PDBsum entry 1cy9

Isomerase

PDB id: 1cy9

Contents

Protein chains

245 a.a. *

Waters ×509

* Residue conservation analysis

PDB id:

1cy9

Name:

Isomerase

Title:

Crystal structure of the 30 kda fragment of e. Coli DNA topoisomerase i. Monoclinic form

Structure:

DNA topoisomerase i. Chain: a, b. Fragment: 30 kda fragment comprising domains ii and iii. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k12. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.80Å R-factor: 0.205 R-free: 0.242

Authors:

H.Feinberg,C.Lima,A.Mondragon

Key ref:

H.Feinberg et al. (1999). Conformational changes in E. coli DNA topoisomerase I. Nat Struct Biol, 6, 918-922. PubMed id: 10504724 DOI: 10.1038/13283

Date:

31-Aug-99 Release date: 08-Mar-00

Protein chains

P06612  (TOP1_ECOLI) -  DNA topoisomerase 1 from Escherichia coli (strain K12)

Seq: 865 a.a.

Struc: 245 a.a.

Enzyme reactions

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

DOI no: 10.1038/13283

Nat Struct Biol 6:918-922 (1999)

PubMed id: 10504724

Conformational changes in E. coli DNA topoisomerase I.

H.Feinberg, C.D.Lima, A.Mondragón.

ABSTRACT

DNA topoisomerases are the enzymes responsible for maintaining the topological states of DNA. In order to change the topology of DNA, topoisomerases pass one or two DNA strands through transient single or double strand breaks in the DNA phosphodiester backbone. It has been proposed that both type IA and type II enzymes change conformation dramatically during the reaction cycle in order to accomplish these transformations. In the case of Escherichia coli DNA topoisomerase I, it has been suggested that a 30 kDa fragment moves away from the rest of the protein to create an entrance into the central hole in the protein. Structures of the 30 kDa fragment reveal that indeed this fragment can change conformation significantly. The fragment is composed of two domains, and while the domains themselves remain largely unchanged, their relative arrangement can change dramatically.

Selected figure(s)

Figure 2.
Figure 2. Stereo view of the structure of the 30 kDa fragment of E. coli DNA topoisomerase I. Two clearly different conformations of the 30 kDa fragment were observed. a, The structure of monomer A in the monoclinic crystal form, and b, the structure of monomer C in the hexagonal crystal form. The orientation of domain II is made identical in both panels to emphasize the large difference in conformation for the two monomers. Domain II is shown in red and domain III is in pink. Tyr 319, the active site tyrosine, and Arg 321 are shown in black. The loop comprising residues 358−364 is only ordered in monomer C and is shown in blue. Drawings were prepared using MOLSCRIPT^13.

Figure 3.
Figure 3. Stereo views of the active site region. a, Domain III of monomer C was superimposed on domain III of the 67 kDa fragment to illustrate the changes around Tyr 319. The structure of the 67 kDa fragment is colored by atom type; monomer C is colored green. Arg 321 is unable to interact with Tyr 319 in the 67 kDa fragment, as it forms hydrogen bonds to the acidic residues in domain I, but the arginine residue has moved in the 30 kDa fragment, and the side chain guanidinium group makes hydrogen bonds to the active site tyrosine. This suggests that Arg 321 could play a role in stabilizing an activated tyrosine. Water molecules were not drawn for clarity. This diagram was prepared using MOLSCRIPT^13 and RASTER3D^14, ^15. b, Electron density maps showing the active site region in the hexagonal crystal form. The 2F[o] - F[c] map is colored in cyan and is contoured at the 1.5 level, while the F[o] - F[c] map is colored in magenta and is contoured at the +3 level. The difference map clearly shows the presence of a second conformation for Arg 321. c, Electron density map showing the active site region in the monoclinic crystal form. The 2F[o] - F[c] map is colored in cyan and is contoured at the 1.5 level. Maps (b) and (c) were prepared using BOBSCRIPT^16 and RASTER3D^14, ^15.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 918-922) copyright 1999.

Figures were selected by an automated process.