P Cramer

Summary

Affiliation: University of Munich
Country: Germany

Publications

  1. ncbi request reprint Functional architecture of RNA polymerase I
    Claus D Kuhn
    Gene Center Munich and Center for Integrated Protein Science CIPSM, Department of Chemistry and Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Str 25, 81377 Munich, Germany
    Cell 131:1260-72. 2007
  2. ncbi request reprint RNA polymerase II structure: from core to functional complexes
    Patrick Cramer
    Institute of Biochemistry and Gene Center, University of Munich, Feodor Lynen Str 25, 81377 Munich, Germany
    Curr Opin Genet Dev 14:218-26. 2004
  3. pmc The spt5 C-terminal region recruits yeast 3' RNA cleavage factor I
    Andreas Mayer
    Gene Center and Department of Biochemistry, Center for Integrated Protein Science Munich, Ludwig Maximilians Universitat Munchen, Munich, Germany
    Mol Cell Biol 32:1321-31. 2012
  4. pmc The phosphatidylserine receptor from Hydra is a nuclear protein with potential Fe(II) dependent oxygenase activity
    Mihai Cikala
    Department Biologie II, Ludwig Maximilians University Munich, Luisenstr, 14 D 80333 Munich, Germany
    BMC Cell Biol 5:26. 2004
  5. ncbi request reprint Recent structural studies of RNA polymerases II and III
    P Cramer
    Gene Center Munich, Department of Chemistry and Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Biochem Soc Trans 34:1058-61. 2006
  6. doi request reprint Structure of eukaryotic RNA polymerases
    P Cramer
    Gene Center Munich and Center for Integrated Protein Science CIPSM, Department of Chemistry and Biochemistry, Ludwig Maximilians Universitat Munchen, 81377 Munich, Germany
    Annu Rev Biophys 37:337-52. 2008
  7. doi request reprint Towards molecular systems biology of gene transcription and regulation
    Patrick Cramer
    Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig Maximilians University, Gene Center, Feodor Lynen Strasse 25, D 81377 Munich, Germany
    Biol Chem 391:731-5. 2010
  8. ncbi request reprint Molecular biology. Self-correcting messages
    Patrick Cramer
    Gene Center Munich, Department of Chemistry and Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Science 313:447-8. 2006
  9. ncbi request reprint Common structural features of nucleic acid polymerases
    P Cramer
    Institute of Biochemistry, Gene Center, University of Munich, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Bioessays 24:724-9. 2002
  10. ncbi request reprint Multisubunit RNA polymerases
    Patrick Cramer
    Institute of Biochemistry, Gene Center, University of Munich, Feodor Lynen Strasse 25, 81377, Munich, Germany
    Curr Opin Struct Biol 12:89-97. 2002

Collaborators

  • Georg Lipps
  • Roland Beckmann
  • T Carell
  • Albert J R Heck
  • Ralf Peter Jansen
  • Andreas Mayer
  • Dmitry G Vassylyev
  • George A Kassavetis
  • Frank C P Holstege
  • M Famulok
  • Roger Kornberg
  • Johannes Söding
  • Florian Brueckner
  • Karim Jean Armache
  • Hubert Kettenberger
  • Anton Meinhart
  • Sonja Baumli
  • Gerke E Damsma
  • Elisabeth Lehmann
  • Alessandro Vannini
  • Stefan Dengl
  • Sebastian R Geiger
  • Kristina Lorenzen
  • Joanna Andrecka
  • Laurent Lariviere
  • Tobias Koschubs
  • Sabine Hoeppner
  • Jasmin F Sydow
  • Michael Thomm
  • Anna J Jasiak
  • Ekaterina Kashkina
  • Dirk Kostrewa
  • Martin Seizl
  • Anselm G Kusser
  • Adam Muschielok
  • Jens Michaelis
  • Souad Naji
  • Claus D Kuhn
  • Katja Strasser
  • Tomislav Kamenski
  • Kirsten Beck
  • Alan C M Cheung
  • Dietmar E Martin
  • Robert Lewis
  • Florian Brückner
  • Shabaz Mohammed
  • Michela G Bertero
  • Michael Micorescu
  • Susanne Röther
  • Michael Anikin
  • William T McAllister
  • Dmitry Temiakov
  • Erika Vojnic
  • Mihai Cikala
  • David A Bushnell
  • Amelie Schreieck
  • Otto Berninghausen
  • Rieke Ringel
  • Patrizia Hanecker
  • Saana Sandström
  • Jasmin Sydow
  • Alan Cheung
  • Julio Ortiz
  • Maria Angeles Izquierdo Arcusa
  • Mai Sun
  • Kristin Leike
  • Barbara Treutlein
  • Fabian Kurth
  • Mirijam E Zeller
  • Andrew Flatley
  • Patrizia Spitalny
  • Sake van Wageningen
  • Thomas Becker
  • Loes van de Pasch
  • Steve Hahn
  • Christoph Leidig
  • Michael Bartlett
  • Andreas Franke
  • Elisabeth Kremmer
  • Bas van Breukelen
  • Holger Hartmann
  • Heidi Feldmann
  • Anass Jawhari
  • Jörg Renkawitz
  • Elena Karakasili
  • Marian Kalocsay
  • Robert Kerkhoven
  • Sebastian Grünberg
  • Ulrich Hennecke
  • Stefan Jennebach

