PDBsum entry 1af5

Endonuclease

PDB id

1af5

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Contents

			Protein chain

					126 a.a. *

			Waters ×8

* Residue conservation analysis

PDB id:

1af5

Links

Name:

Endonuclease

Title:

Group i mobile intron endonuclease

Structure:

I-crei. Chain: a. Synonym: DNA endonuclease i-crei. Engineered: yes. Mutation: yes

Source:

Chlamydomonas reinhardtii. Organism_taxid: 3055. Organelle: chloroplast. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

3.00Å

R-factor:

0.248

R-free:

0.373

Authors:

P.J.Heath,K.M.Stephens,R.J.Monnat Junior,B.L.Stoddard

Key ref:

P.J.Heath et al. (1997). The structure of I-Crel, a group I intron-encoded homing endonuclease. Nat Struct Biol, 4, 468-476. PubMed id: 9187655

Date:

21-Mar-97

Release date:

23-Jul-97

PROCHECK

	Headers

	References

Protein chain

P05725 (DNE1_CHLRE) - DNA endonuclease I-CreI from Chlamydomonas reinhardtii

Seq: Struc:					163 a.a. 126 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

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



		Enzyme reactions

Enzyme class:

E.C.3.1.-.-

[IntEnz] [ExPASy] [KEGG] [BRENDA]

	Nat Struct Biol 4:468-476 (1997)
PubMed id: 9187655

The structure of I-Crel, a group I intron-encoded homing endonuclease.
P.J.Heath, K.M.Stephens, R.J.Monnat, B.L.Stoddard.

ABSTRACT

The structure of I-Crel provides the first view of a protein encoded by a gene within an intron. This endonuclease recognizes a long DNA site approximately 20 base pairs in length and facilitates the lateral transfer of that intron. The protein exhibits a DNA-binding surface consisting of four antiparallel beta-strands that form a 20 A wide groove which is over 70 A long. The architecture of this fold is different from that of the TATA binding protein, TBP, which also contains an antiparallel beta-saddle. The conserved LAGLIDADG motif, which is found in many mobile intron endonucleases, maturases and inteins, forms a novel helical interface and contributes essential residues to the active site.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21047873

S.Arnould, C.Delenda, S.Grizot, C.Desseaux, F.Pâques, G.H.Silva, and J.Smith (2011).
The I-CreI meganuclease and its engineered derivatives: applications from cell modification to gene therapy.

Protein Eng Des Sel, 24, 27-31.

19915993

M.J.Marcaida, I.G.Muñoz, F.J.Blanco, J.Prieto, and G.Montoya (2010).
Homing endonucleases: from basics to therapeutic applications.

Cell Mol Life Sci, 67, 727-748.

20172033

O.Thiéry, B.Börstler, K.Ineichen, and D.Redecker (2010).
Evolutionary dynamics of introns and homing endonuclease ORFs in a region of the large subunit of the mitochondrial rRNA in Glomus species (arbuscular mycorrhizal fungi, Glomeromycota).

Mol Phylogenet Evol, 55, 599-610.

18424798

C.M.Moure, F.S.Gimble, and F.A.Quiocho (2008).
Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway.

Nucleic Acids Res, 36, 3287-3296.

PDB codes:

3c0w 3c0x

17214883

F.Spyrakis, P.Cozzini, C.Bertoli, A.Marabotti, G.E.Kellogg, and A.Mozzarelli (2007).
Energetics of the protein-DNA-water interaction.

BMC Struct Biol, 7, 4.

17452357

J.Prieto, P.Redondo, D.Padró, S.Arnould, J.C.Epinat, F.Pâques, F.J.Blanco, and G.Montoya (2007).
The C-terminal loop of the homing endonuclease I-CreI is essential for site recognition, DNA binding and cleavage.

Nucleic Acids Res, 35, 3262-3271.

PDB code:

2o7m

17410205

L.Zhao, R.P.Bonocora, D.A.Shub, and B.L.Stoddard (2007).
The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif.

