PDBsum entry: 1mk0

Hydrolase

PDB id: 1mk0

Contents

Protein chain

97 a.a. *

Ligands

CIT

BME

Waters ×189

* Residue conservation analysis

PDB id:

1mk0

Name:

Hydrolase

Title:

Catalytic domain of intron endonuclease i-tevi, e75a mutant

Structure:

Intron-associated endonuclease 1. Chain: a. Fragment: catalytic domain (residues 1 to 97). Synonym: i-tevi, irf protein. Engineered: yes. Mutation: yes

Source:

Enterobacteria phage t4. Organism_taxid: 10665. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.60Å R-factor: 0.197 R-free: 0.216

Authors:

P.Van Roey,L.Meehan,J.C.Kowalski,M.Belfort,V.Derbyshire

Key ref:

P.Van Roey et al. (2002). Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI. Nat Struct Biol, 9, 806-811. PubMed id: 12379841 DOI: 10.1038/nsb853

Date:

28-Aug-02 Release date: 30-Oct-02

Protein chain

P13299  (TEV1_BPT4) -  Intron-associated endonuclease 1

Seq: 245 a.a.

Struc: 97 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• Cellular component: intracellular (1 term)
• Biological process: DNA repair (1 term)
• Biochemical function: nuclease activity (1 term)

DOI no: 10.1038/nsb853

Nat Struct Biol 9:806-811 (2002)

PubMed id: 12379841

Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI.

P.Van Roey, L.Meehan, J.C.Kowalski, M.Belfort, V.Derbyshire.

ABSTRACT

I-TevI, a member of the GIY-YIG family of homing endonucleases, consists of an N-terminal catalytic domain and a C-terminal DNA-binding domain joined by a flexible linker. The GIY-YIG motif is in the N-terminal domain of I-TevI, which corresponds to a phylogenetically widespread catalytic cartridge that is often associated with mobile genetic elements. The crystal structure of the catalytic domain of I-TevI, the first of any GIY-YIG endonuclease, reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked by three helices. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site. Similarities in the three-dimensional arrangement of the catalytically important residues and the cation-binding site with those of the His-Cys box endonuclease I-PpoI suggest the possibility of mechanistic relationships among these different families of homing endonucleases despite completely different folds.

Selected figure(s)

Figure 3.
Figure 3. Substrate interaction surface. a, Stereo view of the interaction between the loop joining -helices 1 and 2 (right), the C-terminal loop (left) and -strand 2 (top). The hydrogen bonds (blue dotted lines) between the side chains of Ser 42 and Lys 44 on one side and the main chain carbonyls of Lys 85, Gly 88, Tyr 89 and Asn 90 on the opposite side and the hydrophobic interactions between Leu 45, Tyr 17 and Tyr 89 result in a tight association of the two sides of the molecule. In addition, hydrogen bonds from Asn 90 to the main chain nitrogen and carbonyl of Val 18 on -strand 2 tie the C-terminal loop onto the surface. b, Stereo view of the cluster of basic residues, Arg 30, Arg 27, His 31 and His 40. The final (2F[o] - F[c]) electron density map, contoured at 1.5 , for these residues is shown. c, Stereo view of the residues at the center of the substrate interaction surface, showing all hydrogen bonds in the area as blue dotted lines. The distances between the highly conserved and putative catalytic residues are shown as red dotted lines.

Figure 4.
Figure 4. Structural correspondence between I-TevI and I-PpoI. a, Superposition of the three putative catalytic residues of I-TevI (green) onto those of I-PpoI (orange) showing the similar locations of the divalent cations (Mn^2+ in I-TevI, magenta, and Mg^2+ in I-PpoI, cyan). The superposition was produced by least-squares fitting of the C atoms of the three residue pairs. b, Superposition of the catalytic domain of I-TevI (green) onto the DNA complex of I-PpoI (orange), with the DNA shown as a magenta double helix. The side chains of the I-TevI residues are yellow and those of I-PpoI are cyan. The superposition was produced by overlapping helix 1 of I-TevI onto the Asn 119-containing helix of I-PpoI (lower right), located in the minor groove. This highlights the dramatically different folds adopted by these enzymes, including the addition of a three-stranded -sheet (upper left) in I-PpoI that is inserted in the major groove and contains Arg 61. In this alignment, Asn 119/Glu 75 (I-PpoI/I-TevI numbering) and His 98/Tyr 17 superimpose well, but Arg 61/Arg 27 are widely separated.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2002, 9, 806-811) copyright 2002.

Figures were selected by an automated process.