Detail Information

Publications65

  1. ncbi request reprint Functional architecture of RNA polymerase I
    Claus D Kuhn
    Gene Center Munich and Center for Integrated Protein Science CIPSM, Department of Chemistry and Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Str 25, 81377 Munich, Germany
    Cell 131:1260-72. 2007
    ..In contrast to Pol II, Pol I has a strong intrinsic 3'-RNA cleavage activity, which requires the C-terminal domain of subunit A12.2 and, apparently, enables ribosomal RNA proofreading and 3'-end trimming...
  2. ncbi request reprint RNA polymerase II structure: from core to functional complexes
    Patrick Cramer
    Institute of Biochemistry and Gene Center, University of Munich, Feodor Lynen Str 25, 81377 Munich, Germany
    Curr Opin Genet Dev 14:218-26. 2004
    ..The new studies also show that domains of transcription factors can enter polymerase openings, to modulate function during transcription...
  3. pmc The spt5 C-terminal region recruits yeast 3' RNA cleavage factor I
    Andreas Mayer
    Gene Center and Department of Biochemistry, Center for Integrated Protein Science Munich, Ludwig Maximilians Universitat Munchen, Munich, Germany
    Mol Cell Biol 32:1321-31. 2012
    ..Consistent with this model, the CTR interacts with CFI in vitro but is not required for pA site recognition and transcription termination in vivo...
  4. pmc The phosphatidylserine receptor from Hydra is a nuclear protein with potential Fe(II) dependent oxygenase activity
    Mihai Cikala
    Department Biologie II, Ludwig Maximilians University Munich, Luisenstr, 14 D 80333 Munich, Germany
    BMC Cell Biol 5:26. 2004
    ..Surface exposure of phosphatidylserine is recognised by a specific receptor (phosphatidylserine receptor, PSR) and is required for phagocytosis of apoptotic cells by macrophages and fibroblasts...
  5. ncbi request reprint Recent structural studies of RNA polymerases II and III
    P Cramer
    Gene Center Munich, Department of Chemistry and Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Biochem Soc Trans 34:1058-61. 2006
    ..Finally, we obtained the first structural information on Pol III, in the form of an 11-subunit model obtained by combining a homology model of the nine-subunit core enzyme with a new X-ray structure of the subcomplex C17/25...
  6. doi request reprint Structure of eukaryotic RNA polymerases
    P Cramer
    Gene Center Munich and Center for Integrated Protein Science CIPSM, Department of Chemistry and Biochemistry, Ludwig Maximilians Universitat Munchen, 81377 Munich, Germany
    Annu Rev Biophys 37:337-52. 2008
    ....
  7. doi request reprint Towards molecular systems biology of gene transcription and regulation
    Patrick Cramer
    Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig Maximilians University, Gene Center, Feodor Lynen Strasse 25, D 81377 Munich, Germany
    Biol Chem 391:731-5. 2010
    ..In this article, the efforts of our laboratory to move from an integrated structural biology of gene transcription towards molecular systems biology of gene regulation are reviewed...
  8. ncbi request reprint Molecular biology. Self-correcting messages
    Patrick Cramer
    Gene Center Munich, Department of Chemistry and Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Science 313:447-8. 2006
  9. ncbi request reprint Common structural features of nucleic acid polymerases
    P Cramer
    Institute of Biochemistry, Gene Center, University of Munich, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Bioessays 24:724-9. 2002
    ..All polymerases may undergo "induced fit" upon nucleic acid binding, but the underlying conformational changes differ...
  10. ncbi request reprint Multisubunit RNA polymerases
    Patrick Cramer
    Institute of Biochemistry, Gene Center, University of Munich, Feodor Lynen Strasse 25, 81377, Munich, Germany
    Curr Opin Struct Biol 12:89-97. 2002
    ..Together with a further structure of eukaryotic RNAP bound to DNA and RNA, these results elucidate many aspects of the transcription mechanism, including initiation, elongation, nucleotide addition, processivity and proofreading...
  11. ncbi request reprint Deciphering the RNA polymerase II structure: a personal perspective
    Patrick Cramer
    Gene Center Munich, Department of Chemistry and Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, D 81377 Munich, Germany
