PDBsum entry: 1mw8

Isomerase

PDB id: 1mw8

Contents

Protein chain

561 a.a. *

DNA/RNA

Ligands

SO4 ×5

TMP

Waters ×553

* Residue conservation analysis

PDB id:

1mw8

Name:

Isomerase

Title:

Crystal structure of a complex between h365r mutant of 67 kda n-terminal fragment of e. Coli DNA topoisomerase i and 5'-acttcgggatg-3'

Structure:

5'-d( Ap Cp Tp Tp Cp Gp Gp Gp Ap Tp G)-3'. Chain: y. Engineered: yes. DNA topoisomerase i. Chain: x. Fragment: 67 kda n-terminal fragment. Synonym: omega-protein, relaxing enzyme, untwisting enzyme, swivelase. Engineered: yes.

Source:

Synthetic: yes. Escherichia coli. Organism_taxid: 562. Gene: topa. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.90Å R-factor: 0.226 R-free: 0.273

Authors:

K.Perry,A.Mondragon

Key ref:

K.Perry and A.Mondragón (2003). Structure of a complex between E. coli DNA topoisomerase I and single-stranded DNA. Structure, 11, 1349-1358. PubMed id: 14604525 DOI: 10.1016/j.str.2003.09.013

Date:

27-Sep-02 Release date: 14-Oct-03

Protein chain

P06612  (TOP1_ECOLI) -  DNA topoisomerase 1

Seq: 865 a.a.

Struc: 561 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.5.99.1.2 - Dna topoisomerase.
• Reaction: ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.

 Gene Ontology (GO) functional annotation 

• Cellular component: chromosome (1 term)
• Biological process: DNA metabolic process (3 terms)
• Biochemical function: nucleic acid binding (4 terms)

DOI no: 10.1016/j.str.2003.09.013

Structure 11:1349-1358 (2003)

PubMed id: 14604525

Structure of a complex between E. coli DNA topoisomerase I and single-stranded DNA.

K.Perry, A.Mondragón.

ABSTRACT

In order to gain insights into the mechaism of ssDNA binding and recognition by Escherichia coli DNA topoisomerase I, the structure of the 67 kDa N-terminal fragment of topoisomerase I was solved in complex with ssDNA. The structure reveals a new conformational stage in the multistep catalytic cycle of type IA topoisomerases. In the structure, the ssDNA binding groove leading to the active site is occupied, but the active site is not fully formed. Large conformational changes are not seen; instead, a single helix parallel to the ssDNA binding groove shifts to clamp the ssDNA. The structure helps clarify the temporal sequence of conformational events, starting from an initial empty enzyme and proceeding to a ssDNA-occupied and catalytically competent active site.

Selected figure(s)

Figure 4.
Figure 4. Diagram of Specific Hydrogen Bonds Made between the Oligonucleotide and the Protein in the DNA Binding Groove and at Site IThe coloring of the domains is the same as in Figure 2. Starting at the visible 5' end of the oligonucleotide, the nucleotides are Cyt2, Thy3, Thy4, Cyt5, Gua6, and Gua7. Hydrogen bonds are shown as dashed lines.Top: The shifted a helix has been made transparent, as it directly overlays the oligonucleotide and would prevent visualization of the bonds. The ring stacking between Tyr177 and Thy3, as well as the stacking interaction between Cyt2 and Trp184, are shown.Bottom: Superposition of the topoisomerase III/ssDNA complex on the T67-H365R/11 complex to show the location of the stacking tryptophans. The topoisomerase III/ssDNA complex is colored blue: the protein is dark blue, the ssDNA is light blue, and Trp61 is light blue. The T67-H365R protein is colored green, the ssDNA is in colors, and Trp184 is colored in magenta. The tryptophans are labeled in red, while the ssDNA nucleotides are labeled in black. It can be seen that Trp61 in topoisomerase III comes in from a strand below the base of the 5' nucleotide while Trp184 in topoisomerase I comes in from a helix above the base of the 5' nucleotide.

The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 1349-1358) copyright 2003.

Figure was selected by the author.