Dmitry G Vassylyev

Summary

Affiliation: University of Alabama at Birmingham
Country: USA

Publications

  1. pmc Regulation through the RNA polymerase secondary channel. Structural and functional variability of the coiled-coil transcription factors
    Jindrich Symersky
    Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, School of Medicine, Birmingham, Alabama 35294, USA
    J Biol Chem 281:1309-12. 2006
  2. pmc Elongation by RNA polymerase: a race through roadblocks
    Dmitry G Vassylyev
    Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 402B Kaul Genetics Building, 720 20th Street South, Birmingham, AL 35294, United States
    Curr Opin Struct Biol 19:691-700. 2009
  3. pmc Structural basis for transcription inhibition by tagetitoxin
    Dmitry G Vassylyev
    Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, School of Medicine, Birmingham, Alabama 35294, USA
    Nat Struct Mol Biol 12:1086-93. 2005
  4. ncbi request reprint Crystal structure of the translocation ATPase SecA from Thermus thermophilus reveals a parallel, head-to-head dimer
    Dmitry G Vassylyev
    Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 434 Kaul Genetics Building, 720 20 th Street South, Birmingham, AL 35294, USA
    J Mol Biol 364:248-58. 2006
  5. pmc Crystal structure of pyruvate dehydrogenase phosphatase 1 and its functional implications
    Dmitry G Vassylyev
    Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, School of Medicine and Dentistry, Kaul Genetics Building, Birmingham, AL 35294, USA
    J Mol Biol 370:417-26. 2007
  6. ncbi request reprint Structural basis for transcription elongation by bacterial RNA polymerase
    Dmitry G Vassylyev
    Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 402B Kaul Genetics Building, 720 20th Street South, Birmingham, Alabama 35294, USA
    Nature 448:157-62. 2007
  7. ncbi request reprint Structural basis for substrate loading in bacterial RNA polymerase
    Dmitry G Vassylyev
    Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 402B Kaul Genetics Building, 720 20th Street South, Birmingham, Alabama 35294, USA
    Nature 448:163-8. 2007
  8. pmc The carboxy-terminal coiled-coil of the RNA polymerase beta'-subunit is the main binding site for Gre factors
    Marina N Vassylyeva
    Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
    EMBO Rep 8:1038-43. 2007
  9. pmc Cloning, expression, purification, crystallization and initial crystallographic analysis of the preprotein translocation ATPase SecA from Thermus thermophilus
    Marina N Vassylyeva
    Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 402B Kaul Genetics Building, 720 20th Street South, Birmingham, AL 35294, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 62:909-12. 2006
  10. pmc Crystallization and preliminary crystallographic analysis of the transcriptional regulator RfaH from Escherichia coli and its complex with ops DNA
    Marina N Vassylyeva
    Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, School of Medicine, 402B Kaul Genetics Building, 720 20th Street South, Birmingham, AL 35294, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 62:1027-30. 2006

