PDBsum entry 1vcc

DNA binding

PDB id: 1vcc

Contents

Protein chain

77 a.a. *

Waters ×62

* Residue conservation analysis

PDB id:

1vcc

Name:

DNA binding

Title:

Amino terminal 9kda domain of vaccinia virus DNA topoisomerase i residues 1-77, experimental electron density for residues 1-77

Structure:

DNA topoisomerase i. Chain: a. Fragment: amino terminal 9kda, residues 1 - 77. Engineered: yes. Other_details: domain generated by mild proteolysis of the intact 36kda vaccinia virus DNA topoisomerase i, a member of the eukaryotic- like type i DNA topoisomerases

Source:

Vaccinia virus. Organism_taxid: 10254. Strain: wr. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: active form

Resolution:

1.60Å R-factor: 0.218 R-free: 0.287

Authors:

A.Sharma,R.Hanai,A.Mondragon

Key ref:

A.Sharma et al. (1994). Crystal structure of the amino-terminal fragment of vaccinia virus DNA topoisomerase I at 1.6 A resolution. Structure, 2, 767-777. PubMed id: 7994576 DOI: 10.1016/S0969-2126(94)00077-8

Date:

02-Oct-95 Release date: 08-Mar-96

Protein chain

P68698  (TOP1_VACCW) -  DNA topoisomerase 1B from Vaccinia virus (strain Western Reserve)

Seq: 314 a.a.

Struc: 77 a.a.

Enzyme reactions

• Enzyme class: E.C.5.6.2.1 - Dna topoisomerase.

DOI no: 10.1016/S0969-2126(94)00077-8

Structure 2:767-777 (1994)

PubMed id: 7994576

Crystal structure of the amino-terminal fragment of vaccinia virus DNA topoisomerase I at 1.6 A resolution.

A.Sharma, R.Hanai, A.Mondragón.

ABSTRACT

BACKGROUND: Vaccinia virus, a cytoplasmically-replicating poxvirus, encodes a type I DNA topoisomerase that is biochemically similar to eukaryotic-like DNA topoisomerases I, and which has been widely studied as a model topoisomerase. It is the smallest topoisomerase known and is unusual in that it is resistant to the potent chemotherapeutic agent camptothecin. RESULTS: The crystal structure of a 9 kDa amino-terminal fragment of vaccinia virus DNA topoisomerase I has been determined at 1.6 A resolution. The fragment forms a five-stranded, antiparallel beta-sheet with two short alpha-helices and connecting loops. Residues that are conserved between all eukaryotic-like type I topoisomerases are not clustered in particular regions of the structure. CONCLUSIONS: This is the first atomic structure of any region of a eukaryotic-like DNA topoisomerase I. It has provided insights into the structural bases of the phenotypes of some single-site mutants of the intact topoisomerase. The structure has enabled us to study the interactions within a well-folded protein fragment and the camptothecin resistance of the viral topoisomerase.

Selected figure(s)

Figure 2.
Figure 2. Electron density maps of vaccinia virus DNA topoisomerase I. (a) The original MIRAS map to 2.8 å used for tracing the amino-terminal fragment. The map is contoured at 1.0 σ. (b) 2F[o]– F[c] map at 1.6 å resolution of the cryo-cooled protein model, contoured at 1.2σ. Figure 2. Electron density maps of vaccinia virus DNA topoisomerase I. (a) The original MIRAS map to 2.8 å used for tracing the amino-terminal fragment. The map is contoured at 1.0 σ. (b) 2F[o]– F[c] map at 1.6 å resolution of the cryo-cooled protein model, contoured at 1.2σ.

Figure 4.
Figure 4. Stereo view of the hydrophobic core in the amino terminal fragment of vaccinia virus DNA topoisomerase I. The ribbon diagram is shown in blue. All hydrophobic residues are colored yellow, and hydrophilic residues in orange. The view is looking down the core with the sheet on the right and the helices on the left bottom. Figure 4. Stereo view of the hydrophobic core in the amino terminal fragment of vaccinia virus DNA topoisomerase I. The ribbon diagram is shown in blue. All hydrophobic residues are colored yellow, and hydrophilic residues in orange. The view is looking down the core with the sheet on the right and the helices on the left bottom.

The above figures are reprinted by permission from Cell Press: Structure (1994, 2, 767-777) copyright 1994.

Figures were selected by an automated process.