1rg1: Difference between revisions
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|PDB= 1rg1 |SIZE=350|CAPTION= <scene name='initialview01'>1rg1</scene>, resolution 2.10Å | |PDB= 1rg1 |SIZE=350|CAPTION= <scene name='initialview01'>1rg1</scene>, resolution 2.10Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand= | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=OTS:4-(2S-AMINO-1-HYDROXYETHYL)PHENOL'>OTS</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=VO4:VANADATE+ION'>VO4</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= TDP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]) | |GENE= TDP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]) | ||
|DOMAIN= | |||
|RELATEDENTRY=[[1nop|1NOP]], [[1jy1|1JY1]], [[1rff|1RFF]], [[1rfi|1RFI]], [[1rg2|1RG2]], [[1rgt|1RGT]], [[1rgu|1RGU]], [[1rh0|1RH0]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rg1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rg1 OCA], [http://www.ebi.ac.uk/pdbsum/1rg1 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1rg1 RCSB]</span> | |||
}} | }} | ||
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[[Category: Hol, W G.]] | [[Category: Hol, W G.]] | ||
[[Category: Interthal, H.]] | [[Category: Interthal, H.]] | ||
[[Category: protein-dna complex]] | [[Category: protein-dna complex]] | ||
[[Category: transition state mimic]] | [[Category: transition state mimic]] | ||
[[Category: vanadate complex]] | [[Category: vanadate complex]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:27:38 2008'' | ||
Revision as of 23:27, 30 March 2008
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| , resolution 2.10Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , | ||||||
| Gene: | TDP1 (Homo sapiens) | ||||||
| Related: | 1NOP, 1JY1, 1RFF, 1RFI, 1RG2, 1RGT, 1RGU, 1RH0
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTT
OverviewOverview
Tyrosyl-DNA phosphodiesterase (Tdp1) catalyzes the hydrolysis of a phosphodiester bond between a tyrosine residue and a DNA 3' phosphate and functions as a DNA repair enzyme that cleaves stalled topoisomerase I-DNA complexes. We previously determined a procedure to crystallize a quaternary complex containing Tdp1, vanadate, a DNA oligonucleotide, and a tyrosine-containing peptide that mimics the transition state for hydrolysis of the Tdp1 substrate. Here, the ability of vanadate to accept a variety of different ligands is exploited to produce several different quaternary complexes with a variety of oligonucleotides, and peptides or a tyrosine analogue, in efforts to explore the binding properties of the Tdp1 DNA and peptide binding clefts. Eight crystal structures of Tdp1 with vanadate, oligonucleotides, and peptides or peptide analogues were determined. These structures demonstrated that Tdp1 is able to bind substituents with limited sequence variation in the polypeptide moiety and also bind oligonucleotides with sequence variation at the 3' end. Additionally, the tyrosine analogue octopamine can replace topoisomerase I derived peptides as the apical ligand to vanadate. The versatility of this system suggests that the formation of quaternary complexes around vanadate could be adapted to become a useful method for structure-based inhibitor design and has the potential to be generally applicable to other enzymes that perform chemistry on phosphate esters.
DiseaseDisease
Known disease associated with this structure: Spinocerebellar ataxia, autosomal recessive with axonal neuropathy OMIM:[607198]
About this StructureAbout this Structure
1RG1 is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.
ReferenceReference
Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes., Davies DR, Interthal H, Champoux JJ, Hol WG, J Med Chem. 2004 Feb 12;47(4):829-37. PMID:14761185
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