EMBO J, 26, 2432-2442.

PDB code:

2ost

17720189

M.Scalley-Kim, A.McConnell-Smith, and B.L.Stoddard (2007).
Coevolution of a homing endonuclease and its host target sequence.

J Mol Biol, 372, 1305-1319.

PDB code:

2qoj

17426121

P.Volná, J.Jarjour, S.Baxter, S.R.Roffler, R.J.Monnat, B.L.Stoddard, and A.M.Scharenberg (2007).
Flow cytometric analysis of DNA binding and cleavage by cell surface-displayed homing endonucleases.

Nucleic Acids Res, 35, 2748-2758.

16738662

J.Ashworth, J.J.Havranek, C.M.Duarte, D.Sussman, R.J.Monnat, B.L.Stoddard, and D.Baker (2006).
Computational redesign of endonuclease DNA binding and cleavage specificity.

Nature, 441, 656-659.

PDB code:

2fld

16456032

J.C.Samuelson, R.D.Morgan, J.S.Benner, T.E.Claus, S.L.Packard, and S.Y.Xu (2006).
Engineering a rare-cutting restriction enzyme: genetic screening and selection of NotI variants.

Nucleic Acids Res, 34, 796-805.

16698548

P.C.Spiegel, B.Chevalier, D.Sussman, M.Turmel, C.Lemieux, and B.L.Stoddard (2006).
The structure of I-CeuI homing endonuclease: Evolving asymmetric DNA recognition from a symmetric protein scaffold.

Structure, 14, 869-880.

PDB code:

2ex5

16116439

A.Longo, C.W.Leonard, G.S.Bassi, D.Berndt, J.M.Krahn, T.M.Hall, and K.M.Weeks (2005).
Evolution from DNA to RNA recognition by the bI3 LAGLIDADG maturase.

Nat Struct Mol Biol, 12, 779-787.

PDB code:

2ab5

15020462

A.Bakhrat, M.S.Jurica, B.L.Stoddard, and D.Raveh (2004).
Homology modeling and mutational analysis of Ho endonuclease of yeast.

Genetics, 166, 721-728.

15190132

G.H.Silva, and M.Belfort (2004).
Analysis of the LAGLIDADG interface of the monomeric homing endonuclease I-DmoI.

Nucleic Acids Res, 32, 3156-3168.

15189989

J.D.Wuitschick, P.R.Lindstrom, A.E.Meyer, and K.M.Karrer (2004).
Homing endonucleases encoded by germ line-limited genes in Tetrahymena thermophila have APETELA2 DNA binding domains.

Eukaryot Cell, 3, 685-694.

15280510

K.L.Posey, V.Koufopanou, A.Burt, and F.S.Gimble (2004).
Evolution of divergent DNA recognition specificities in VDE homing endonucleases from two yeast species.

Nucleic Acids Res, 32, 3947-3956.

15502310

T.Imagawa, H.Nakayama, N.Katunuma, H.Sakuraba, T.Ohshima, T.Itoh, Y.Sako, N.Nomura, and H.Tsuge (2004).
Crystallization and preliminary X-ray diffraction analysis of homing endonuclease I-Tsp061I.

Acta Crystallogr D Biol Crystallogr, 60, 2006-2008.

12771221

J.C.Epinat, S.Arnould, P.Chames, P.Rochaix, D.Desfontaines, C.Puzin, A.Patin, A.Zanghellini, F.Pâques, and E.Lacroix (2003).
A novel engineered meganuclease induces homologous recombination in yeast and mammalian cells.

Nucleic Acids Res, 31, 2952-2962.

14633971

J.M.Bolduc, P.C.Spiegel, P.Chatterjee, K.L.Brady, M.E.Downing, M.G.Caprara, R.B.Waring, and B.L.Stoddard (2003).
Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor.

Genes Dev, 17, 2875-2888.

