PDBsum entry 2f5g

Gene regulation

PDB id: 2f5g

Contents

Protein chains

130 a.a. *

Waters ×308

* Residue conservation analysis

PDB id:

2f5g

Name:

Gene regulation

Title:

Crystal structure of is200 transposase

Structure:

Transposase, putative. Chain: a, b. Synonym: is200 transposase. Engineered: yes

Source:

Sulfolobus solfataricus. Organism_taxid: 2287. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.70Å R-factor: 0.213 R-free: 0.225

Authors:

H.H.Lee,J.Y.Yoon,H.S.Kim,J.Y.Kang,K.H.Kim,D.J.Kim,S.W.Suh

Key ref:

H.H.Lee et al. (2006). Crystal structure of a metal ion-bound IS200 transposase. J Biol Chem, 281, 4261-4266. PubMed id: 16340015 DOI: 10.1074/jbc.M511567200

Date:

25-Nov-05 Release date: 13-Dec-05

Protein chains

Q97Y68  (Q97Y68_SULSO) -  Transposase, putative from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Seq: 133 a.a.

Struc: 130 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1074/jbc.M511567200

J Biol Chem 281:4261-4266 (2006)

PubMed id: 16340015

Crystal structure of a metal ion-bound IS200 transposase.

H.H.Lee, J.Y.Yoon, H.S.Kim, J.Y.Kang, K.H.Kim, D.J.Kim, J.Y.Ha, B.Mikami, H.J.Yoon, S.W.Suh.

ABSTRACT

IS200 transposases, present in many bacteria and Archaea, appear to be distinct from other groups of transposases. To provide a structural basis for understanding the action of IS200 transposases, we have determined the crystal structure of the SSO1474 protein from Sulfolobus solfataricus, a member of the IS200 family, in both Mn(2+)-bound and Mn(2+)-free forms. Its monomer fold is distinct from other classes of structurally characterized transposases. Two monomers form a tight dimer by exchanging the C-terminal alpha-helix and by merging the two central beta-sheets into a large beta-sheet. Glu(55), His(62), and four water molecules provide the direct coordination sphere of the catalytically essential metal ion in the Mn(2+)-bound structure. His(16), Asp(59), and His(60) also play important roles in maintaining the metal binding site. The catalytic site is formed at the interface between monomers. The candidate nucleophile in the transposition mechanism, strictly conserved Tyr(121) coming from the other monomer, is turned away from the active site, suggesting that a conformational change is likely to occur during the catalytic cycle.

Selected figure(s)

Figure 3.
A close-up view of a metal ion binding by the HUH motif. A, 2F[o] - F[c] electron density map around the Mn^2+ binding site. Residues near the HUH motif (His^60 and His^62) are shown in sticks. Octahedral coordination of Mn^2+ is represented by black dotted lines, whereas blue dotted lines denote hydrogen bonds. Red balls represent water molecules. B, superposition of the Mn^2+-bound (orange sticks) and Mn^2+-free (cyan sticks) S. solfataricus transposase structures. Black dotted lines indicate Mn^2+ coordination, whereas green dotted lines denote hydrogen bonds. C, superposition of the Mn^2+-bound S. solfataricus transposase (orange sticks) and Mn^2+-free structure of the H. pylori IS608 transposase (green sticks). Black dotted lines denote Mn^2+ coordination and blue dotted lines, hydrogen bonds. D, binding of a divalent metal ion by the HUH motif in other proteins. Black dotted lines denote Mn^2+ coordination and hydrogen bonds.

Figure 4.
A surface view of a dimer and DNA binding model of S. solfataricus transposase. A, the electrostatic potential at the molecular surface of a dimer of S. solfataricus transposase is shown (blue, positive; red, negative). B, stem-loop DNA binding to S. solfataricus transposase modeled by superposition of S. solfataricus transposase (Mn^2+-free, blue) and the H. pylori IS608 transposase (PDB code 2A6O, orange).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 4261-4266) copyright 2006.

Figures were selected by an automated process.