Domain Swapping in Allosteric Modulation of DNA Specificity

The structure of two DNA-bound SgrAI enzyme dimers is presented, along with mutagenesis experiments supporting a role for this structure in polymer formation and the activation of DNA cleavage by SgrAI.

[1]  S. Moore,et al.  On the aggregation of bovine pancreatic ribonuclease. , 1962, Archives of biochemistry and biophysics.

[2]  G. Fasman.  CRC Handbook of Biochemistry and Molecular Biology , 1975 .

[3]  W. Kabsch.  A solution for the best rotation to relate two sets of vectors , 1976 .

[4]  G. D'alessio,et al.  Co-operativity in seminal ribonuclease function. Kinetic studies. , 1987, The Biochemical journal.

[5]  G. Teebor,et al.  Purification and characterization of 5-hydroxymethyluracil-DNA glycosylase from calf thymus. Its possible role in the maintenance of methylated cytosine residues. , 1989, The Journal of biological chemistry.

[6]  A. Aggarwal.  Crystallization of DNA binding proteins with oligodeoxynucleotides. , 1990, Methods.

[7]  N. Tautz,et al.  SgrAI, a novel class-II restriction endonuclease from Streptomyces griseus recognizing the octanucleotide sequence 5'-CR/CCGGYG-3' [corrected]. , 1990, Nucleic acids research.

[8]  N. Tautz,et al.  SgrAl, a novel class-II restriction endonuclease from Streptomyces griseus recognizing the octanucleotide sequence 5′-CR/CCGGYG-3′ , 1990 .

[9]  G. D'alessio,et al.  The antitumor action of seminal ribonuclease and its quaternary conformations , 1995, FEBS letters.

[10]  D Eisenberg,et al.  3D domain swapping: A mechanism for oligomer assembly , 1995, Protein science : a publication of the Protein Society.

[11]  M. Bertoldi,et al.  The activity on double-stranded RNA of aggregates of ribonuclease A higher than dimers increases as a function of the size of the aggregates. , 1996, The Biochemical journal.

[12]  M. Bowman,et al.  Crystal structure of the complex of diphtheria toxin with an extracellular fragment of its receptor. , 1997, Molecular cell.

[13]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[14]  D Eisenberg,et al.  The crystal structure of a 3D domain-swapped dimer of RNase A at a 2.1-A resolution. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[15]  C Urbanke,et al.  The Cfr10I restriction enzyme is functional as a tetramer. , 1999, Journal of molecular biology.

[16]  D E McRee,et al.  XtalView/Xfit--A versatile program for manipulating atomic coordinates and electron density. , 1999, Journal of structural biology.

[17]  K. Wilson,et al.  Efficient anisotropic refinement of macromolecular structures using FFT. , 1999, Acta crystallographica. Section D, Biological crystallography.

[18]  S. Halford,et al.  Reactions of Type II Restriction Endonucleases with 8-Base Pair Recognition Sites* , 1999, The Journal of Biological Chemistry.

[19]  M. Bertoldi,et al.  Structural versatility of bovine ribonuclease A. Distinct conformers of trimeric and tetrameric aggregates of the enzyme. , 1999, European journal of biochemistry.

[20]  R. Huber,et al.  Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA , 2000, Nature Structural Biology.

[21]  R. Raines,et al.  Dimer formation by a “monomeric” protein , 2000, Protein science : a publication of the Protein Society.

[22]  A. Pingoud,et al.  Sau3AI, a Monomeric Type II Restriction Endonuclease That Dimerizes on the DNA and Thereby Induces DNA Loops* , 2001, The Journal of Biological Chemistry.

[23]  B. Connolly,et al.  Binding and recognition of GATATC target sequences by the EcoRV restriction endonuclease: a study using fluorescent oligonucleotides and fluorescence polarization. , 2001, Biochemistry.

[24]  David Eisenberg,et al.  A domain-swapped RNase A dimer with implications for amyloid formation , 2001, Nature Structural Biology.

[25]  R J Read,et al.  Pushing the boundaries of molecular replacement with maximum likelihood. , 2003, Acta crystallographica. Section D, Biological crystallography.

[26]  A. Jeltsch,et al.  Structure and function of type II restriction endonucleases. , 2001, Nucleic acids research.

[27]  David Eisenberg,et al.  3D domain swapping: As domains continue to swap , 2002, Protein science : a publication of the Protein Society.

[28]  J. Bitinaite,et al.  Self-generated DNA termini relax the specificity of SgrAI restriction endonuclease , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[29]  D. Eisenberg,et al.  Structures of the two 3D domain‐swapped RNase A trimers , 2002, Protein science : a publication of the Protein Society.

[30]  Randy J Read,et al.  Electronic Reprint Biological Crystallography Phenix: Building New Software for Automated Crystallographic Structure Determination Biological Crystallography Phenix: Building New Software for Automated Crystallographic Structure Determination , 2022 .

[31]  Laurence H. Pearl,et al.  Structural basis for uracil recognition by archaeal family B DNA polymerases , 2002, Nature Structural Biology.

[32]  S. Halford,et al.  Subunit assembly for DNA cleavage by restriction endonuclease SgrAI. , 2003, Journal of molecular biology.

[33]  J. Bitinaite,et al.  Kinetic Analysis of the Coordinated Interaction of SgrAI Restriction Endonuclease with Different DNA Targets* , 2003, Journal of Biological Chemistry.

[34]  A. Pingoud,et al.  Type II restriction endonucleases: structure and mechanism , 2005, Cellular and Molecular Life Sciences.

[35]  Michael D. Abràmoff,et al.  Image processing with ImageJ , 2004 .

[36]  S. Halford,et al.  Dynamics of DNA loop capture by the SfiI restriction endonuclease on supercoiled and relaxed DNA. , 2004, Journal of molecular biology.

[37]  Randy J Read,et al.  Electronic Reprint Biological Crystallography Likelihood-enhanced Fast Rotation Functions Biological Crystallography Likelihood-enhanced Fast Rotation Functions , 2003 .

[38]  H. Viadiu,et al.  A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA , 2005, The EMBO journal.

[39]  V. Šikšnys,et al.  Conversion of the tetrameric restriction endonuclease Bse634I into a dimer: oligomeric structure-stability-function correlations. , 2005, Journal of molecular biology.

[40]  S. Halford,et al.  Long-range communications between DNA sites by the dimeric restriction endonuclease SgrAI. , 2005, Journal of molecular biology.

[41]  David Eisenberg,et al.  Deposition diseases and 3D domain swapping. , 2006, Structure.

[42]  V. Šikšnys,et al.  Allosteric communication network in the tetrameric restriction endonuclease Bse634I. , 2006, Journal of molecular biology.

[43]  Romualdas Vaisvila,et al.  USER™ friendly DNA engineering and cloning method by uracil excision , 2007, Nucleic acids research.

[44]  R. Sessions,et al.  A Switch in the Mechanism of Communication between the Two DNA-Binding Sites in the SfiI Restriction Endonuclease , 2007, Journal of molecular biology.

[45]  M. Gregory,et al.  The structure of SgrAI bound to DNA; recognition of an 8 base pair target , 2008, Nucleic acids research.

[46]  Roger L. Lundblad,et al.  Handbook of Biochemistry and Molecular Biology, Fifth Edition , 2010 .

[47]  N. Horton,et al.  Activation of DNA cleavage by oligomerization of DNA-bound SgrAI. , 2010, Biochemistry.