Primary Citation PubMed: 9488652
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Effect on DNA relaxation of the single Thr718Ala mutation in human topoisomerase I: a functional and molecular dynamics study.
(2005) Nucleic Acids Res 33
PubMed: 15944452 | PubMedCentral: PMC1145191 | DOI: 10.1093/nar/gki642
A hydrogen bond between the side chain of Thr-718 and the G+2 phosphate group of the scissile strand has been detected in several crystallographic structures of topo70 (PDB id 1a36, 1k4s, 1k4t) ( 6 ... 02013; 8 ).
MD simulations The topo70–DNA covalent complex was modeled obtaining the starting position for residues 215–633 and 641–765 from the crystal structure 1a36 ( 6 ), and those for residues 203–214 from the crystal structure 1ej9 ( 5 ).
The seven residues constituting the loop region that connects the linker to the core domain [residues 634–640, which are lacking in the 1a36 Protein Data Bank (PDB) structure because of thermal fluctuation] and the covalent bond between Tyr-723 and the DNA-1 base were added to the system by molecular modeling using the SYBYL program (Tripos Inc., St Louis, MO).
Publication Year: 2005
Rotation of DNA around intact strand in human topoisomerase I implies distinct mechanisms for positive and negative supercoil relaxation.
PubMed: 16314322 | PubMedCentral: PMC1298917 | DOI: 10.1093/nar/gki935
A covalent model of the DNA–topoisomerase complex was set-up, with the position of the linker domain (missing in the covalent structure, PDB code 1a31) built using the non-covalent structure (... DB code 1a36).
An overview of the structures of protein-DNA complexes.
(2000) Genome Biol 1
PubMed: 11104519 | PubMedCentral: PMC138832 | DOI: 10.1186/gb-2000-1-1-reviews001
Topoisomerase I 1a31 * A Topoisomerase I H. sapiens 2.1 AAAAAGACCCTGAAAAACCCCT 1a35 A Topoisomerase I H. sapiens 2.5 AAAAAGACCCTGAAAAACCCCT 1a36 A Topoisomerase I H. sapiens 2.8 AAAAAGACTTAGAAAAATTTTT... Each entry is provided with the four-digit PDB code, the name, the source, resolution and the aligned sequences of DNA to which the protein is bound in the crystal structure.
Publication Year: 2000
The open state of human topoisomerase I as probed by molecular dynamics simulation.
(2007) Nucleic Acids Res 35
PubMed: 17439970 | PubMedCentral: PMC1888835 | DOI: 10.1093/nar/gkm199
METHODS The initial configuration of hTop1 was modeled obtaining the starting position for residues 215–633 and 641–765 from the crystal structure 1a36 ( 6 ), and those for residues 20... –214 from the crystal structure 1ej9 ( 17 ).
The seven residues constituting the loop region that connects the linker to the core domain (residues 634–640, which are lacking in the 1a36 PDB structure because of thermal fluctuation) were added to the system by molecular modeling, as already described ( 14 ), using the SYBYL program (St Louis, MO).
As a matter of fact, the largest deviation of the active site backbone atoms from the 1a36 crystallographic structure is only 1.7 Å.
Publication Year: 2007
Thr729 in human topoisomerase I modulates anti-cancer drug resistance by altering protein domain communications as suggested by molecular dynamics simulations.
(2008) Nucleic Acids Res 36
PubMed: 18765473 | PubMedCentral: PMC2553568 | DOI: 10.1093/nar/gkn558
In particular, the starting positions for residues 215–633 and 641–765 were obtained from the crystal structure 1a36 ( 5 ), and those for residues 203–214 from the crystal stru... ture 1ej9 ( 13 ).
Publication Year: 2008
Peptide Inhibition of Topoisomerase IB from Plasmodium falciparum.
(2011) Mol Biol Int 2011
PubMed: 22091414 | PubMedCentral: PMC3200115 | DOI: 10.4061/2011/854626
Docking Experiment The three-dimensional structure for residues Pro140-Phe839 of pfTopoI was obtained through homology modeling using the SwissModel server [ 44 ] and the crystal structure of hTopoI (... K4T and 1A36 PDBs) as a template [ 45 , 46 ].
Publication Year: 2011
Role of Flexibility in Protein-DNA-Drug Recognition: The Case of Asp677Gly-Val703Ile Topoisomerase Mutant Hypersensitive to Camptothecin.
(2012) J Amino Acids 2012
PubMed: 22315664 | PubMedCentral: PMC3270393 | DOI: 10.1155/2012/206083
MD Simulation The DNA-Topo70 covalent complex, without the N-terminal domain, has been modelled obtaining the starting positions from the X-ray structure of 1a36 for residues 215–633 and 641... 02013;765 [ 6 ], and from the X-ray structure 1ej9 for residues 203–214 [ 19 ].
The five residues 636–640 that form the loop connecting the linker domain and the C-terminal domain, lacking in the 1a36 structure in the Protein Data Bank (PDB http://www.rscb.org/pdb/ ), and the covalent bond between the catalytic Tyr723 and the −1 base, Thy10, have been added to the structure via molecular modelling.
