Thomas A Steitz

Summary

Affiliation: Yale University
Country: USA

Publications

  1. ncbi request reprint Collecting butterflies and the protein structure initiative: the right questions?
    Thomas A Steitz
    Department of Molecular Biophysics, Yale University, New Haven, CT 06520 8114, USA
    Structure 15:1523-4. 2007
  2. doi request reprint A structural understanding of the dynamic ribosome machine
    Thomas A Steitz
    Department of Molecular Biophysics and Biochemistry, Department of Chemistry, Yale University, and the Howard Hughes Medical Institute, New Haven, Connecticut 06520 8114, USA
    Nat Rev Mol Cell Biol 9:242-53. 2008
  3. pmc Insights into the replisome from the structure of a ternary complex of the DNA polymerase III alpha-subunit
    Richard A Wing
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    J Mol Biol 382:859-69. 2008
  4. pmc Cross-crystal averaging reveals that the structure of the peptidyl-transferase center is the same in the 70S ribosome and the 50S subunit
    Miljan Simonovic
    Howard Hughes Medical Institute, Yale University, New Haven, CT 06520 8114, USA
    Proc Natl Acad Sci U S A 105:500-5. 2008
  5. pmc The phi29 DNA polymerase:protein-primer structure suggests a model for the initiation to elongation transition
    Satwik Kamtekar
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA
    EMBO J 25:1335-43. 2006
  6. ncbi request reprint An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA
    T Martin Schmeing
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Nature 438:520-4. 2005
  7. ncbi request reprint Structure of hexameric DnaB helicase and its complex with a domain of DnaG primase
    Scott Bailey
    Department of Molecular Biophysics and Biochemistry and Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
    Science 318:459-63. 2007
  8. pmc How the CCA-adding enzyme selects adenine over cytosine at position 76 of tRNA
    Baocheng Pan
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Science 330:937-40. 2010
  9. pmc The structure of LepA, the ribosomal back translocase
    Robin N Evans
    Departments of Molecular Biophysics and Biochemistry and Chemistry and Howard Hughes Medical Institute, Yale University, New Haven, CT 06520 8114, USA
    Proc Natl Acad Sci U S A 105:4673-8. 2008
  10. pmc Revisiting the structures of several antibiotics bound to the bacterial ribosome
    David Bulkley
    Departments of Chemistry, Yale University, Howard Hughes Medical Institute, New Haven, CT 06511, USA
    Proc Natl Acad Sci U S A 107:17158-63. 2010

Collaborators

Detail Information

Publications73

  1. ncbi request reprint Collecting butterflies and the protein structure initiative: the right questions?
    Thomas A Steitz
    Department of Molecular Biophysics, Yale University, New Haven, CT 06520 8114, USA
    Structure 15:1523-4. 2007
  2. doi request reprint A structural understanding of the dynamic ribosome machine
    Thomas A Steitz
    Department of Molecular Biophysics and Biochemistry, Department of Chemistry, Yale University, and the Howard Hughes Medical Institute, New Haven, Connecticut 06520 8114, USA
    Nat Rev Mol Cell Biol 9:242-53. 2008
    ..Together, these studies have revolutionized our understanding of the mechanism of protein synthesis...
  3. pmc Insights into the replisome from the structure of a ternary complex of the DNA polymerase III alpha-subunit
    Richard A Wing
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    J Mol Biol 382:859-69. 2008
    ..Finally, superimposing a recent structure of the clamp bound to DNA on this Pol IIIalpha complex with DNA places a loop of the beta-binding domain into the appropriate clamp cleft and supports a mechanism of polymerase switching...
  4. pmc Cross-crystal averaging reveals that the structure of the peptidyl-transferase center is the same in the 70S ribosome and the 50S subunit
    Miljan Simonovic
    Howard Hughes Medical Institute, Yale University, New Haven, CT 06520 8114, USA
    Proc Natl Acad Sci U S A 105:500-5. 2008
    ..8 A 70S model as well as that of the H. marismortui 50S subunit. We conclude that the structure of the PTC is the same in the functionally equivalent 70S ribosome and the 50S subunit...
