PDBsum entry 2gaj

Isomerase

PDB id: 2gaj

Contents

Protein chains

581 a.a.

Waters ×877

References listed in PDB file

Key reference

Title

Crystal structure of full length topoisomerase i from thermotoga maritima.

Authors

G.Hansen, A.Harrenga, B.Wieland, D.Schomburg, P.Reinemer.

Ref.

J Mol Biol, 2006, 358, 1328-1340. [DOI no: 10.1016/j.jmb.2006.03.012]

PubMed id

16600296

Abstract

DNA topoisomerases are a family of enzymes altering the topology of DNA by concerted breakage and rejoining of the phosphodiester backbone of DNA. Bacterial and archeal type IA topoisomerases, including topoisomerase I, topoisomerase III, and reverse gyrase, are crucial in regulation of DNA supercoiling and maintenance of genetic stability. The crystal structure of full length topoisomerase I from Thermotoga maritima was determined at 1.7A resolution and represents an intact and fully active bacterial topoisomerase I. It reveals the torus-like structure of the conserved transesterification core domain comprising domains I-IV and a tightly associated C-terminal zinc ribbon domain (domain V) packing against domain IV of the core domain. The previously established zinc-independence of the functional activity of T.maritima topoisomerase I is further supported by its crystal structure as no zinc ion is bound to domain V. However, the structural integrity is preserved by the formation of two disulfide bridges between the four Zn-binding cysteine residues. A functional role of domain V in DNA binding and recognition is suggested and discussed in the light of the structure and previous biochemical findings. In addition, implications for bacterial topoisomerases I are provided.

Figure 1.
Figure 1. Overall structure of topoisomerase I from T. maritima. Domains are colour-coded: domain I (yellow), II (green), III (red), IV (blue) and V (purple). For simplification in domains I–IV only β-strands of more than two residues length are indicated. (a) Topology cartoon of the structure. Cysteine residues 559, 561, 578 and 580 in domain V are indicated by circles. (b) Stereo representation of the molecule. To enable easy orientation secondary structure elements are labelled according to the E. coli topoisomerase I scheme.^4 Helices are represented by letters A–R and β-sheets by numbers 1–20.

Figure 5.
Figure 5. Schematic representation of single-stranded DNA binding to T. maritima topoisomerase I. Molecular surface of the molecule showing the DNA binding region of the protein. The individual domains are coloured as in Figure 1. The broken line marks the postulated elongated interaction surface path for single-stranded DNA. The DNA occupies the binding cleft in vicinity of the active site, travels across the interface of domains I and IV and interacts with the positively charged surface of domain V.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 358, 1328-1340) copyright 2006.