PDBsum entry 1nop

Hydrolase/DNA

PDB id: 1nop

Contents

Protein chain

425 a.a. *

DNA/RNA

Ligands

_DT

LYS-LEU-ASN-TYR-LEU

VO4 ×2

Waters ×96

* Residue conservation analysis

PDB id:

1nop

Name:

Hydrolase/DNA

Title:

Crystal structure of human tyrosyl-DNA phosphodiesterase (tdp1) in complex with vanadate, DNA and a human topoisomerase i-derived peptide

Structure:

5'-d( Ap Gp Ap Gp Tp T)-3'. Chain: d, f. Engineered: yes. Tyrosyl-DNA phosphodiesterase 1. Chain: a, b. Fragment: residues 149-608. Synonym: tdp1. Engineered: yes. Mutation: yes.

Source:

Synthetic: yes. Other_details: this sequence is derived from a sequence known to be a target for topoisomerase i. Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Other_details: this sequence occurs naturally in human topoisomerase

Biol. unit:

Trimer (from PQS)

Resolution:

2.30Å R-factor: 0.208 R-free: 0.252

Authors:

D.R.Davies,H.Interthal,J.J.Champoux,W.G.J.Hol

Key ref:

D.R.Davies et al. (2003). Crystal structure of a transition state mimic for Tdp1 assembled from vanadate, DNA, and a topoisomerase I-derived peptide. Chem Biol, 10, 139-147. PubMed id: 12618186 DOI: 10.1016/S1074-5521(03)00021-8

Date:

16-Jan-03 Release date: 11-Mar-03

Protein chains

Q9NUW8  (TYDP1_HUMAN) -  Tyrosyl-DNA phosphodiesterase 1 from Homo sapiens

Seq: 608 a.a.

Struc: 425 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DNA/RNA chain

G-T-T 3 bases

Enzyme reactions

• Enzyme class: E.C.3.1.4.- - ?????

DOI no: 10.1016/S1074-5521(03)00021-8

Chem Biol 10:139-147 (2003)

PubMed id: 12618186

Crystal structure of a transition state mimic for Tdp1 assembled from vanadate, DNA, and a topoisomerase I-derived peptide.

D.R.Davies, H.Interthal, J.J.Champoux, W.G.Hol.

ABSTRACT

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.

Selected figure(s)

Figure 3.
Figure 3. Hydrogen Bonding Contacts between Tdp1 and the Vanadate-Peptide-DNA Substrate Transition State AnalogTdp1, peptide, and DNA are colored as in Figure 1A, with the vanadate moiety in green and hydrogen bonds indicated by dashed lines. Residues 232–242 of Tdp1 have been omitted for clarity. Hydrogen bonds to the vanadate moiety are displayed in (A), hydrogen bonds to the peptide moiety are displayed in (B), and hydrogen bonds to the DNA moiety in (C).

Figure 4.
Figure 4. Electrostatic Potential Surface of Tdp1The molecular surface is colored between −10kT (red) and +10kT (blue) and was generated with the program GRASP [35]. The orientation of the Tdp1 structure is the same as in Figure 1A. The peptide-vanadate-DNA substrate mimic is displayed as a stick structure. The yellow V indicates the position of the vanadate residue in the active site. The DNA moiety extends above the active site, bound in the narrow, positively charged half of the substrate binding groove. The peptide moiety is located below the active site in a relatively neutral portion of the wider substrate binding cleft.

The above figures are reprinted by permission from Cell Press: Chem Biol (2003, 10, 139-147) copyright 2003.

Figures were selected by an automated process.