3D domain swapping: As domains continue to swap

Three‐dimensional (3D) domain swapping creates a bond between two or more protein molecules as they exchange their identical domains. Since the term '3D domain swapping' was first used to describe the dimeric structure of diphtheria toxin, the database of domain‐swapped proteins has greatly expanded. Analyses of the now about 40 structurally characterized cases of domain‐swapped proteins reveal that most swapped domains are at either the N or C terminus and that the swapped domains are diverse in their primary and secondary structures. In addition to tabulating domain‐swapped proteins, we describe in detail several examples of 3D domain swapping which show the swapping of more than one domain in a protein, the structural evidence for 3D domain swapping in amyloid proteins, and the flexibility of hinge loops. We also discuss the physiological relevance of 3D domain swapping and a possible mechanism for 3D domain swapping. The present state of knowledge leads us to suggest that 3D domain swapping can occur under appropriate conditions in any protein with an unconstrained terminus. As domains continue to swap, this review attempts not only a summary of the known domain‐swapped proteins, but also a framework for understanding future findings of 3D domain swapping.

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

[2]  Witold K. Surewicz,et al.  Crystal structure of the human prion protein reveals a mechanism for oligomerization , 2002, Nature Structural Biology.

[3]  W. Lim,et al.  Structure of the SH3-guanylate kinase module from PSD-95 suggests a mechanism for regulated assembly of MAGUK scaffolding proteins. , 2001, Molecules and Cells.

[4]  L. Itzhaki,et al.  Observation of signal transduction in three-dimensional domain swapping , 2001, Nature Structural Biology.

[5]  A. Benito,et al.  The structure of an engineered domain-swapped ribonuclease dimer and its implications for the evolution of proteins toward oligomerization. , 2001, Structure.

[6]  M. J. Conroy,et al.  Three‐dimensional domain swapping in the folded and molten‐globule states of cystatins, an amyloid‐forming structural superfamily , 2001, The EMBO journal.

[7]  Kam Y. J. Zhang,et al.  Conversion of monomeric protein L to an obligate dimer by computational protein design , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[8]  L. Itzhaki,et al.  Three-dimensional domain swapping in p13suc1 occurs in the unfolded state and is controlled by conserved proline residues , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[9]  S. Linse,et al.  An extended hudrophobic core induces EF‐hand swapping , 2001, Protein science : a publication of the Protein Society.

[10]  U. Jakob,et al.  The 2.2 A crystal structure of Hsp33: a heat shock protein with redox-regulated chaperone activity. , 2001, Structure.

[11]  A. Minton,et al.  The Influence of Macromolecular Crowding and Macromolecular Confinement on Biochemical Reactions in Physiological Media* , 2001, The Journal of Biological Chemistry.

[12]  Zbigniew Grzonka,et al.  Human cystatin C, an amyloidogenic protein, dimerizes through three-dimensional domain swapping , 2001, Nature Structural Biology.

[13]  D Baker,et al.  Biological Crystallography Structures of the B1 Domain of Protein L from Peptostreptococcus Magnus with a Tyrosine to Tryptophan Substitution , 2022 .

[14]  D. Rees,et al.  Crystal Structure of the “cab”-type β Class Carbonic Anhydrase from the Archaeon Methanobacterium thermoautotrophicum * , 2001, The Journal of Biological Chemistry.

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

[16]  D. Eisenberg,et al.  Design of three-dimensional domain-swapped dimers and fibrous oligomers. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[17]  J. Valentine,et al.  Molecular confinement influences protein structure and enhances thermal protein stability , 2001, Protein science : a publication of the Protein Society.

[18]  Markus R. Wenk,et al.  Structural and biochemical characterization of the type III secretion chaperones CesT and SigE , 2001, Nature Structural Biology.

[19]  E. Casale,et al.  Dimer formation through domain swapping in the crystal structure of the Grb2-SH2-Ac-pYVNV complex. , 2000, Biochemistry.

[20]  B. Matthews,et al.  Determination of the structure of Escherichia coli glyoxalase I suggests a structural basis for differential metal activation. , 2000, Biochemistry.