PDB code:

1p8k

12654010

W.J.Geese, Y.K.Kwon, X.Wen, and R.B.Waring (2003).
In vitro analysis of the relationship between endonuclease and maturase activities in the bi-functional group I intron-encoded protein, I-AniI.

Eur J Biochem, 270, 1543-1554.

11729187

A.J.Bath, S.E.Milsom, N.A.Gormley, and S.E.Halford (2002).
Many type IIs restriction endonucleases interact with two recognition sites before cleaving DNA.

J Biol Chem, 277, 4024-4033.

12419232

B.S.Chevalier, T.Kortemme, M.S.Chadsey, D.Baker, R.J.Monnat, and B.L.Stoddard (2002).
Design, activity, and structure of a highly specific artificial endonuclease.

Mol Cell, 10, 895-905.

PDB code:

1mow

12219083

C.M.Moure, F.S.Gimble, and F.A.Quiocho (2002).
Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence.

Nat Struct Biol, 9, 764-770.

PDB codes:

1lws 1lwt

12235380

E.Werner, W.Wende, A.Pingoud, and U.Heinemann (2002).
High resolution crystal structure of domain I of the Saccharomyces cerevisiae homing endonuclease PI-SceI.

Nucleic Acids Res, 30, 3962-3971.

PDB code:

1gpp

11897024

L.M.Iyer, E.V.Koonin, and L.Aravind (2002).
Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors.

Genome Biol, 3, RESEARCH0012.

12202772

L.M.Seligman, K.M.Chisholm, B.S.Chevalier, M.S.Chadsey, S.T.Edwards, J.H.Savage, and A.L.Veillet (2002).
Mutations altering the cleavage specificity of a homing endonuclease.

Nucleic Acids Res, 30, 3870-3879.

12239210

L.Thion, E.Laurine, M.Erard, O.Burlet-Schiltz, B.Monsarrat, J.M.Masson, and I.Saves (2002).
The two-step cleavage activity of PI-TfuI intein endonuclease demonstrated by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

J Biol Chem, 277, 45442-45450.

11850426

N.Guhan, and K.Muniyappa (2002).
Mycobacterium tuberculosis RecA intein possesses a novel ATP-dependent site-specific double-stranded DNA endonuclease activity.

J Biol Chem, 277, 16257-16264.

12379841

P.Van Roey, L.Meehan, J.C.Kowalski, M.Belfort, and V.Derbyshire (2002).
Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI.

Nat Struct Biol, 9, 806-811.

PDB codes:

1ln0 1mk0

11600710

F.S.Gimble (2001).
Degeneration of a homing endonuclease and its target sequence in a wild yeast strain.

Nucleic Acids Res, 29, 4215-4223.

11344334

J.M.Bujnicki, and L.Rychlewski (2001).
Unusual evolutionary history of the tRNA splicing endonuclease EndA: relationship to the LAGLIDADG and PD-(D/E)XK deoxyribonucleases.

Protein Sci, 10, 656-660.

11160929

P.Lucas, C.Otis, J.P.Mercier, M.Turmel, and C.Lemieux (2001).
Rapid evolution of the DNA-binding site in LAGLIDADG homing endonucleases.

Nucleic Acids Res, 29, 960-969.

10666469

C.Monteilhet, D.Dziadkowiec, T.Szczepanek, and J.Lazowska (2000).
Purification and characterization of the DNA cleavage and recognition site of I-ScaI mitochondrial group I intron encoded endonuclease produced in Escherichia coli.

Nucleic Acids Res, 28, 1245-1251.

10644733

D.Hu, M.Crist, X.Duan, F.A.Quiocho, and F.S.Gimble (2000).
Probing the structure of the PI-SceI-DNA complex by affinity cleavage and affinity photocross-linking.

J Biol Chem, 275, 2705-2712.

PDB code:

1dfa

10754232

F.S.Gimble (2000).
Invasion of a multitude of genetic niches by mobile endonuclease genes.

