PDBsum entry: 1a74

Hydrolase/DNA

PDB id: 1a74

Contents

Protein chains

162 a.a.

DNA/RNA

Metals

_ZN ×4

Waters ×226

PDB id:

1a74

Name:

Hydrolase/DNA

Title:

I-ppol homing endonuclease/DNA complex

Structure:

DNA (5'- d( Tp Tp Gp Ap Cp Tp Cp Tp Cp Tp Tp Ap Ap Gp Ap Gp A p Gp Tp Cp A)-3'). Chain: c, d. Engineered: yes. Intron-encoded endonuclease i-ppoi. Chain: a, b. Synonym: intron-encoded endonuclease i-ppoi. Engineered: yes

Source:

Synthetic: yes. Physarum polycephalum. Organism_taxid: 5791. Cellular_location: nucleus. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.20Å R-factor: 0.216 R-free: 0.265

Authors:

B.L.Jurica,K.E.Flick,R.J.Monnat Junior,M.S.Stoddard

Key ref:

K.E.Flick et al. (1998). DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI. Nature, 394, 96. PubMed id: 9665136 DOI: 10.1038/27952

Date:

19-Mar-98 Release date: 22-Jun-98

Protein chains

Q94702  (PPO1_PHYPO) -  Intron-encoded endonuclease I-PpoI

Seq: 163 a.a.

Struc: 162 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: intron homing (1 term)
• Biochemical function: hydrolase activity (3 terms)

DOI no: 10.1038/27952

Nature 394:96 (1998)

PubMed id: 9665136

DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI.

K.E.Flick, M.S.Jurica, R.J.Monnat, B.L.Stoddard.

ABSTRACT

Homing endonucleases are a diverse collection of proteins that are encoded by genes with mobile, self-splicing introns. They have also been identified in self-splicing inteins (protein introns). These enzymes promote the movement of the DNA sequences that encode them from one chromosome location to another; they do this by making a site-specific double-strand break at a target site in an allele that lacks the corresponding mobile intron. The target sites recognized by these small endonucleases are generally long (14-44 base pairs). Four families of homing endonucleases have been identified, including the LAGLIDADG, the His-Cys box, the GIY-YIG and the H-N-H endonucleases. The first identified His-Cys box homing endonuclease was I-PpoI from the slime mould Physarum polycephalum. Its gene resides in one of only a few nuclear introns known to exhibit genetic mobility. Here we report the structure of the I-PpoI homing endonuclease bound to homing-site DNA determined to 1.8 A resolution. I-PpoI displays an elongated fold of dimensions 25 x 35 x 80 A, with mixed alpha/beta topology. Each I-PpoI monomer contains three antiparallel beta-sheets flanked by two long alpha-helices and a long carboxy-terminal tail, and is stabilized by two bound zinc ions 15 A apart. The enzyme possesses a new zinc-bound fold and endonuclease active site. The structure has been determined in both uncleaved substrate and cleaved product complexes.

Selected figure(s)

Figure 2.
Figure 2 Structure of the dimer interface. a, The central dimer interface is composed primarily of Van der Waals contacts between Trp 124 and 124'. This interface buries a total of less than 700 ?2 of protein surface. Lys 120 and 120' make direct contacts with thymine bases in the minor groove of the central cleavage site. b, The domain-swapped C-terminal tail (red) crosses the dimer interface at Gly 146 and proceeds across the surface of the second subunit. Each arm results in an additional 900 ?2 of buried surface area. Residues 150-153 form a short -strand interaction with residues 111'-113'. Each of the C-terminal oxygens forms a hydrogen bond with His 40. Phe 160 is also buried in this interface.

Figure 5.
Figure 5 The endonuclease DNA-binding surface. a, Schematic diagram of contacts between an endonuclease monomer and a half-homing site. Residues 61, 63, 65 and 67 are all from the same face of a single -strand and form a series of contacts down the major groove. b, The DNA-binding interactions of the I-PpoI -ribbon in a homing half-site major groove. The alternating side chains from 4 are shown.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1998, 394, 96-0) copyright 1998.

Figures were selected by an automated process.