[21]  Michael R Sawaya,et al.  Crystal Structure of T7 Gene 4 Ring Helicase Indicates a Mechanism for Sequential Hydrolysis of Nucleotides , 2000, Cell.

[22]  G. Leonard,et al.  Domain swapping in the sporulation response regulator Spo0A. , 2000, Journal of molecular biology.

[23]  K Wüthrich,et al.  NMR solution structure of the human prion protein. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

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

[25]  A. Wilkinson,et al.  Phosphorylated aspartate in the structure of a response regulator protein. , 1999, Journal of molecular biology.

[26]  Charles C. Richardson,et al.  Crystal Structure of the Helicase Domain from the Replicative Helicase-Primase of Bacteriophage T7 , 1999, Cell.

[27]  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.

[28]  Christian Wiesmann,et al.  Crystal structure of nerve growth factor in complex with the ligand-binding domain of the TrkA receptor , 1999, Nature.

[29]  Alfonso Mondragón,et al.  Structures of Two Repeats of Spectrin Suggest Models of Flexibility , 1999, Cell.

[30]  S. Bass,et al.  Crystal structures of the neurotrophin-binding domain of TrkA, TrkB and TrkC. , 1999, Journal of molecular biology.

[31]  G. Rivas,et al.  Direct observation of the self-association of dilute proteins in the presence of inert macromolecules at high concentration via tracer sedimentation equilibrium: theory, experiment, and biological significance. , 1999, Biochemistry.

[32]  O. Herzberg,et al.  Helix swapping between two α/β barrels: crystal structure of phosphoenolpyruvate mutase with bound Mg2+–oxalate , 1999 .

[33]  A. Gronenborn,et al.  Crystal structure of cyanovirin-N, a potent HIV-inactivating protein, shows unexpected domain swapping. , 1999, Journal of molecular biology.

[34]  D. Suck,et al.  X‐ray structure of T4 endonuclease VII: a DNA junction resolvase with a novel fold and unusual domain‐swapped dimer architecture , 1999, The EMBO journal.

[35]  L. Wyns,et al.  Trimeric domain-swapped barnase. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[36]  R. Sessions,et al.  Engineered assembly of intertwined oligomers of an immunoglobulin chain. , 1999, Journal of molecular biology.

[37]  O. Herzberg,et al.  Helix swapping between two alpha/beta barrels: crystal structure of phosphoenolpyruvate mutase with bound Mg(2+)-oxalate. , 1999, Structure.

[38]  G. Privé,et al.  Crystal structure of the BTB domain from PLZF. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[39]  M. Stone,et al.  Active monomeric and dimeric forms of Pseudomonas putida glyoxalase I: evidence for 3D domain swapping. , 1998, Biochemistry.

[40]  K. Baradaran,et al.  An N-terminal fragment of the gene 4 helicase/primase of bacteriophage T7 retains primase activity in the absence of helicase activity. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[41]  A. Gronenborn,et al.  Solution structure of cyanovirin-N, a potent HIV-inactivating protein , 1998, Nature Structural Biology.

[42]  P. Colman,et al.  Three-dimensional structures of single-chain Fv-neuraminidase complexes. , 1998, Journal of molecular biology.

[43]  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.

[44]  F E Cohen,et al.  Pathologic conformations of prion proteins. , 1998, Annual review of biochemistry.

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

[46]  A. Murzin,et al.  The 2.0-A resolution crystal structure of a trimeric antibody fragment with noncognate VH-VL domain pairs shows a rearrangement of VH CDR3. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[47]  K. Kishan,et al.  The SH3 domain of Eps8 exists as a novel intertwined dimer , 1997, Nature Structural Biology.

[48]  Hu Pan,et al.  Characterization and crystallization of the helicase domain of bacteriophage T7 gene 4 protein , 1997, Nucleic Acids Res..

[49]  T A Jones,et al.  Crystal structure of human glyoxalase I—evidence for gene duplication and 3D domain swapping , 1997, The EMBO journal.

[50]  W R Taylor,et al.  Three-dimensional domain duplication, swapping and stealing. , 1997, Current opinion in structural biology.

[51]  M. Koizumi,et al.  Structure of coagulation factors IX/X-binding protein, a heterodimer of C-type lectin domains , 1997, Nature Structural Biology.

