1K4T | pdb_00001k4t

HUMAN DNA TOPOISOMERASE I (70 KDA) IN COMPLEX WITH THE POISON TOPOTECAN AND COVALENT COMPLEX WITH A 22 BASE PAIR DNA DUPLEX

PDB DOI: https://doi.org/10.2210/pdb1K4T/pdb
NAKB: 1K4T

Classification: ISOMERASE/DNA
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2001-10-08 Released: 2002-12-04
Deposition Author(s): Staker, B.L., Hjerrild, K., Feese, M.D., Behnke, C.A., Burgin Jr., A.B., Stewart, L.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.269 (Depositor)
R-Value Work:
0.229 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

The mechanism of topoisomerase I poisoning by a camptothecin analog

Staker, B.L., Hjerrild, K., Feese, M.D., Behnke, C.A., Burgin Jr., A.B., Stewart, L.J.

(2002) Proc Natl Acad Sci U S A 99: 15387-15392

PubMed: 12426403 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.242259599
Primary Citation Related Structures:
1K4S, 1K4T

PubMed Abstract:
We report the x-ray crystal structure of human topoisomerase I covalently joined to double-stranded DNA and bound to the clinically approved anticancer agent Topotecan. Topotecan mimics a DNA base pair and binds at the site of DNA cleavage by intercalating between the upstream (-1) and downstream (+1) base pairs. Intercalation displaces the downstream DNA, thus preventing religation of the cleaved strand. By specifically binding to the enzyme-substrate complex, Topotecan acts as an uncompetitive inhibitor. The structure can explain several of the known structure-activity relationships of the camptothecin family of anticancer drugs and suggests that there are at least two classes of mutations that can produce a drug-resistant enzyme. The first class includes changes to residues that contribute to direct interactions with the drug, whereas a second class would alter interactions with the DNA and thereby destabilize the drug-binding site.

Organizational Affiliation

deCODE genetics, Incorporated, BioStructures Group, 7869 Northeast Day Road West, Bainbridge Island, WA 98110, USA.

Macromolecule Content

Total Structure Weight: 84.97 kDa
Atom Count: 5,883
Modeled Residue Count: 609
Deposited Residue Count: 636
Unique protein chains: 1
Unique nucleic acid chains: 3

Macromolecules

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase I	D [auth A]	592	Homo sapiens	Mutation(s): 1 EC: 5.99.1.2 (PDB Primary Data), 5.6.2.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P11387 (Homo sapiens) Explore P11387 Go to UniProtKB: P11387
PHAROS: P11387 GTEx: ENSG00000198900
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11387
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 1
5'-D(APAPAPAPAPGPAPCPTPT)-3'	A [auth B]	10	N/A
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
5'-D((TGP)PGPAPAPAPAPAPTPTPTPTPT)-3'	B [auth C]	12	N/A
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 3
5'-D(APAPAPAPAPTPTPTPTPTPCPCPAPAPGPTPCPTPTPTPTPT)-3'	C [auth D]	22	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TTG Query on TTG Download:Ideal Coordinates CCD File SDF format, chain E [auth C] MOL2 format, chain E [auth C] mmCIF format, chain E [auth C]	E [auth C]	2-(1-DIMETHYLAMINOMETHYL-2-HYDROXY-8-HYDROXYMETHYL-9-OXO-9,11-DIHYDRO-INDOLIZINO[1,2-B]QUINOLIN-7-YL)-2-HYDROXY-BUTYRIC ACID C₂₃ H₂₅ N₃ O₆ DPQJTQJZJNYUEC-QHCPKHFHSA-N		Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]
TTC Query on TTC Download:Ideal Coordinates CCD File SDF format, chain F [auth D] MOL2 format, chain F [auth D] mmCIF format, chain F [auth D]	F [auth D]	(S)-10-[(DIMETHYLAMINO)METHYL]-4-ETHYL-4,9-DIHYDROXY-1H-PYRANO[3',4':6,7]INOLIZINO[1,2-B]-QUINOLINE-3,14(4H,12H)-DIONE C₂₃ H₂₃ N₃ O₅ UCFGDBYHRUNTLO-QHCPKHFHSA-N		Interactions Focus chain F [auth D] Interactions & Density Focus chain F [auth D]
HG Query on HG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR Query on PTR	D [auth A]	L-PEPTIDE LINKING	C₉ H₁₂ N O₆ P		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.269 (Depositor)
R-Value Work: 0.229 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.093	α = 90
b = 116.26	β = 94.16
c = 75.217	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNX	refinement
CNX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2002-12-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2002-12-04
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-11-15
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2024-10-30
Changes: Structure summary