D'Annessa, P.Fiorani, C.Losasso, P.Benedetti, and A.Desideri (2008).
Thr729 in human topoisomerase I modulates anti-cancer drug resistance by altering protein domain communications as suggested by molecular dynamics simulations.
  Nucleic Acids Res, 36, 5645-5651.  
18508107 H.Kim, J.H.Cardellina, R.Akee, J.J.Champoux, and J.T.Stivers (2008).
Arylstibonic acids: novel inhibitors and activators of human topoisomerase IB.
  Bioorg Chem, 36, 190-197.  
18318502 J.E.Deweese, A.B.Burgin, and N.Osheroff (2008).
Using 3'-bridging phosphorothiolates to isolate the forward DNA cleavage reaction of human topoisomerase IIalpha.
  Biochemistry, 47, 4129-4140.  
18693244 K.Palle, L.Pattarello, M.van der Merwe, C.Losasso, P.Benedetti, and M.A.Bjornsti (2008).
Disulfide Cross-links Reveal Conserved Features of DNA Topoisomerase I Architecture and a Role for the N Terminus in Clamp Closure.
  J Biol Chem, 283, 27767-27775.  
17943230 M.K.Gounder, A.S.Nazar, A.Saleem, P.Pungaliya, D.Kulkarni, R.Versace, and E.H.Rubin (2008).
Effects of drug efflux proteins and topoisomerase I mutations on the camptothecin analogue gimatecan.
  Invest New Drugs, 26, 205-213.  
18056711 M.van der Merwe, and M.A.Bjornsti (2008).
Mutation of gly721 alters DNA topoisomerase I active site architecture and sensitivity to camptothecin.
  J Biol Chem, 283, 3305-3315.  
18443285 S.Sirikantaramas, M.Yamazaki, and K.Saito (2008).
Mutations in topoisomerase I as a self-resistance mechanism coevolved with the production of the anticancer alkaloid camptothecin in plants.
  Proc Natl Acad Sci U S A, 105, 6782-6786.  
17589503 D.A.Koster, K.Palle, E.S.Bot, M.A.Bjornsti, and N.H.Dekker (2007).
Antitumour drugs impede DNA uncoiling by topoisomerase I.
  Nature, 448, 213-217.  
17355975 D.Montaudon, K.Palle, L.P.Rivory, J.Robert, C.Douat-Casassus, S.Quideau, M.A.Bjornsti, and P.Pourquier (2007).
Inhibition of topoisomerase I cleavage activity by thiol-reactive compounds: importance of vicinal cysteines 504 and 505.
  J Biol Chem, 282, 14403-14412.  
18254239 I.Choi, C.Kim, and S.Choi (2007).
Binding mode analysis of topoisomerase inhibitors, 6-arylamino-7-chloro-quinazoline-5,8-diones, within the cleavable complex of human topoisomerase I and DNA.
  Arch Pharm Res, 30, 1526-1535.  
16368685 A.Patel, S.Shuman, and A.Mondragón (2006).
Crystal structure of a bacterial type IB DNA topoisomerase reveals a preassembled active site in the absence of DNA.
  J Biol Chem, 281, 6030-6037.
PDB code: 2f4q
16505102 C.Marchand, S.Antony, K.W.Kohn, M.Cushman, A.Ioanoviciu, B.L.Staker, A.B.Burgin, L.Stewart, and Y.Pommier (2006).
A novel norindenoisoquinoline structure reveals a common interfacial inhibitor paradigm for ternary trapping of the topoisomerase I-DNA covalent complex.
  Mol Cancer Ther, 5, 287-295.  
16885024 K.Perry, Y.Hwang, F.D.Bushman, and G.D.Van Duyne (2006).
Structural basis for specificity in the poxvirus topoisomerase.
  Mol Cell, 23, 343-354.
PDB codes: 2h7f 2h7g
16990249 P.Fiorani, G.Chillemi, C.Losasso, S.Castelli, and A.Desideri (2006).
The different cleavage DNA sequence specificity explains the camptothecin resistance of the human topoisomerase I Glu418Lys mutant.
  Nucleic Acids Res, 34, 5093-5100.  
16990856 Y.Pommier (2006).
Topoisomerase I inhibitors: camptothecins and beyond.
  Nat Rev Cancer, 6, 789-802.  
16891172 Y.Pommier, J.M.Barcelo, V.A.Rao, O.Sordet, A.G.Jobson, L.Thibaut, Z.H.Miao, J.A.Seiler, H.Zhang, C.Marchand, K.Agama, J.L.Nitiss, and C.Redon (2006).
Repair of topoisomerase I-mediated DNA damage.
  Prog Nucleic Acid Res Mol Biol, 81, 179-229.  
15749159 Y.Pommier, and J.Cherfils (2005).
Interfacial inhibition of macromolecular interactions: nature's paradigm for drug discovery.
  Trends Pharmacol Sci, 26, 138-145.  
15347588 G.Chillemi, M.Redinbo, A.Bruselles, and A.Desideri (2004).
Role of the linker domain and the 203-214 N-terminal residues in the human topoisomerase I DNA complex dynamics.
  Biophys J, 87, 4087-4097.  
15489506 W.C.Colley, M.van der Merwe, J.R.Vance, A.B.Burgin, and M.A.Bjornsti (2004).
Substitution of conserved residues within the active site alters the cleavage religation equilibrium of DNA topoisomerase I.
  J Biol Chem, 279, 54069-54078.  
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.