Publication Year: 2012
Analysis of conformational variation in macromolecular structural models.
(2012) PLoS One 7
PubMed: 22808083 | PubMedCentral: PMC3392262 | DOI: 10.1371/journal.pone.0039993
Unstructured inindividual protein structure α-helix 634 10 1K4S/1A36 633–710: QRAPPKTFEKSMMNLQTKIDAKKEQLADARRDLKSAKADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDREE α-helix in one comp... ex and unstructuredin the other α-helix 633–636,639–640,669–687,700–701,703–710 11 1SER/1SRY 36–86: EVQELKKRLQEVQTERNQVAKRVPKAPPEEKEALIARGKALGEEAKRLEEA Unstructured in complex and α-helix inindividual structure Α-helix 48, 50–69 12 1HLO/1R05 12–27: ADKRAHHNALERKRRD α-helix in the complex (crystal) andunstructured in the individual protein(NMR) α-helix 27-Dec 13 1B70/1EIY 6–85: LAAIQNARDLEELKALKARYLGKKGLLTQEMKGLSALPLEERRKRGQELNAIKAALEAALEAREKALEEAALKEALERER α-helix in one complex and unstructuredin the other α-helix – 14 1JYE/1EFA 5–13: TLYDVAEYA α-helix in complex, unstructured inindividual protein α-helix 11 16–25: SYQTVSRVVN α-helix in complex, unstructured inindividual protein α-helix and β-strand 16–17 32–46: AKTREKVEAAMAELN α-helix in complex, unstructured inindividual protein α-helix 32–37 15 1D1U/1D0E 67–84: SQEARLGIKPHIQRLLDQ α-helix in one complex and unstructuredin other α-helix 69–71, 83–84 99–114: LPVKKPGTNDYRPVQD α-helix in one complex, β-strand and coilin other Coil 99–114 237–273: QQGTRALLQTLGNLGYRASAKKAQICQ α-helix and coil in one complex, β-strandin the other α-helix 238–241, 264 16 1VS5/2QOU 19–30: SIVVAIERFVKH β-strand in one complex, mostlyunstructured in other β-strand and α-helix - 34–46: GKFIKRTTKLHVH β-strand in one complex, mostlyunstructured in other β-strand 34–35, 45–46 57–67: VVEIRECRPLS β-strand in one complex, mostlyunstructured in other β-strand – 10.1371/journal.pone.0039993.
A small organic compound enhances the religation reaction of human topoisomerase I and identifies crucial elements for the religation mechanism.
(2013) Biosci Rep 33
PubMed: 23368812 | PubMedCentral: PMC3590572 | DOI: 10.1042/BSR20120118
The molecular geometry of the Top1 non-covalent binary complex was obtained by modelling the 1A36 PDB entry; after removing the DNA, the same structure was used to obtain a model of the Top1 enzyme in... the absence of DNA.
Publication Year: 2013
Replacement of the human topoisomerase linker domain with the plasmodial counterpart renders the enzyme camptothecin resistant.
(2013) PLoS One 8
PubMed: 23844196 | PubMedCentral: PMC3699648 | DOI: 10.1371/journal.pone.0068404
Based on the sequence alignment, the template considered for the homology modeling was the crystal structures 1A36 of the hTop1 in complex with a 22 bp DNA [ 6 ].
Theoretical and experimental studies of new modified isoflavonoids as potential inhibitors of topoisomerase I from Plasmodium falciparum.
(2014) PLoS One 9
PubMed: 24651068 | PubMedCentral: PMC3961230 | DOI: 10.1371/journal.pone.0091191
The 3D structure of Pf TopoI ( Figure S1 ) was built in the Swiss Model server  , according to the procedure reported by Roy et al  , using as templates the PDB structures of Hss TopoI 1K4T [1... ] and 1A36  .
Publication Year: 2014
PubMed ID is not available.
Published in 2015
DNA topoisomerase (Protein Data Bank ID 1A36) was used as a structural template to build the model.
Publication Year: 2015
( d ) SQDG (shown in orange) docks in the DNA binding region of topo I protein (PDB ID: 1A36) (shown in purple).
SQDG docks in the DNA binding region of topo I by forming non-covalent interactions Molecular docking was performed between human topoisomerase I (PDB ID: 1A36) 48 and SQDG (Pubchem, CID 50898453) 20 ( Fig. 6d ).
Molecular docking Crystal structure of the receptor molecule i.e. human topoisomerase I complexed with its substrate DNA and inhibitor camptothecin was collected from Protein Data Bank (PDB) (PDB ID: 1A36) 48 .
Probable binding cavities of 1A36 were identified using the CASTp web server 62 and molecular docking of SQDG with topo I was performed using the GOLD v5.0.1 package from Cambridge Crystallographic Data Centre 63 .
Three-dimensional (3D) coordinates of DNA and camptothecin were removed from the 1A36 structure for docking of SQDG.
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