  5. pmc The phi29 DNA polymerase:protein-primer structure suggests a model for the initiation to elongation transition
    Satwik Kamtekar
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA
    EMBO J 25:1335-43. 2006
    ..The model indicates that terminal protein should dissociate from polymerase after the incorporation of approximately six nucleotides...
  6. ncbi request reprint An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA
    T Martin Schmeing
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Nature 438:520-4. 2005
    ..Protein release factors may also function, in part, by inducing an active-site rearrangement similar to that produced by the A-site aminoacyl-tRNA, allowing the carbonyl group and water to be positioned for hydrolysis...
  7. ncbi request reprint Structure of hexameric DnaB helicase and its complex with a domain of DnaG primase
    Scott Bailey
    Department of Molecular Biophysics and Biochemistry and Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
    Science 318:459-63. 2007
    ..Three positive, conserved electrostatic patches on the N-terminal domain of DnaB may also serve as a binding site for DNA and thereby guide the DNA to a DnaG active site...
  8. pmc How the CCA-adding enzyme selects adenine over cytosine at position 76 of tRNA
    Baocheng Pan
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Science 330:937-40. 2010
    ....
  9. pmc The structure of LepA, the ribosomal back translocase
    Robin N Evans
    Departments of Molecular Biophysics and Biochemistry and Chemistry and Howard Hughes Medical Institute, Yale University, New Haven, CT 06520 8114, USA
    Proc Natl Acad Sci U S A 105:4673-8. 2008
    ..In this model, the very electrostatically positive CTD of LepA is placed in the direct vicinity of the A site of the large ribosomal subunit, suggesting a possible interaction between the CTD and the back translocated tRNA or 23S rRNA...
  10. pmc Revisiting the structures of several antibiotics bound to the bacterial ribosome
    David Bulkley
    Departments of Chemistry, Yale University, Howard Hughes Medical Institute, New Haven, CT 06511, USA
    Proc Natl Acad Sci U S A 107:17158-63. 2010
    ....
  11. ncbi request reprint Crystal structures of an archaeal class I CCA-adding enzyme and its nucleotide complexes
    Yong Xiong
    Department of Molecular Biophysics and Biochemistry, New Haven, CT 06520, USA
    Mol Cell 12:1165-72. 2003
    ..The structures of the AfCCA enzyme and the eukaryotic poly(A) polymerase are very similar, implying a close evolutionary relationship between them...
  12. ncbi request reprint Gene replacement in Haloarcula marismortui: construction of a strain with two of its three chromosomal rRNA operons deleted
    Daqi Tu
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, P O Box 208114, New Haven, CT 06520 8114, USA
    Extremophiles 9:427-35. 2005
    ..The structural consequences of these and other such mutations can be determined with unusual accuracy because crystals of the large ribosomal subunit of H. marismortui diffract to atomic resolution...
  13. pmc Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases
    Andrea J Berman
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    EMBO J 26:3494-505. 2007
    ..Polymerases from the two families also interact with downstream single-stranded template DNA in very different ways...
  14. pmc Toward understanding phosphoseryl-tRNACys formation: the crystal structure of Methanococcus maripaludis phosphoseryl-tRNA synthetase
    Satwik Kamtekar
    Department of Molecular Biophysics and Biochemistry and Chemistry and Howard Hughes Medical Institute, Yale University, New Haven, CT 06520 8114, USA
    Proc Natl Acad Sci U S A 104:2620-5. 2007
    ..Using a complex with tungstate as a marker for the position of the phosphate moiety of Sep, we suggest that SepRS and PheRS bind their respective amino acid substrates in dissimilar orientations by using different residues...
  15. pmc The structure of a transcribing T7 RNA polymerase in transition from initiation to elongation
    Kimberly J Durniak
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520 8114, USA
    Science 322:553-7. 2008
    ..The C-helix subdomain moves modestly toward its elongation conformation, whereas subdomain H remains in its initiation- rather than its elongation-phase location, more than 70 angstroms away...
