Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule

被引:97
作者
Changela, A
DiGate, RJ
Mondragón, A
机构
[1] Northwestern Univ, Dept Biochem Mol Biol & Cell Biol, Evanston, IL 60208 USA
[2] Univ Maryland, Sch Med, Dept Pharmaceut Sci, Baltimore, MD 21201 USA
关键词
D O I
10.1038/35082615
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
A variety of cellular processes, including DNA replication, transcription, and chromosome condensation, require enzymes that can regulate the ensuing topological changes occurring in DNA. Such enzymes-DNA topoisomerases-alter DNA topology by catalysing the cleavage of single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA), the passage of DNA through the resulting break, and the rejoining of the broken phosphodiester backbone(1). DNA topoisomerase III from Escherichia coli belongs to the type IA family of DNA topoisomerases, which transiently cleave ssDNA via formation of a covalent 5' phosphotyrosine intermediate. Here we report the crystal structure, at 2.05 Angstrom resolution, of an inactive mutant of E. coli DNA topoisomerase III in a non-covalent complex with an 8-base ssDNA molecule. The enzyme undergoes a conformational change that allows the oligonucleotide to bind within a groove leading to the active site. We note that the ssDNA molecule adopts a conformation like that of B-DNA while bound to the enzyme. The position of the DNA within the realigned active site provides insight into the role of several highly conserved residues during catalysis. These findings confirm various aspects of the type IA topoisomerase mechanism while suggesting functional implications for other topoisomerases and proteins that perform DNA rearrangements.
引用
收藏
页码:1077 / 1081
页数:5
相关论文
共 30 条
[1]   Toprim - a conserved catalytic domain in type IA and II topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins [J].
Aravind, L ;
Leipe, DD ;
Koonin, EV .
NUCLEIC ACIDS RESEARCH, 1998, 26 (18) :4205-4213
[2]   THE CCP4 SUITE - PROGRAMS FOR PROTEIN CRYSTALLOGRAPHY [J].
BAILEY, S .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1994, 50 :760-763
[3]   Structure and mechanism of DNA topoisomerase II [J].
Berger, JM ;
Gamblin, SJ ;
Harrison, SC ;
Wang, JC .
NATURE, 1996, 379 (6562) :225-232
[4]   Structural similarities between topoisomerases that cleave one or both DNA strands [J].
Berger, JM ;
Fass, D ;
Wang, JC ;
Harrison, SC .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1998, 95 (14) :7876-7881
[5]   Crystallography & NMR system:: A new software suite for macromolecular structure determination [J].
Brunger, AT ;
Adams, PD ;
Clore, GM ;
DeLano, WL ;
Gros, P ;
Grosse-Kunstleve, RW ;
Jiang, JS ;
Kuszewski, J ;
Nilges, M ;
Pannu, NS ;
Read, RJ ;
Rice, LM ;
Simonson, T ;
Warren, GL .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1998, 54 :905-921
[6]   Identification of active site residues in Escherichia coli DNA topoisomerase I [J].
Chen, SJ ;
Wang, JC .
JOURNAL OF BIOLOGICAL CHEMISTRY, 1998, 273 (11) :6050-6056
[7]   MECHANISTIC STUDIES ON ESCHERICHIA-COLI DNA TOPOISOMERASE .1. DIVALENT ION EFFECTS [J].
DOMANICO, PL ;
TSEDINH, YC .
JOURNAL OF INORGANIC BIOCHEMISTRY, 1991, 42 (02) :87-96
[8]   SETOR - HARDWARE-LIGHTED 3-DIMENSIONAL SOLID MODEL REPRESENTATIONS OF MACROMOLECULES [J].
EVANS, SV .
JOURNAL OF MOLECULAR GRAPHICS, 1993, 11 (02) :134-&
[9]  
Fass D, 1999, NAT STRUCT BIOL, V6, P322
[10]   Macromolecular crystal annealing: Overcoming increased mosaicity associated with cryocrystallography [J].
Harp, JM ;
Timm, DE ;
Bunick, GJ .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 1998, 54 :622-628