High resolution crystal structure of domain I of the Saccharomyces cerevisiae homing endonuclease PI-SceI.

The homing endonuclease PI-SceI from Saccharo myces cerevisiae consists of two domains. The protein splicing domain I catalyzes the excision of the mature endonuclease (intein) from a precursor protein and the religation of the flanking amino acid sequences (exteins) to a functional protein. Furthermore, domain I is involved in binding and recognition of the specific DNA substrate. Domain II of PI-SceI, the endonuclease domain, which is structurally homologous to other homing endonucleases from the LAGLIDADG family, harbors the endonucleolytic center of PI-SceI, which in vivo initiates the homing process by introducing a double-strand cut in the approximately 35 bp recognition sequence. At 1.35 A resolution, the crystal structure of PI-SceI domain I provides a detailed view of the part of the protein that is responsible for tight and specific DNA binding. A geometry-based docking of the 75 degrees bent recognition sequence to the full-length protein implies a conformational change or hinge movement of a subdomain of domain I, the tongs part, that is predicted to reach into the major groove near base pairs +16 to +18.

[1]  A. Pingoud,et al.  A Mutational Analysis of DNA Binding and Cleavage by the Homing Endonuclease PI-SceI , 2000, Molecular Biology.

[2]  Y. Anraku,et al.  Protein-splicing reaction via a thiazolidine intermediate: crystal structure of the VMA1-derived endonuclease bearing the N and C-terminal propeptides. , 2002, Journal of molecular biology.

[3]  F. S. Gimble.  Degeneration of a homing endonuclease and its target sequence in a wild yeast strain. , 2001, Nucleic acids research.

[4]  B. Stoddard,et al.  Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility. , 2001, Nucleic acids research.

[5]  H. Paulus,et al.  Reversible Inhibition of Protein Splicing by Zinc Ion* , 2001, The Journal of Biological Chemistry.

[6]  M. Weiss,et al.  Global Indicators of X-ray Data Quality , 2000 .

[7]  K Morikawa,et al.  Crystal structure of an archaeal intein-encoded homing endonuclease PI-PfuI. , 2000, Journal of molecular biology.

[8]  A. Pingoud,et al.  A model for the PI-SceIxDNA complex based on multiple base and phosphate backbone-specific photocross-links. , 2000, Journal of molecular biology.

[9]  F A Quiocho,et al.  Structural Insights into the Protein Splicing Mechanism of PI-SceI* , 2000, The Journal of Biological Chemistry.

[10]  Noren,et al.  Dissecting the Chemistry of Protein Splicing and Its Applications. , 2000, Angewandte Chemie.

[11]  F. Quiocho,et al.  Probing the Structure of the PI-SceI-DNA Complex by Affinity Cleavage and Affinity Photocross-linking* , 2000, The Journal of Biological Chemistry.

[12]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 , 2000, Nucleic Acids Res..

[13]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[14]  A. Pingoud,et al.  The monomeric homing endonuclease PI‐SceI has two catalytic centres for cleavage of the two strands of its DNA substrate , 1999, The EMBO journal.

[15]  M. Crist,et al.  Mapping of a DNA binding region of the PI-sceI homing endonuclease by affinity cleavage and alanine-scanning mutagenesis. , 1999, Biochemistry.

[16]  B. Stoddard,et al.  Homing endonucleases: structure, function and evolution , 1999, Cellular and Molecular Life Sciences CMLS.

[17]  A. Pingoud,et al.  Photocross-linking of the Homing Endonuclease PI-SceI to Its Recognition Sequence* , 1999, The Journal of Biological Chemistry.

[18]  B. Stoddard,et al.  DNA recognition and cleavage by the LAGLIDADG homing endonuclease I-CreI. , 1998, Molecular cell.

[19]  Barry L. Stoddard,et al.  DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI , 1998, Nature.

[20]  A. Pingoud,et al.  Structural and functional analysis of the homing endonuclease PI-sceI by limited proteolytic cleavage and molecular cloning of partial digestion products. , 1998, Biochemistry.