  16. pmc The structure of the ankyrin-binding site of beta-spectrin reveals how tandem spectrin-repeats generate unique ligand-binding properties
    Paul R Stabach
    Department of Pathology, Yale University, New Haven, CT 06520, USA
    Blood 113:5377-84. 2009
    ..The putative coupling of flexibility and ligand binding suggests a mechanism by which spectrin might participate in mechanosensory regulation...
  17. ncbi request reprint Structural insights into the roles of water and the 2' hydroxyl of the P site tRNA in the peptidyl transferase reaction
    T Martin Schmeing
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Mol Cell 20:437-48. 2005
    ....
  18. pmc The structures of antibiotics bound to the E site region of the 50 S ribosomal subunit of Haloarcula marismortui: 13-deoxytedanolide and girodazole
    Susan J Schroeder
    Department of Chemistry, Yale University, New Haven, CT 06520 8107, USA
    J Mol Biol 367:1471-9. 2007
    ..Girodazole is specific for eukarytes and archaea because it makes interactions with L15 that are not possible in eubacteria...
  19. pmc The human SepSecS-tRNASec complex reveals the mechanism of selenocysteine formation
    Sotiria Palioura
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Science 325:321-5. 2009
    ..The tRNA binding is likely to induce a conformational change in the enzyme's active site that allows a phosphoserine covalently attached to tRNA(Sec), but not free phosphoserine, to be oriented properly for the reaction to occur...
  20. pmc Peptidyl-CCA deacylation on the ribosome promoted by induced fit and the O3'-hydroxyl group of A76 of the unacylated A-site tRNA
    Miljan Simonovic
    Howard Hughes Medical Institute, New Haven, Connecticut 06520 8114, USA
    RNA 14:2372-8. 2008
    ....
  21. pmc Mutations outside the anisomycin-binding site can make ribosomes drug-resistant
    Gregor Blaha
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    J Mol Biol 379:505-19. 2008
    ..The conformational effects of some mutations of the second kind propagate through the ribosome for considerable distances and are reversed when A-site substrates bind to the ribosome...
  22. ncbi request reprint Correction of X-ray intensities from single crystals containing lattice-translocation defects
    Jimin Wang
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520 8114, USA
    Acta Crystallogr D Biol Crystallogr 61:67-74. 2005
    ..An application of this procedure is made to determine the crystal structure of phi29 DNA polymerase at 2.2 A resolution using multiple isomorphous replacement and multiwavelength anomalous dispersion methods...
  23. ncbi request reprint Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit
    Jeffrey L Hansen
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520 8114, USA
    J Mol Biol 330:1061-75. 2003
    ..Virginiamycin M occupies portions of both the A and P-site, and induces a conformational change in the ribosome. Blasticidin S base-pairs with the P-loop and thereby mimics C74 and C75 of a P-site bound tRNA...
  24. pmc Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome
    Gregor Blaha
    Department of Molecular Biophysics, Yale University, New Haven, CT 06520, USA
    Science 325:966-70. 2009
    ..EF-P facilitates the proper positioning of the fMet-tRNA(i)(fMet) for the formation of the first peptide bond during translation initiation...
  25. ncbi request reprint RNA, the first macromolecular catalyst: the ribosome is a ribozyme
    Thomas A Steitz
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Trends Biochem Sci 28:411-8. 2003
    ..The structures of the large subunit bound to a variety of antibiotics explain the effects of antibiotic resistance mutations and provide promise for the development of new antibiotics...
  26. ncbi request reprint On the structural basis of peptide-bond formation and antibiotic resistance from atomic structures of the large ribosomal subunit
    Thomas A Steitz
    Department of Molecular Biophysics and Biochemistry, Yale University, and Howard Hughes Medical Institute, P O Box 208114, New Haven, CT 06520 8114, USA
    FEBS Lett 579:955-8. 2005
    ..The structure shows that the ribosome is indeed a ribozyme...
  27. ncbi request reprint Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template
    Yong Xiong
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Nature 430:640-5. 2004
    ..Discrimination between CTP or ATP at a given addition step and at termination arises from changes in the size and shape of the nucleotide binding site that is progressively altered by the elongating 3' end of the tRNA...