Research Grants

  1. Molecular mechanisms of transcription elongation
    Dmitry Vassylyev; Fiscal Year: 2009

Collaborators

Detail Information

Publications45

  1. pmc Regulation through the RNA polymerase secondary channel. Structural and functional variability of the coiled-coil transcription factors
    Jindrich Symersky
    Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, School of Medicine, Birmingham, Alabama 35294, USA
    J Biol Chem 281:1309-12. 2006
    ..The excess of the acidic residues and inherent flexibility of the coiled-coil tip might allow Gfh1 to adjust its activity to structurally distinct substrates, thereby inhibiting diverse catalytic reactions of RNA polymerase...
  2. pmc Elongation by RNA polymerase: a race through roadblocks
    Dmitry G Vassylyev
    Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 402B Kaul Genetics Building, 720 20th Street South, Birmingham, AL 35294, United States
    Curr Opin Struct Biol 19:691-700. 2009
    ..The available structural information suggests a number of general mechanistic predictions that provide a reference point and direction for future studies of transcription regulation...
  3. pmc Structural basis for transcription inhibition by tagetitoxin
    Dmitry G Vassylyev
    Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, School of Medicine, Birmingham, Alabama 35294, USA
    Nat Struct Mol Biol 12:1086-93. 2005
    ..Remodeling of the active site by metal ions could be a common theme in the regulation of catalysis by nucleic acid enzymes...
  4. ncbi request reprint Crystal structure of the translocation ATPase SecA from Thermus thermophilus reveals a parallel, head-to-head dimer
    Dmitry G Vassylyev
    Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 434 Kaul Genetics Building, 720 20 th Street South, Birmingham, AL 35294, USA
    J Mol Biol 364:248-58. 2006
    ....
  5. pmc Crystal structure of pyruvate dehydrogenase phosphatase 1 and its functional implications
    Dmitry G Vassylyev
    Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, School of Medicine and Dentistry, Kaul Genetics Building, Birmingham, AL 35294, USA
    J Mol Biol 370:417-26. 2007
    ....
  6. ncbi request reprint Structural basis for transcription elongation by bacterial RNA polymerase
    Dmitry G Vassylyev
    Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 402B Kaul Genetics Building, 720 20th Street South, Birmingham, Alabama 35294, USA
    Nature 448:157-62. 2007
    ..The RNA is threaded through the RNA exit channel, where it adopts a conformation mimicking that of a single strand within a double helix, providing insight into a mechanism for hairpin-dependent pausing and termination...
  7. ncbi request reprint Structural basis for substrate loading in bacterial RNA polymerase
    Dmitry G Vassylyev
    Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 402B Kaul Genetics Building, 720 20th Street South, Birmingham, Alabama 35294, USA
    Nature 448:163-8. 2007
    ..Second, freezing of the preinsertion state is an attractive target for the design of novel antibiotics. Last, the TL emerges as a prominent target whose refolding can be modulated by regulatory factors...
  8. pmc The carboxy-terminal coiled-coil of the RNA polymerase beta'-subunit is the main binding site for Gre factors
    Marina N Vassylyeva
    Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
    EMBO Rep 8:1038-43. 2007
    ..We show that substitutions of these residues and those in the GreB C-terminal domain cavity confer defects in GreB activity and binding to RNAP, and present a plausible model for the RNAP-GreB complex...
  9. pmc Cloning, expression, purification, crystallization and initial crystallographic analysis of the preprotein translocation ATPase SecA from Thermus thermophilus
    Marina N Vassylyeva
    Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 402B Kaul Genetics Building, 720 20th Street South, Birmingham, AL 35294, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 62:909-12. 2006
    ..The crystals, improved by macroseeding, diffracted to beyond 2.8 and 3.5 A resolution for the trigonal and hexagonal crystal forms, respectively. Structure determination using the multiple isomorphous replacement method is in progress...
  10. pmc Crystallization and preliminary crystallographic analysis of the transcriptional regulator RfaH from Escherichia coli and its complex with ops DNA
    Marina N Vassylyeva
    Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, School of Medicine, 402B Kaul Genetics Building, 720 20th Street South, Birmingham, AL 35294, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 62:1027-30. 2006
    ..Crystals of selenomethionine-labeled proteins in both crystal forms were obtained by cross-microseeding using the native microcrystals. The structure determination of RfaH and its complex with DNA is in progress...
  11. pmc Cloning, expression, purification, crystallization and initial crystallographic analysis of transcription elongation factors GreB from Escherichia coli and Gfh1 from Thermus thermophilus
    Anna A Perederina
    Department of Biochemistry and Molecular Genetics, University of Alabama, School of Medicine, Birmingham, AL 35294, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 62:44-6. 2006
    ..Crystals of the selenomethionine proteins were obtained by microseeding using the native protein crystals and diffract as well as the native ones. The structure determination of these proteins is now in progress...
  12. ncbi request reprint Tracking RNA polymerase, one step at a time
    Dmitry G Vassylyev
    Department of Biochemistry and Molecular Genetics, University of Alabama, Birmingham, Alabama 35294, USA
    Cell 123:977-9. 2005
    ....
  13. doi request reprint Structural insights into mechanisms of the small RNA methyltransferase HEN1
    Ying Huang
    Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
    Nature 461:823-7. 2009
    ..Metal ion coordination by both 2' and 3' hydroxyls on the 3'-terminal nucleotide and four invariant residues in the active site of the methyltransferase domain suggests a novel Mg(2+)-dependent 2'-O-methylation mechanism...
  14. pmc The binding site and mechanism of the RNA polymerase inhibitor tagetitoxin: an issue open to debate
    Sergiy Klyuyev
    Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, AL, USA
    Transcription 3:46-50. 2012
    ....
  15. pmc Crystal structure of an asymmetric complex of pyruvate dehydrogenase kinase 3 with lipoyl domain 2 and its biological implications
    Yancho Devedjiev
    Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, School of Medicine and Dentistry, Kaul Genetics Building, Birmingham, AL 35294, USA
    J Mol Biol 370:407-16. 2007
    ..Thus, the L2-domains likely act not only as the structural anchors but also modulate the catalytic cycle of PDHK...
  16. pmc Allosteric control of the RNA polymerase by the elongation factor RfaH
    Vladimir Svetlov
    Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
    Nucleic Acids Res 35:5694-705. 2007
    ....
  17. pmc Elongation complexes of Thermus thermophilus RNA polymerase that possess distinct translocation conformations
    Ekaterina Kashkina
    Department of Cell Biology, University of Medicine and Dentistry of New Jersey, School of Osteopathic Medicine, Stratford, NJ 08084, USA
    Nucleic Acids Res 34:4036-45. 2006
    ..Crystals of a posttranslocated complex were used to collect diffraction data at atomic resolution...
  18. pmc Still looking for the magic spot: the crystallographically defined binding site for ppGpp on RNA polymerase is unlikely to be responsible for rRNA transcription regulation
    Catherine E Vrentas
    Department of Bacteriology, University of Wisconsin Madison, 1550 Linden Drive, Madison, WI 53706, USA
    J Mol Biol 377:551-64. 2008
    ..coli ribosomal RNA transcription initiation and highlight the importance of inclusion of omega in bacterial RNAP preparations...
  19. pmc ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding
    Shun ichi Sekine
    Cellular Signaling Laboratory and Structurome Group, RIKEN Harima Institute at SPring 8, 1 1 1 Kouto, Mikazuki cho, Sayo, Hyogo 679 5148, Japan
    EMBO J 22:676-88. 2003
    ..Therefore, tRNA binding to GluRS switches the ATP-binding mode. The interactions of the three tRNA(Glu) regions with GluRS cause conformational changes around the ATP-binding site, and allow ATP to bind to the 'productive' subsite...
  20. pmc A mechanism of nucleotide misincorporation during transcription due to template-strand misalignment
    Richard T Pomerantz
    Department of Microbiology and Immunology, The State University of New York Downstate Medical Center, 450 Clarkson Avenue, Brooklyn, New York 11203, USA
    Mol Cell 24:245-55. 2006
    ..Our findings for T7 RNAP are in contrast to related DNA polymerases of the Pol I type, which fail to extend mismatches efficiently and generate predominantly deletion errors as a result of template-strand misalignment...
  21. pmc The transition to an elongation complex by T7 RNA polymerase is a multistep process
    Rajiv P Bandwar
    Department of Biochemistry, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
    J Biol Chem 282:22879-86. 2007
    ..The results indicate that the transition to an EC is a multistep process and that the movement of the core subdomain and reorganization of certain elements in the N-terminal domain commence prior to promoter release (at 8-9 nt)...