    Nat Struct Mol Biol 13:1042-4. 2006
    ..This year's Nobel laureate in chemistry is Roger Kornberg. Patrick Cramer gives a personal account of how the Kornberg laboratory determined the structure of the RNA polymerase II core enzyme...
  12. doi request reprint Structure of an archaeal RNA polymerase
    Anselm G Kusser
    Gene Center Munich and Center for integrated Protein Science CiPS M, Department of Chemistry and Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Str 25, 81377 Munich, Germany
    J Mol Biol 376:303-7. 2008
    ..The structural organization of the archaeal RNA polymerase serves as a reference for future structure-function analysis of the transcription mechanism and allows for evolutionary comparisons...
  13. doi request reprint Structure and in vivo requirement of the yeast Spt6 SH2 domain
    Stefan Dengl
    Gene Center and Center for Integrated Protein Science Munich, Department of Chemistry and Biochemistry, Ludwig Maximilians Universitat Munchen, Munich, Germany
    J Mol Biol 389:211-25. 2009
    ..Differential gene expression analysis reveals that the SH2 domain is required for normal expression of a subset of yeast genes, and is consistent with multiple functions of Spt6 in chromatin transcription...
  14. pmc Structure-function studies of the RNA polymerase II elongation complex
    Florian Brueckner
    Department of Chemistry and Biochemistry, Gene Center Munich and Center for Integrated Protein Science CIPSM, Ludwig Maximilians Universitat Munchen, Munich, Germany
    Acta Crystallogr D Biol Crystallogr 65:112-20. 2009
    ....
  15. doi request reprint Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation
    Florian Brueckner
    Gene Center and Center for Integrated Protein Science Munich CIPSM, Department of Chemistry and Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Nat Struct Mol Biol 15:811-8. 2008
    ....
  16. ncbi request reprint Molecular basis of RNA-dependent RNA polymerase II activity
    Elisabeth Lehmann
    Gene Center Munich and Center for Integrated Protein Science CIPSM, Department of Chemistry and Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Nature 450:445-9. 2007
    ..The RdRP activity of Pol II provides a missing link in molecular evolution, because it suggests that Pol II evolved from an ancient replicase that duplicated RNA genomes...
  17. ncbi request reprint Recognition of RNA polymerase II carboxy-terminal domain by 3'-RNA-processing factors
    Anton Meinhart
    Department of Chemistry and Biochemistry, Gene Center, University of Munich, 81377 Munich, Germany
    Nature 430:223-6. 2004
    ..The model suggests that, during the mRNA transcription-processing cycle, compact spiral regions in the CTD are unravelled and regenerated in a phosphorylation-dependent manner...
  18. doi request reprint RNA polymerase I contains a TFIIF-related DNA-binding subcomplex
    Sebastian R Geiger
    Gene Center and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Mol Cell 39:583-94. 2010
    ..Thus, Pol I/III subunits that have no counterparts in Pol II are evolutionarily related to Pol II initiation factors and may have evolved to mediate promoter specificity and transcription processivity...
  19. ncbi request reprint Structure and function of RNA polymerase II
    Patrick Cramer
    Institute of Biochemistry and Gene Center, University of Munich, 81377 Munich, Germany
    Adv Protein Chem 67:1-42. 2004
  20. ncbi request reprint CPD damage recognition by transcribing RNA polymerase II
    Florian Brueckner
    Munich Center for Integrated Protein Science CiPS, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Science 315:859-62. 2007
    ..This is consistent with nonallosteric recruitment of repair factors and excision of a lesion-containing DNA fragment in the presence of Pol II...
  21. ncbi request reprint Fluorescence detection of nucleic acids and proteins in multi-component crystals
    Hubert Kettenberger
    Gene Center, University of Munich, Department of Chemistry and Biochemistry, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Acta Crystallogr D Biol Crystallogr 62:146-50. 2006
    ..Additional experiments suggest the general applicability of these fluorescence assays for the characterization of crystal contents...
