Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 81.14 kDa 
• Atom Count: 5,386 
• Modelled Residue Count: 538 
• Deposited Residue Count: 609 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 1RR8

Structural Mechanisms of Camptothecin Resistance by Mutations in Human Topoisomerase I

• PDB DOI: 10.2210/pdb1RR8/pdb
• NDB: PD0498

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


• Deposited: 2003-12-08 Released: 2004-07-06 
• Deposition Author(s): Chrencik, J.E., Staker, B.L., Burgin, A.B., Stewart, L., Redinbo, M.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.294 
• R-Value Work: 0.242 
• R-Value Observed: 0.292 

Literature

Mechanisms of camptothecin resistance by human topoisomerase I mutations

Chrencik, J.E., Staker, B.L., Burgin, A.B., Pourquier, P., Pommier, Y., Stewart, L., Redinbo, M.R.

(2004) J Mol Biol 339: 773-784

• PubMed: 15165849 
• DOI: 10.1016/j.jmb.2004.03.077
• Primary Citation of Related Structures:  
  1RR8, 1RRJ


• PubMed Abstract: 
  

Human topoisomerase I relaxes superhelical tension associated with DNA replication, transcription and recombination by reversibly nicking one strand of duplex DNA and forming a covalent 3'-phosphotyrosine linkage. This enzyme is the sole target of the camptothecin family of anticancer compounds, which acts by stabilizing the covalent protein-DNA complex and enhancing apoptosis through blocking the advancement of replication forks. Mutations that impart resistance to camptothecin have been identified in several regions of human topoisomerase I. We present the crystal structures of two camptothecin-resistant forms of human topoisomerase I (Phe361Ser at 2.6A resolution and Asn722Ser at 2.3A resolution) in ternary complexes with DNA and topotecan (Hycamtin), a camptothecin analogue currently in widespread clinical use. While the alteration of Asn722 to Ser leads to the elimination of a water-mediated contact between the enzyme and topotecan, we were surprised to find that a well-ordered water molecule replaces the hydrophobic phenylalanine side-chain in the Phe361Ser structure. We further consider camptothecin-resistant mutations at seven additional sites in human topoisomerase I and present structural evidence explaining their possible impact on drug binding. These results advance our understanding of the mechanism of cell poisoning by camptothecin and suggest specific modifications to the drug that may improve efficacy.

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Organizational Affiliation: 

Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase I	C	565	Homo sapiens	Mutation(s): 3  Gene Names: TOP1 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

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T*GP*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'	A	22	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*CP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3'	B	22	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TTG	D [auth A]	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
TTC	E [auth A]	(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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	C	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
TTC	BindingDB:  1RR8	Kd: 26.5 (nM) from 1 assay(s)
		IC50: min: 21, max: 2.00e+4 (nM) from 11 assay(s)
		EC50: min: 54, max: 71.3 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.294 
• R-Value Work: 0.242 
• R-Value Observed: 0.292 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.59	α = 90
b = 115.585	β = 96.29
c = 75.01	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
TRUNCATE	data reduction
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-07-06 
Deposition Author(s): Chrencik, J.E., Staker, B.L., Burgin, A.B., Stewart, L., Redinbo, M.R.

Revision History  

• Version 1.0: 2004-07-06
  Type: Initial release
  
• Version 1.1: 2008-05-05
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations