PDBsum entry: 1d6m

Isomerase

PDB-id: 1d6m

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PROCHECK

Protein chain

603 a.a. *

* Residue conservation analysis

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Clefts Calculation

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PDB id:

1d6m

Name:

Isomerase

Title:

Crystal structure of e. Coli DNA topoisomerase iii

Structure:

DNA topoisomerase iii. Chain: a. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.

UniProt:

P14294 (TOP3_ECOLI)

Seq:

Struc:

Seq:

Struc:

Seq:

653 a.a.

Struc:

603 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Enzyme class:

E.C.5.99.1.2   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.

Resolution:

3.00Å

R-factor:

0.239

R-free:

0.268

Authors:

A.Mondragon,R.Digate

Key ref:

A.Mondragón and R.DiGate (1999). The structure of Escherichia coli DNA topoisomerase III.. Structure, 7, 1373-1383. [PubMed id: 10574789] [DOI: 10.1016/S0969-2126(00)80027-1]

Date:

14-Oct-99

Release date:

14-Oct-00

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Key reference

DOI no: 10.1016/S0969-2126(00)80027-1

Structure 7:1373-1383 (1999)

PubMed id: 10574789

The structure of Escherichia coli DNA topoisomerase III.

A.Mondragón, R.DiGate.

ABSTRACT

BACKGROUND: DNA topoisomerases are enzymes that change the topology of DNA. Type IA topoisomerases transiently cleave one DNA strand in order to pass another strand or strands through the break. In this manner, they can relax negatively supercoiled DNA and catenate and decatenate DNA molecules. Structural information on Escherichia coli DNA topoisomerase III is important for understanding the mechanism of this type of enzyme and for studying the mechanistic differences among different members of the same subfamily. RESULTS: The structure of the intact and fully active E. coli DNA topoisomerase III has been solved to 3.0 A resolution. The structure shows the characteristic fold of the type IA topoisomerases that is formed by four domains, creating a toroidal protein. There is remarkable structural similarity to the 67 kDa N-terminal fragment of E. coli DNA topoisomerase I, although the relative arrangement of the four domains is significantly different. A major difference is the presence of a 17 amino acid insertion in topoisomerase III that protrudes from the side of the central hole and could be involved in the catenation and decatenation reactions. The active site is formed by highly conserved amino acids, but the structural information and existing biochemical and mutagenesis data are still insufficient to assign specific roles to most of them. The presence of a groove in one side of the protein is suggestive of a single-stranded DNA (ssDNA)-binding region. CONCLUSIONS: The structure of E. coli DNA topoisomerase III resembles the structure of E. coli DNA topoisomerase I except for the presence of a positively charged loop that may be involved in catenation and decatenation. A groove on the side of the protein leads to the active site and is likely to be involved in DNA binding. The structure helps to establish the overall mechanism for the type IA subfamily of topoisomerases with greater confidence and expands the structural basis for understanding these proteins.

Selected figure(s)

Figure 5.
Figure 5. Stereo representation of the active site of E. coli DNA topoisomerase III. The mainchain of the protein is colored using the same color scheme as in Figure 1. This region contains some of the most highly conserved residues among all type IA topoisomerases. The active-site tyrosine, Tyr328, is surrounded by several acidic residues in domain I. In the open conformation, these acidic residues may serve to bind magnesium and through it ssDNA. The drawing was made with the program MolScript [38].

The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 1373-1383) copyright 1999.

Figure was selected by an automated process.