1nop
From Proteopedia
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|PDB= 1nop |SIZE=350|CAPTION= <scene name='initialview01'>1nop</scene>, resolution 2.30Å | |PDB= 1nop |SIZE=350|CAPTION= <scene name='initialview01'>1nop</scene>, resolution 2.30Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=VO4:VANADATE ION'>VO4</scene> | + | |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=VO4:VANADATE+ION'>VO4</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1jy1|1JY1]], [[1mu7|1MU7]], [[1mu9|1MU9]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nop OCA], [http://www.ebi.ac.uk/pdbsum/1nop PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1nop RCSB]</span> | ||
}} | }} | ||
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[[Category: Hol, W G.J.]] | [[Category: Hol, W G.J.]] | ||
[[Category: Interthal, H.]] | [[Category: Interthal, H.]] | ||
| - | [[Category: VO4]] | ||
[[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 22:33:20 2008'' |
Revision as of 19:33, 30 March 2008
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| , resolution 2.30Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||
| Related: | 1JY1, 1MU7, 1MU9
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of human tyrosyl-DNA phosphodiesterase (Tdp1) in complex with vanadate, DNA and a human topoisomerase I-derived peptide
Overview
Tyrosyl-DNA phosphodiesterase (Tdp1) is a member of the phospholipase D superfamily and acts as a DNA repair enzyme that removes stalled topoisomerase I- DNA complexes by hydrolyzing the bond between a tyrosine side chain and a DNA 3' phosphate. Despite the complexity of the substrate of this phosphodiesterase, vanadate succeeded in linking human Tdp1, a tyrosine-containing peptide, and a single-stranded DNA oligonucleotide into a quaternary complex that mimics the transition state for the first step of the catalytic reaction. The conformation of the bound substrate mimic gives compelling evidence that the topoisomerase I-DNA complex must undergo extensive modification prior to cleavage by Tdp1. The structure also illustrates that the use of vanadate as the central moiety in high-order complexes has the potential to be a general method for capturing protein-substrate interactions for phosphoryl transfer enzymes, even when the substrates are large, complicated, and unusual.
About this Structure
1NOP is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.
Reference
Crystal structure of a transition state mimic for Tdp1 assembled from vanadate, DNA, and a topoisomerase I-derived peptide., Davies DR, Interthal H, Champoux JJ, Hol WG, Chem Biol. 2003 Feb;10(2):139-47. PMID:12618186
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