[52]  D Eisenberg,et al.  Oligomer formation by 3D domain swapping: a model for protein assembly and misassembly. , 1997, Advances in protein chemistry.

[53]  E A Merritt,et al.  Raster3D: photorealistic molecular graphics. , 1997, Methods in enzymology.

[54]  C. Cambillau,et al.  Domain swapping creates a third putative combining site in bovine odorant binding protein dimer , 1996, Nature Structural Biology.

[55]  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.

[56]  P. Nyman,et al.  Crystal structure of the Escherichia coli dUTPase in complex with a substrate analogue (dUDP) , 1996, Nature Structural Biology.

[57]  M. James,et al.  Crystal structure of the yeast cell-cycle control protein, p13suc1, in a strand-exchanged dimer. , 1996, Structure.

[58]  S. Harrison,et al.  The structure of simian virus 40 refined at 3.1 A resolution. , 1996, Structure.

[59]  B. Matthews,et al.  High-resolution structure of an engineered Cro monomer shows changes in conformation relative to the native dimer. , 1996, Biochemistry.

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

[61]  R. Lindner,et al.  Effects of dextran on the self-association of human spectrin. , 1995, Biophysical chemistry.

[62]  Eaton E. Lattman,et al.  One-step evolution of a dimer from a monomeric protein , 1995, Nature Structural Biology.

[63]  R L Brady,et al.  One sequence, two folds: a metastable structure of CD2. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[64]  J. Tainer,et al.  Crystal structure of the human cell cycle protein CksHs1: single domain fold with similarity to kinase N-lobe domain. , 1995, Journal of molecular biology.

[65]  L. Presta,et al.  An immunoglobulin‐like domain determines the specificity of neurotrophin receptors. , 1995, The EMBO journal.

[66]  A Wlodawer,et al.  Crystal structure of interleukin-10 reveals the functional dimer with an unexpected topological similarity to interferon gamma. , 1995, Structure.

[67]  A. Ducruix,et al.  Crystal structure of the mammalian Grb2 adaptor. , 1995, Science.

[68]  L. Johnson,et al.  The crystal structure of p13suc1, a p34cdc2‐interacting cell cycle control protein. , 1995, The EMBO journal.

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

[70]  R. Williams,et al.  Crystal structure of a diabody, a bivalent antibody fragment. , 1994, Structure.

[71]  David Eisenberg,et al.  Refined structure of dimeric diphtheria toxin at 2.0 Å resolution , 1994, Protein science : a publication of the Protein Society.

[72]  D Eisenberg,et al.  Refined structure of monomelic diphtheria toxin at 2.3 Å resolution , 1994, Protein science : a publication of the Protein Society.

[73]  Andrea Musacchio,et al.  High-resolution crystal structures of tyrosine kinase SH3 domains complexed with proline-rich peptides , 1994, Nature Structural Biology.

[74]  P. Dumas,et al.  Crystal structure and site‐directed mutagenesis of a bleomycin resistance protein and their significance for drug sequestering. , 1994, The EMBO journal.

[75]  G. Ralston,et al.  Enhancement of self-association of human spectrin by polyethylene glycol. , 1994, The International journal of biochemistry.

[76]  D. Eisenberg,et al.  Domain swapping: entangling alliances between proteins. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[77]  R. Webster,et al.  Recombinant anti-sialidase single-chain variable fragment antibody. Characterization, formation of dimer and higher-molecular-mass multimers and the solution of the crystal structure of the single-chain variable fragment/sialidase complex. , 1994, European journal of biochemistry.

[78]  A. Fersht,et al.  Subsite binding in an RNase: structure of a barnase-tetranucleotide complex at 1.76-A resolution. , 1994, Biochemistry.

[79]  D. Branton,et al.  Crystal structure of the repetitive segments of spectrin. , 1993, Science.

[80]  N. Hilschmann,et al.  Reduction of disulfide bonds in an amyloidogenic Bence Jones protein leads to formation of "amyloid-like" fibrils in vitro. , 1993, Biological chemistry Hoppe-Seyler.

[81]  J. Tainer,et al.  Human CksHs2 atomic structure: a role for its hexameric assembly in cell cycle control. , 1993, Science.