  22. pmc Structural basis for converting a general transcription factor into an operon-specific virulence regulator
    Georgiy A Belogurov
    Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
    Mol Cell 26:117-29. 2007
    ..Finally, we argue that RfaH binds to the beta' subunit coiled coil, the major target site for the initiation sigma factors...
  23. pmc Conformational transition of Sec machinery inferred from bacterial SecYE structures
    Tomoya Tsukazaki
    Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta cho, Midori ku, Yokohama shi, Kanagawa 226 8501, Japan
    Nature 455:988-91. 2008
    ....
  24. ncbi request reprint Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins
    Irina Artsimovitch
    Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, USA
    Cell 122:351-63. 2005
    ..Based on structural predictions, we designed enzyme substitutions that apparently interrupt this allosteric signal...
  25. ncbi request reprint Crystal structure of a lysine biosynthesis enzyme, LysX, from Thermus thermophilus HB8
    Hiroaki Sakai
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama, 230 0045, Japan
    J Mol Biol 332:729-40. 2003
    ..This observation strongly suggests that LysX is an ATP-utilizing enzyme that shares a common evolutionary ancestor with other ATP-grasp fold proteins possessing a carboxylate-amine/thiol ligase activity...
  26. ncbi request reprint Cloning, expression, purification, crystallization and initial crystallographic analysis of the lysine-biosynthesis LysX protein from Thermus thermophilus HB8
    Marina N Vassylyeva
    Genomic Sciences Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    Acta Crystallogr D Biol Crystallogr 59:1651-2. 2003
    ..5 and 3.1 A resolution, respectively. Crystals of selenomethionine-containing LysX protein were obtained by cross-microseeding, using the native microcrystals as a seed. Structure determination is now in progress...
  27. ncbi request reprint [Structure of the bacterial RNA polymerase holoenzyme]
    Shun ichi Sekine
    Tanpakushitsu Kakusan Koso 48:1-8. 2003
  28. ncbi request reprint Crystallization and preliminary crystallographic analysis of T7 RNA polymerase elongation complex
    Dmitry Temiakov
    Morse Institute of Molecular Genetics, Department of Microbiology and Immunology, SUNY Health Science Center at Brooklyn, 450 Clarkson Avenue, Brooklyn, New York 11203 2098, USA
    Acta Crystallogr D Biol Crystallogr 59:185-7. 2003
    ..An unambiguous molecular-replacement solution was found using the C-terminal portion of the T7 RNA polymerase structure from the early initiation complex as a search model. Model building and structure refinement are now in progress...
  29. ncbi request reprint Structure of a T7 RNA polymerase elongation complex at 2.9 A resolution
    Tahir H Tahirov
    High Throughput Factory, RIKEN Harima Institute at SPring 8, 1 1 1 Kouto, Mikazuki cho, Sayo, Hyogo 679 5148, Japan
    Nature 420:43-50. 2002
    ..The structure implies plausible mechanisms for the various phases of the transcription cycle, and reveals important structural similarities with the multisubunit RNA polymerases...
  30. ncbi request reprint Purification, crystallization and initial crystallographic analysis of RNA polymerase holoenzyme from Thermus thermophilus
    Marina N Vassylyeva
    Genomic Sciences Center RIKEN, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan
    Acta Crystallogr D Biol Crystallogr 58:1497-500. 2002
    ..aquaticus RNA polymerase core enzyme as a search model. The refinement of structure and model building of the sigma(70) subunit is now in progress...
  31. ncbi request reprint An enzyme with a deep trefoil knot for the active-site architecture
    Osamu Nureki
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Japan
    Acta Crystallogr D Biol Crystallogr 58:1129-37. 2002
    ..On the other hand, the amino-terminal domain exhibits a geometrical similarity to the ribosomal proteins which recognize an internal loop of RNA...
  32. ncbi request reprint Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution
    Dmitry G Vassylyev
    Cellular Signaling Laboratory, RIKEN Harima Institute at SPring 8, 1 1 1 Kouto, Mikazuki cho, Sayo, Hyogo 679 5148, Japan
    Nature 417:712-9. 2002
    ..The holoenzyme structure provides insight into the structural organization of transcription intermediate complexes and into the mechanism of transcription initiation...
  33. ncbi request reprint Structural basis for substrate selection by t7 RNA polymerase
    Dmitry Temiakov
    Morse Institute for Molecular Genetics, Department of Microbiology, SUNY Health Science Center, 450 Clarkson Avenue, Brooklyn, New York 11203, USA
    Cell 116:381-91. 2004
    ..Modeling of multisubunit RNAPs suggests that this mechanism might be universal for all RNAPs...
