PDBsum entry 2csd

Isomerase

PDB id: 2csd

Contents

Protein chains

516 a.a.

PDB id:

2csd

Name:

Isomerase

Title:

Crystal structure of topoisomerase v (61 kda fragment)

Structure:

Topoisomerase v. Chain: a, b. Fragment: n-term 61 kda fragment. Synonym: top61. Engineered: yes

Source:

Methanopyrus kandleri. Organism_taxid: 2320. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.90Å R-factor: 0.240 R-free: 0.308

Authors:

B.Taneja,A.Patel,A.Slesarev,A.Mondragon

Key ref:

B.Taneja et al. (2006). Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerases. EMBO J, 25, 398-408. PubMed id: 16395333 DOI: 10.1038/sj.emboj.7600922

Date:

21-May-05 Release date: 31-Jan-06

Protein chains

Q977W1  (Q977W1_9EURY) -  Topoisomerase V from Methanopyrus kandleri

Seq: 984 a.a.

Struc: 516 a.a.

DOI no: 10.1038/sj.emboj.7600922

EMBO J 25:398-408 (2006)

PubMed id: 16395333

Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerases.

B.Taneja, A.Patel, A.Slesarev, A.Mondragón.

ABSTRACT

Topoisomerases are involved in controlling and maintaining the topology of DNA and are present in all kingdoms of life. Unlike all other types of topoisomerases, similar type IB enzymes have only been identified in bacteria and eukarya. The only putative type IB topoisomerase in archaea is represented by Methanopyrus kandleri topoisomerase V. Despite several common functional characteristics, topoisomerase V shows no sequence similarity to other members of the same type. The structure of the 61 kDa N-terminal fragment of topoisomerase V reveals no structural similarity to other topoisomerases. Furthermore, the structure of the active site region is different, suggesting no conservation in the cleavage and religation mechanism. Additionally, the active site is buried, indicating the need of a conformational change for activity. The presence of a topoisomerase in archaea with a unique structure suggests the evolution of a separate mechanism to alter DNA.

Selected figure(s)

Figure 2.
Figure 2 The multiHhH domain is flexible, while the topoisomerase domain is rigid. Schematic diagram showing the superposition of the two monomers in the asymmetric unit of crystal Form I. The active site residues are shown in yellow. In (A) only the multiHhH domains were used for the superposition, while in (B) the topoisomerase domains were used for the superposition. The figure illustrates the variability in the multiHhH domains (Supplementary data). For clarity, in each monomer the topoisomerase domain and the multiHhH domain are shown in different shades of the same color.

Figure 4.
Figure 4 Model for a topoisomerase domain-DNA complex. (A) Electrostatic surface representation of the topoisomerase domain. The diagram shows that the topoisomerase has a large positively charged groove in one face of the protein centered around the active site. The insets correspond to 90° views of the molecule and show that there are no additional large positively charged regions in the protein. The electrostatic potential was calculated with the program APBS (Baker et al, 2001), with a dielectric constant of 80 for the solvent and 20 for the protein. The surface is colored with a blue to red gradient from +5 to -5 K[b]T/e. (B) The diagram shows a model of the topoisomerase domain in complex with B-DNA. The coloring scheme is the same as in Figure 1. To create the model, the linker helix and the multiHhH domain were removed. DNA was docked using the HTH motif of human Pax6-paired domain-DNA complex (Xu et al, 1999), but replacing the DNA with a canonical, straight B-DNA model. No attempts were made to prevent steric clashes. In the model, the active site tyrosine is ideally placed to interact with the phosphodiester backbone and the other putative active site residues are also in the vicinity of DNA. The model suggests a potential way for topo-61 to interact with DNA, making extensive interactions.

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2006, 25, 398-408) copyright 2006.

Figures were selected by an automated process.