[82]  L. Mazzarella,et al.  Bovine seminal ribonuclease: structure at 1.9 A resolution. , 1993, Acta crystallographica. Section D, Biological crystallography.

[83]  M. Lambert,et al.  A novel dimer configuration revealed by the crystal structure at 2.4 Å resolution of human interleukin-5 , 1993, Nature.

[84]  T. Toni.  The Machinery of Life , 1993, Springer New York.

[85]  David I. Stuart,et al.  Crystal structure at 2.8 Å resolution of a soluble form of the cell adhesion molecule CD2 , 1992, Nature.

[86]  A. North,et al.  Pheromone binding to two rodent urinary proteins revealed by X-ray crystallography , 1992, Nature.

[87]  Y. Mitsui,et al.  Three‐dimensional crystal structure of recombinant murine interferon‐beta. , 1992, The EMBO journal.

[88]  A. Parente,et al.  The dual-mode quaternary structure of seminal RNase. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[89]  S. Forsén,et al.  Proline cis-trans isomers in calbindin D9k observed by X-ray crystallography. , 1992, Journal of Molecular Biology.

[90]  Irene T. Weber,et al.  The structure of the E. coli recA protein monomer and polymer , 1992, Nature.

[91]  B. Welch.  The structure , 1992 .

[92]  W. Weis,et al.  Structure of the calcium-dependent lectin domain from a rat mannose-binding protein determined by MAD phasing. , 1991, Science.

[93]  K. Diederichs,et al.  Low-resolution structure of recombinant human granulocyte-macrophage colony stimulating factor. , 1991, Journal of molecular biology.

[94]  E. W. Miles,et al.  Structural basis for catalysis by tryptophan synthase. , 1991, Advances in enzymology and related areas of molecular biology.

[95]  T. L. Blundell,et al.  X-ray analysis of βB2-crystallin and evolution of oligomeric lens proteins , 1990, Nature.

[96]  T L Blundell,et al.  X-ray analysis of beta B2-crystallin and evolution of oligomeric lens proteins. , 1990, Nature.

[97]  E. Lattman,et al.  The crystal structure of the ternary complex of staphylococcal nuclease, Ca2+ and the inhibitor pdTp, refined at 1.65 Å , 1989, Proteins.

[98]  W. Bode,et al.  The 2.0 A X‐ray crystal structure of chicken egg white cystatin and its possible mode of interaction with cysteine proteinases. , 1988, The EMBO journal.

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

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

[101]  R. Collier,et al.  Dimeric form of diphtheria toxin: purification and characterization. , 1986, Biochemistry.

[102]  M G Rossmann,et al.  The NADPH binding site on beef liver catalase. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[103]  R. Huber,et al.  Crystallographic refinement and atomic models of two different forms of citrate synthase at 2.7 and 1.7 A resolution. , 1984, Journal of molecular biology.

[104]  A Wlodawer,et al.  The refined crystal structure of ribonuclease A at 2.0 A resolution. , 1982, The Journal of biological chemistry.

[105]  B. Matthews,et al.  Structure of the cro repressor from bacteriophage λ and its interaction with DNA , 1981, Nature.

[106]  Graeme Wistow,et al.  The molecular structure and stability of the eye lens: X-ray analysis of γ-crystallin II , 1981, Nature.

[107]  B. Matthews,et al.  Structure of the cro repressor from bacteriophage lambda and its interaction with DNA. , 1981, Nature.

[108]  T. Blundell,et al.  The molecular structure and stability of the eye lens: x-ray analysis of gamma-crystallin II. , 1981, Nature.

[109]  M. Goldberg,et al.  Renaturation of Escherichia coli tryptophanase after exposure to 8 M urea. Evidence for the existence of nucleation centers. , 1974, European journal of biochemistry.

[110]  C. Yanofsky,et al.  Restoration of Enzymic Activity by Complementation in Vitro between Mutant α Subunits of Tryptophan Synthetase and between Mutant Subunits and Fragments of the α Subunit , 1969 .

[111]  C. Yanofsky,et al.  Restoration of enzymic activity by complementation in vitro between mutant alpha subunits of tryptophan synthetase and between mutant subunits and fragments of the alpha subunit. , 1969, The Journal of biological chemistry.

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