  34. ncbi request reprint Structural basis for transcription regulation by alarmone ppGpp
    Irina Artsimovitch
    Department of Microbiology, Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
    Cell 117:299-310. 2004
    ..We present experimental evidence highlighting the importance of base-specific contacts between ppGpp and specific cytosine residues during both transcription initiation and elongation...
  35. pmc Discrimination against deoxyribonucleotide substrates by bacterial RNA polymerase
    Vladimir Svetlov
    Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
    J Biol Chem 279:38087-90. 2004
    ....
  36. ncbi request reprint Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription
    Anna Perederina
    Cellular Signaling Laboratory, Mikazuki cho, Sayo, Hyogo 679 5148, Japan
    Cell 118:297-309. 2004
    ..Substitution of these residues eliminates the synergy between DksA and ppGpp. Thus, the secondary channel emerges as a common regulatory entrance for transcription factors...
  37. ncbi request reprint Structural basis for template-independent RNA polymerization
    Kozo Tomita
    Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, 1 1 1, Higashi, Tsukuba shi, Ibaragi 305 8666, Japan
    Nature 430:700-4. 2004
    ..Our structure represents the 'pre-insertion' stage of selecting the incoming nucleotide and provides the structural basis for the mechanism underlying template-independent RNA polymerization...
  38. ncbi request reprint Structural basis of transcription inhibition by antibiotic streptolydigin
    Dmitry Temiakov
    Department of Cell Biology, School of Osteopathic Medicine, University of Medicine and Dentistry of New Jersey, Stratford, New Jersey 08084, USA
    Mol Cell 19:655-66. 2005
    ..The results provide a basis for a design of new antibiotics utilizing the Stl-like mechanism...
  39. ncbi request reprint RNA displacement and resolution of the transcription bubble during transcription by T7 RNA polymerase
    Manli Jiang
    Morse Institute of Molecular Genetics, Department of Microbiology and Immunology, SUNY Health Science Center at Brooklyn, 450 Clarkson Avenue, Brooklyn, NY 11203, USA
    Mol Cell 15:777-88. 2004
    ..The results indicate that the transition is a multistep process and reveal a critical role for the nontemplate strand of the DNA...
  40. pmc Purification, crystallization and preliminary X-ray diffraction of SecDF, a translocon-associated membrane protein, from Thermus thermophilus
    Tomoya Tsukazaki
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 62:376-80. 2006
    ..These results provide information that is essential for the determination of the three-dimensional structure of this important membrane component of the protein-translocation machinery...
  41. ncbi request reprint Is it easy to stop RNA polymerase?
    Irina Artsimovitch
    Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
    Cell Cycle 5:399-404. 2006
    ....
  42. ncbi request reprint Cloning, expression, purification, crystallization and initial crystallographic analysis of transcription factor DksA from Escherichia coli
    Marina N Vassylyeva
    Genomic Sciences Center, RIKEN Yokohama Institute, 1 7 22 Suehiro cho, Tsurumi Yokohama 230 0045, Japan
    Acta Crystallogr D Biol Crystallogr 60:1611-3. 2004
    ..0 A at a synchrotron. Three complete atomic resolution multiple anomalous dispersion diffraction data sets were collected from the same crystal of the P2(1)2(1)2(1) crystal form at the absorption edge for Zn atoms...
  43. ncbi request reprint Merging the RNA and DNA worlds
    Irina Artsimovitch
    Nat Struct Mol Biol 14:1122-3. 2007
  44. pmc Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase
    Shuya Fukai
    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo ku, Japan
    RNA 9:100-11. 2003
    ..Therefore, the coiled-coil domain of ValRS is likely to stabilize the L-shaped tRNA structure during the aminoacylation reaction...
  45. pmc The elongation factor RfaH and the initiation factor sigma bind to the same site on the transcription elongation complex
    Anastasiya Sevostyanova
    Department of Microbiology, Ohio State University, 484 West Twelfth Avenue, Columbus, OH 43210, USA
    Proc Natl Acad Sci U S A 105:865-70. 2008
    ..Our findings highlight the key regulatory role played by the clamp helices during both initiation and elongation stages of transcription...

Research Grants1

  1. Molecular mechanisms of transcription elongation
    Dmitry Vassylyev; Fiscal Year: 2009
    ..the facile translocation upon nucleotide addition, the effects of systematic variation of the scaffold components and substitutions of the key RNA polymerase residues that are highlighted by the structure will be analyzed ..