  28. pmc Structure of the RAG1 nonamer binding domain with DNA reveals a dimer that mediates DNA synapsis
    Fang Fang Yin
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
    Nat Struct Mol Biol 16:499-508. 2009
    ..These findings reveal a previously unsuspected function for the NBD in DNA synapsis and have implications for the regulation of DNA binding and cleavage by RAG1 and RAG2...
  29. pmc Structures of triacetyloleandomycin and mycalamide A bind to the large ribosomal subunit of Haloarcula marismortui
    Güliz Gürel
    Department of Chemistry, Yale University, New Haven, CT 06520, USA
    Antimicrob Agents Chemother 53:5010-4. 2009
    ..Mycalamide A binds to the E site and inhibits protein synthesis by occupying the space normally occupied by the CCA end of E-site-bound tRNAs...
  30. pmc The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome
    Robin E Stanley
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
    Nat Struct Mol Biol 17:289-93. 2010
    ....
  31. pmc Insights into base selectivity from the 1.8 Å resolution structure of an RB69 DNA polymerase ternary complex
    Mina Wang
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 96520 8114, USA
    Biochemistry 50:581-90. 2011
    ..These interactions are optimized in the dehydrated environment that envelops Watson-Crick nascent base pairs and serve to enhance base selectivity in wild-type RB69 pol...
  32. ncbi request reprint Insights into strand displacement and processivity from the crystal structure of the protein-primed DNA polymerase of bacteriophage phi29
    Satwik Kamtekar
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Mol Cell 16:609-18. 2004
    ..The high processivity of phi29 DNA polymerase may be explained by its topological encirclement of both the downstream template and the upstream duplex DNA...
  33. pmc How hibernation factors RMF, HPF, and YfiA turn off protein synthesis
    Yury S Polikanov
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA
    Science 336:915-8. 2012
    ..The binding of RMF and HPF, but not YfiA, to the ribosome induces a conformational change of the 30S head domain that promotes 100S dimer formation...
  34. pmc Structure of apo-CAP reveals that large conformational changes are necessary for DNA binding
    Hitesh Sharma
    Departments of Chemistry and Molecular Biophysics and Biochemistry, Yale University, Howard Hughes Medical Institute, New Haven, CT 06511, USA
    Proc Natl Acad Sci U S A 106:16604-9. 2009
    ..These interactions are associated with the reorientation and elongation of the C-helices that precludes the formation of the inactive structure...
  35. doi request reprint Crystal structure of the oxazolidinone antibiotic linezolid bound to the 50S ribosomal subunit
    Joseph A Ippolito
    Department of Structure Based Drug Design, Rib X Pharmaceuticals Inc, 300 George Street, Suite 301, New Haven, CT 06511, USA
    J Med Chem 51:3353-6. 2008
    ..These results provide a structural basis for the discovery of improved oxazolidinones active against emerging drug-resistant clinical strains...
  36. pmc U2504 determines the species specificity of the A-site cleft antibiotics: the structures of tiamulin, homoharringtonine, and bruceantin bound to the ribosome
    Güliz Gürel
    Department of Chemistry, Yale University, New Haven, CT 06520, USA
    J Mol Biol 389:146-56. 2009
    ..In the ribosome, the position of U2504 is controlled by its interactions with neighboring nucleotides, whose identities vary among kingdoms...
  37. pmc Implications of structures of synaptic tetramers of gamma delta resolvase for the mechanism of recombination
    Satwik Kamtekar
    Departments of Molecular Biophysics, and Howard Hughes Medical Institute, Yale University, New Haven, CT 06520 8114, USA
    Proc Natl Acad Sci U S A 103:10642-7. 2006
    ....
  38. pmc Structures of deacylated tRNA mimics bound to the E site of the large ribosomal subunit
    T Martin Schmeing
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 8114, USA
    RNA 9:1345-52. 2003
    ..It appears that the E site on the 50S subunit was formed by only RNA in the last common ancestor of the three kingdoms, since the proteins at the E sites of H. marismortui and Deinucoccus radiodurans large subunits are not homologous...
  39. ncbi request reprint Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance
    Daqi Tu
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Cell 121:257-70. 2005
    ..coli) that stacks between them. The structure of large subunit containing a three residue deletion mutant of L22 shows a change in the L22 structure and exit tunnel shape that illuminates its macrolide resistance phenotype...