FEMS Microbiol Lett, 185, 99.

10944393

H.Ponstingl, K.Henrick, and J.M.Thornton (2000).
Discriminating between homodimeric and monomeric proteins in the crystalline state.

Proteins, 41, 47-57.

11142386

S.B.Rho, and S.A.Martinis (2000).
The bI4 group I intron binds directly to both its protein splicing partners, a tRNA synthetase and maturase, to facilitate RNA splicing activity.

RNA, 6, 1882-1894.

11123916

S.Schöttler, W.Wende, V.Pingoud, and A.Pingoud (2000).
Identification of Asp218 and Asp326 as the principal Mg2+ binding ligands of the homing endonuclease PI-SceI.

Biochemistry, 39, 15895-15900.

10601013

F.Christ, S.Schoettler, W.Wende, S.Steuer, A.Pingoud, and V.Pingoud (1999).
The monomeric homing endonuclease PI-SceI has two catalytic centres for cleavage of the two strands of its DNA substrate.

EMBO J, 18, 6908-6916.

10438738

K.D.Everett, S.Kahane, R.M.Bush, and M.G.Friedman (1999).
An unspliced group I intron in 23S rRNA links Chlamydiales, chloroplasts, and mitochondria.

J Bacteriol, 181, 4734-4740.

10187809

V.Pingoud, H.Thole, F.Christ, W.Grindl, W.Wende, and A.Pingoud (1999).
Photocross-linking of the homing endonuclease PI-SceI to its recognition sequence.

J Biol Chem, 274, 10235-10243.

9519292

A.K.Aggarwal, and D.A.Wah (1998).
Novel site-specific DNA endonucleases.

Curr Opin Struct Biol, 8, 19-25.

9804821

F.S.Gimble, X.Duan, D.Hu, and F.A.Quiocho (1998).
Identification of Lys-403 in the PI-SceI homing endonuclease as part of a symmetric catalytic center.

J Biol Chem, 273, 30524-30529.

9609720

V.Pingoud, W.Grindl, W.Wende, H.Thole, and A.Pingoud (1998).
Structural and functional analysis of the homing endonuclease PI-sceI by limited proteolytic cleavage and molecular cloning of partial digestion products.

Biochemistry, 37, 8233-8243.

9518476

W.Grindl, W.Wende, V.Pingoud, and A.Pingoud (1998).
The protein splicing domain of the homing endonuclease PI-sceI is responsible for specific DNA binding.

Nucleic Acids Res, 26, 1857-1862.

9468518

Z.He, M.Crist, H.Yen, X.Duan, F.A.Quiocho, and F.S.Gimble (1998).
Amino acid residues in both the protein splicing and endonuclease domains of the PI-SceI intein mediate DNA binding.

J Biol Chem, 273, 4607-4615.

9358175

J.Z.Dalgaard, A.J.Klar, M.J.Moser, W.R.Holley, A.Chatterjee, and I.S.Mian (1997).
Statistical modeling and analysis of the LAGLIDADG family of site-specific endonucleases and identification of an intein that encodes a site-specific endonuclease of the HNH family.

Nucleic Acids Res, 25, 4626-4638.

9416623

K.E.Flick, D.McHugh, J.D.Heath, K.M.Stephens, R.J.Monnat, and B.L.Stoddard (1997).
Crystallization and preliminary X-ray studies of I-PpoI: a nuclear, intron-encoded homing endonuclease from Physarum polycephalum.

Protein Sci, 6, 2677-2680.

9409828

L.M.Seligman, K.M.Stephens, J.H.Savage, and R.J.Monnat (1997).
Genetic analysis of the Chlamydomonas reinhardtii I-CreI mobile intron homing system in Escherichia coli.

Genetics, 147, 1653-1664.

9254693

M.Belfort, and R.J.Roberts (1997).
Homing endonucleases: keeping the house in order.

Nucleic Acids Res, 25, 3379-3388.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.