[21]  A. Pingoud,et al.  The protein splicing domain of the homing endonuclease PI-sceI is responsible for specific DNA binding. , 1998, Nucleic acids research.

[22]  F. Quiocho,et al.  Amino Acid Residues in Both the Protein Splicing and Endonuclease Domains of the PI-SceI Intein Mediate DNA Binding* , 1998, The Journal of Biological Chemistry.

[23]  Amalio Telenti,et al.  Crystal structure of GyrA intein from Mycobacterium xenopi reveals structural basis of protein splicing , 1998, Nature Structural Biology.

[24]  E. Koonin,et al.  Crystal Structure of a Hedgehog Autoprocessing Domain: Homology between Hedgehog and Self-Splicing Proteins , 1997, Cell.

[25]  R J Roberts,et al.  Homing endonucleases: keeping the house in order. , 1997, Nucleic acids research.

[26]  David C. Jones,et al.  CATH--a hierarchic classification of protein domain structures. , 1997, Structure.

[27]  B. Stoddard,et al.  The structure of I-Crel, a Group I intron-encoded homing endonuclease , 1997, Nature Structural Biology.

[28]  F. Quiocho,et al.  Crystal Structure of PI-SceI, a Homing Endonuclease with Protein Splicing Activity , 1997, Cell.

[29]  Z. Otwinowski,et al.  Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[30]  N. Guex,et al.  SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling , 1997, Electrophoresis.

[31]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence data bank and its supplement TrEMBL , 1997, Nucleic Acids Res..

[32]  A. Pingoud,et al.  Binding, bending and cleavage of DNA substrates by the homing endonuclease Pl-SceI. , 1996, Nucleic acids research.

[33]  J. Wang,et al.  Substrate recognition and induced DNA distortion by the PI-SceI endonuclease, an enzyme generated by protein splicing. , 1996, Journal of molecular biology.

[34]  T. Koch,et al.  Mechanistic Studies of the 5-Iodouracil Chromophore Relevant to Its Use in Nucleoprotein Photo-Cross-Linking , 1996 .

[35]  M. Billeter,et al.  MOLMOL: a program for display and analysis of macromolecular structures. , 1996, Journal of molecular graphics.

[36]  C. S. Tung,et al.  NAMOT2 - a redesigned nucleic acid modeling tool: construction of non-canonical DNA structures , 1996, Comput. Appl. Biosci..

[37]  J. Thornton,et al.  PROMOTIF—A program to identify and analyze structural motifs in proteins , 1996, Protein science : a publication of the Protein Society.

[38]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[39]  Frederick S. Gimble,et al.  Substitutions in Conserved Dodecapeptide Motifs That Uncouple the DNA Binding and DNA Cleavage Activities of PI-SceI Endonuclease (*) , 1995, The Journal of Biological Chemistry.

[40]  H. Nash,et al.  Specific photocrosslinking of DNA-protein complexes: identification of contacts between integration host factor and its target DNA. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[41]  Collaborative Computational,et al.  The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

[42]  J. Navaza,et al.  AMoRe: an automated package for molecular replacement , 1994 .

[43]  J. Thorner,et al.  Purification and characterization of VDE, a site-specific endonuclease from the yeast Saccharomyces cerevisiae. , 1993, The Journal of biological chemistry.

[44]  C. Sander,et al.  Protein structure comparison by alignment of distance matrices. , 1993, Journal of molecular biology.

[45]  M. Belfort,et al.  4 Homing Endonucleases , 1993 .

[46]  M. Belfort,et al.  Introns as mobile genetic elements. , 1993, Annual review of biochemistry.

[47]  V S Lamzin,et al.  Automated refinement of protein models. , 1993, Acta crystallographica. Section D, Biological crystallography.

[48]  J. Thorner,et al.  Homing of a DNA endonuclease gene by meiotic gene conversion in Saccharomyces cerevisiae , 1992, Nature.

[49]  Sung-Hou Kim,et al.  Sparse matrix sampling: a screening method for crystallization of proteins , 1991 .

[50]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.