  40. ncbi request reprint The structure of T. aquaticus DNA polymerase III is distinct from eukaryotic replicative DNA polymerases
    Scott Bailey
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Cell 126:893-904. 2006
    ..Although other possibilities have been proposed, the plausibility of a ribozyme DNA polymerase should be considered...
  41. ncbi request reprint The structural basis of large ribosomal subunit function
    Peter B Moore
    Departments of Molecular Biophysics and Biochemistry, Chemistry, Yale University, New Haven, Connecticut 06520, USA
    Annu Rev Biochem 72:813-50. 2003
    ..The work reviewed, taken as a whole, proves beyond doubt that the ribosome is an RNA enzyme, as had long been surmised on the basis of less conclusive evidence...
  42. ncbi request reprint Structure of a synaptic gammadelta resolvase tetramer covalently linked to two cleaved DNAs
    Weikai Li
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Science 309:1210-5. 2005
    ..The two dimers linked to the DNAs that are to be recombined are held together by a flat interface. This may allow a 180 degrees rotation of one dimer relative to the other in order to reposition the DNA duplexes for strand exchange...
  43. pmc Structural basis for the rescue of stalled ribosomes: structure of YaeJ bound to the ribosome
    Matthieu G Gagnon
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA
    Science 335:1370-2. 2012
    ..This structure gives insights into the mechanism of YaeJ function and provides a basis for understanding how it rescues stalled ribosomes...
  44. ncbi request reprint Structure of the base of the L7/L12 stalk of the Haloarcula marismortui large ribosomal subunit: analysis of L11 movements
    Jennifer M Kavran
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    J Mol Biol 371:1047-59. 2007
    ..These three states are represented by the orientations of the L11 NTD relative to the ribosome and suggest that L11 may play a more specialized role in the factor binding cycle than previously appreciated...
  45. pmc Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation
    Jennifer M Kavran
    Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, CT 06520 8114, USA
    Proc Natl Acad Sci U S A 104:11268-73. 2007
    ..The PylRS structure provides an excellent framework for designing new aaRSs with altered amino acid specificity...
  46. ncbi request reprint The structural mechanism of translocation and helicase activity in T7 RNA polymerase
    Y Whitney Yin
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Cell 116:393-404. 2004
    ..We propose that the dissociation of the product PPi after nucleotide addition produces the protein conformational change resulting in translocation and strand separation...
  47. pmc The contribution of metal ions to the structural stability of the large ribosomal subunit
    Daniel J Klein
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Ave, New Haven, CT 06520 8114, USA
    RNA 10:1366-79. 2004
    ....
  48. ncbi request reprint The structures of four macrolide antibiotics bound to the large ribosomal subunit
    Jeffrey L Hansen
    Department of Molecular Biophysics and Biochemistry, New Haven, Connecticut 06520, USA
    Mol Cell 10:117-28. 2002
    ..coli). Mutations in 23S rRNA that result in clinical resistance render the binding site less complementary to macrolides...
  49. pmc Crystal structure of an intermediate of rotating dimers within the synaptic tetramer of the G-segment invertase
    Christopher J Ritacco
    Department of Molecular Biophysics and Biochemistry, Department of Chemistry and Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
    Nucleic Acids Res 41:2673-82. 2013
    ..Thus, our structure provides direct evidence for the proposed rotational mechanism of site-specific recombination...
  50. pmc The hexameric helicase DnaB adopts a nonplanar conformation during translocation
    Ornchuma Itsathitphaisarn
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Cell 151:267-77. 2012
    ..We propose a hand-over-hand mechanism in which sequential hydrolysis of NTP causes a sequential 5' to 3' movement of the subunits along the helical axis of the staircase, resulting in the unwinding of two nucleotides per subunit...
  51. pmc The roles of RNA in the synthesis of protein
    Peter B Moore
    Department of Molecular Biophysics, Yale University, New Haven, Connecticut 208114, USA
    Cold Spring Harb Perspect Biol 3:a003780. 2011
    ..This review emphasizes what has been learned about the mechanism of peptide bond formation, the antibiotics that inhibit ribosome function, and the fidelity of decoding...
  52. pmc Accuracy, lesion bypass, strand displacement and translocation by DNA polymerases
    Thomas A Steitz
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520 8114, USA
    Philos Trans R Soc Lond B Biol Sci 359:17-23. 2004
    ....
  53. pmc Visualizing polynucleotide polymerase machines at work
    Thomas A Steitz
    Department of Molecular Biophysics, Yale University, and Howard Hughes Medical Institute, New Haven, CT 06520 8114, USA
    EMBO J 25:3458-68. 2006
    ..Movies are shown that allow the direct visualization of the conformational changes that the polymerases undergo during the different steps of polymerization...
  54. pmc Structural insights into peptide bond formation
    Jeffrey L Hansen
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520 8114, USA
    Proc Natl Acad Sci U S A 99:11670-5. 2002
    ..These interactions position the alpha amino group adjacent to the carbonyl carbon of esterified P site substrate in an orientation suitable for a nucleophilic attack...
  55. ncbi request reprint The crystal structure of yeast fatty acid synthase, a cellular machine with eight active sites working together
    Ivan B Lomakin
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA
    Cell 129:319-32. 2007
    ..The phosphopantetheinyl transferase domain lies outside the shell of the assembly, inaccessible to ACP that lies inside, suggesting that the attachment of the pantetheine arm to ACP must occur before complete assembly of the complex...
  56. pmc Structure of HIV-1 reverse transcriptase bound to an inhibitor active against mutant reverse transcriptases resistant to other nonnucleoside inhibitors
    Janice D Pata
    Department of Molecular Biophysics and Biochemistry, Yale University, Howard Hughes Medical Institute, New Haven, CT 06520 8114, USA
    Proc Natl Acad Sci U S A 101:10548-53. 2004
    ....
  57. pmc After the ribosome structures: how does peptidyl transferase work?
    Peter B Moore
    Department of Chemistry, Howard Hughes Medical Institute, Yale University, 350 Edwards Street, New Haven, CT 06520 8107, USA
    RNA 9:155-9. 2003
    ..of the site enhance the rate of peptide-bond formation chemically? Do intact ribosomes make peptide bonds the same way as the isolated large subunits that have been the source of all this atomic resolution structural information?..
  58. ncbi request reprint Structure of the calmodulin alphaII-spectrin complex provides insight into the regulation of cell plasticity
    Miljan Simonovic
    Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520, USA
    J Biol Chem 281:34333-40. 2006
    ..The structure of this complex provides insight into the mechanisms by which calmodulin, calpain, caspase, and tyrosine phosphorylation act on spectrin to regulate essential cellular processes...
  59. ncbi request reprint Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase
    Y Whitney Yin
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520 8114, USA
    Science 298:1387-95. 2002
    ..Downstream duplex DNA binds to the fingers domain, and its orientation relative to upstream DNA in the initiation complex implies an unwinding that could facilitate formation of the open promoter complex...
  60. pmc The antibiotic thermorubin inhibits protein synthesis by binding to inter-subunit bridge B2a of the ribosome
    David Bulkley
    Department of Chemistry, Yale University, New Haven, CT 06520 8107, USA
    J Mol Biol 416:571-8. 2012
    ....
  61. ncbi request reprint The structural basis of the transition from initiation to elongation phases of transcription, as well as translocation and strand separation, by T7 RNA polymerase
    Thomas A Steitz
    Department of Molecular Biophysics and Biochemistry, Yale University, and Howard Hughes Medical Institute, New Haven, CT 06520 8114, USA
    Curr Opin Struct Biol 14:4-9. 2004
    ..The rotation that results in translocation is powered by the release of the pyrophosphate product...
  62. pmc The crystal structure of the Thermus aquaticus DnaB helicase monomer
    Scott Bailey
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Nucleic Acids Res 35:4728-36. 2007
    ..Comparison of hexameric homology models of DnaB with the structure of the papillomavirus E1 helicase suggests the two helicases may function through different mechanisms despite their sharing a common ancestor...
  63. pmc Assembly, purification and crystallization of an active HIV-1 reverse transcriptase initiation complex
    Janice D Pata
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA
    Nucleic Acids Res 30:4855-63. 2002
    ..Thus, in vitro transcribed tRNA can be used efficiently as a primer by HIV-1 RT. We have also obtained crystals of the HIV-1 initiation complex that require the precisely defined ends of this in vitro transcribed tRNA(Lys3) to grow...
  64. ncbi request reprint A novel method of determining the number of macromolecules per asymmetric unit from accurate crystal-volume measurements
    Fang Li
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520 8114, USA
    Acta Crystallogr D Biol Crystallogr 59:1793-6. 2003
    ..The method has been tested successfully on three different crystals of known structures...
  65. pmc Poly(A) tail recognition by a viral RNA element through assembly of a triple helix
    Rachel M Mitton-Fry
    Department of Molecular Biophysics and Biochemistry MB and B, Howard Hughes Medical Institute HHMI, Yale University School of Medicine, Boyer Center for Molecular Medicine, 295 Congress Avenue, New Haven, CT 06536 9812, USA
    Science 330:1244-7. 2010
    ..Deadenylation assays confirm the functional importance of the triple helix. Thus, the ENE acts as an intramolecular RNA clamp, sequestering the PAN poly(A) tail and preventing the initiation of RNA decay...
  66. ncbi request reprint The involvement of RNA in ribosome function
    Peter B Moore
    Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208107, New Haven, Connecticut 06520 8107, USA
    Nature 418:229-35. 2002
    ..Recent structural work has demonstrated a profound involvement of the ribosome's RNA component in all aspects of its function, supporting the hypothesis that proteins were added to the ribosome late in its evolution...
  67. pmc The structural changes of T7 RNA polymerase from transcription initiation to elongation
    Thomas A Steitz
    Department of Molecular Biophysics and Biochemistry, Yale University, and Howard Hughes Medical Institute, New Haven, CT 06520 8114, United States
    Curr Opin Struct Biol 19:683-90. 2009
    ..A conformational change in the 'fingers' domain that results from the binding or dissociation of incoming NTP or PPi appears to be associated with the state of translocation of T7 RNAP...
  68. ncbi request reprint A pre-translocational intermediate in protein synthesis observed in crystals of enzymatically active 50S subunits
    T Martin Schmeing
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 8114, USA
    Nat Struct Biol 9:225-30. 2002
    ..Thus, this structure represents a state that occurs after peptide bond formation but before the hybrid state of protein synthesis...
  69. ncbi request reprint Crystal structures of the Bacillus stearothermophilus CCA-adding enzyme and its complexes with ATP or CTP
    Fang Li
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Cell 111:815-24. 2002
    ..Each subunit has one active site capable of switching its base specificity between ATP and CTP, an important component of the CCA-adding mechanism...
  70. pmc The structural basis of cysteine aminoacylation of tRNAPro by prolyl-tRNA synthetases
    Satwik Kamtekar
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520 8114, USA
    Proc Natl Acad Sci U S A 100:1673-8. 2003
    ..jannaschii ProRS misacylates tRNA(Pro) with cysteine, and argue against the proposal that these archaeal ProRS enzymes possess the dual capacity to aminoacylate both tRNA(Pro) and tRNA(Cys) with their cognate amino acids...
  71. ncbi request reprint Structural insights into the functions of the large ribosomal subunit, a major antibiotic target
    Thomas A Steitz
    Howard Hughes Medical Institute, USA
    Keio J Med 57:1-14. 2008
  72. ncbi request reprint The ribosome revealed
    Peter B Moore
    Trends Biochem Sci 30:281-3. 2005
  73. pmc A specific subdomain in phi29 DNA polymerase confers both processivity and strand-displacement capacity
    Irene Rodríguez
    Instituto de Biología Molecular Eladio Viñuela, Consejo Superior de Investigaciones Cientificas, Centro de Biologia Molecular Severo Ochoa, Universidad Autonoma de Madrid, Canto Blanco, 28049 Madrid, Spain
    Proc Natl Acad Sci U S A 102:6407-12. 2005
    ..Therefore, the biochemical results described here directly demonstrate that TPR2 plays a critical role in strand displacement and processivity...