  22. ncbi request reprint Structure and carboxyl-terminal domain (CTD) binding of the Set2 SRI domain that couples histone H3 Lys36 methylation to transcription
    Erika Vojnic
    Gene Center, Department of Chemistry and Biochemistry, Ludwig Maximilians University of Munich, Feodor Lynen Strasse 25, 81377 Munich, Germany
    J Biol Chem 281:13-5. 2006
    ..Unexpectedly, the SRI domain fold resembles the structure of an RNA polymerase-interacting domain in bacterial sigma factors (domain sigma2 in sigma70)...
  23. pmc Architecture of initiation-competent 12-subunit RNA polymerase II
    Karim Jean Armache
    Institute of Biochemistry and Gene Center, University of Munich, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Proc Natl Acad Sci U S A 100:6964-8. 2003
    ..The core-Rpb7 interaction and some functions of Rpb4/7 are apparently conserved in all eukaryotic and archaeal RNA polymerases but not in the bacterial enzyme...
  24. ncbi request reprint An extended winged helix domain in general transcription factor E/IIE alpha
    Anton Meinhart
    Institute of Biochemistry, Gene Center, University of Munich, Feodor Lynen Strasse 25, 81377 Munich, Germany
    J Biol Chem 278:48267-74. 2003
    ..Homology modeling shows that the TFE domain is conserved in TFIIE alpha, including the potential functional surfaces...
  25. ncbi request reprint Structure and TBP binding of the Mediator head subcomplex Med8-Med18-Med20
    Laurent Lariviere
    Gene Center Munich, Department of Chemistry and Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Str 25, 81377 Munich, Germany
    Nat Struct Mol Biol 13:895-901. 2006
    ....
  26. ncbi request reprint Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS
    Hubert Kettenberger
    Gene Center, Department of Chemistry and Biochemistry, Ludwig Maximilians University of Munich, Feodor Lynen Str 25, 81377 Munich, Germany
    Mol Cell 16:955-65. 2004
    ..Binding of the elongation factor TFIIS realigns RNA in the active center, possibly converting the elongation complex to an alternative state less prone to stalling...
  27. ncbi request reprint Mechanism of transcriptional stalling at cisplatin-damaged DNA
    Gerke E Damsma
    Center for Integrated Protein Science CIPSM, Department of Chemistry and Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Nat Struct Mol Biol 14:1127-33. 2007
    ..The stalling mechanism differs from that of Pol II stalling at a photolesion, which involves delivery of the lesion to the active site and lesion-templated misincorporation that blocks transcription...
  28. pmc Identification, structure, and functional requirement of the Mediator submodule Med7N/31
    Tobias Koschubs
    Gene Center and Center for Integrated Protein Science Munich CIPSM, Department of Chemistry and Biochemistry, Ludwig Maximilians Universität LMU München, Munich, Germany
    EMBO J 28:69-80. 2009
    ..Comparative phenotyping and transcriptome profiling identify specific and overlapping functions of different Mediator submodules...
  29. doi request reprint RNA polymerase fidelity and transcriptional proofreading
    Jasmin F Sydow
    Gene Center Munich and Center for Integrated Protein Science Munich, Department of Chemistry and Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Str 25, 81377 Munich, Germany
    Curr Opin Struct Biol 19:732-9. 2009
    ..Since cleavage occurs at the same active site that is used for polymerization, the RNAP proofreading mechanism differs from that used by DNAPs, which contain a distinct nuclease specific active site...
  30. pmc Molecular basis of transcriptional mutagenesis at 8-oxoguanine
    Gerke E Damsma
    Gene Center and Center for Integrated Protein Science Munich CIPSM, Department of Chemistry and Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, 81377 Munich, Germany
    J Biol Chem 284:31658-63. 2009
    ..The misincorporated adenine escapes intrinsic proofreading, resulting in transcriptional mutagenesis that is observed directly by mass spectrometric RNA analysis...
  31. pmc Nano positioning system reveals the course of upstream and nontemplate DNA within the RNA polymerase II elongation complex
    Joanna Andrecka
    Department of Chemistry and Biochemistry and Center for Integrated Protein Science München, Ludwig Maximilians Universitat Munchen, Butenandtstr 11, 81377 Munchen, Germany
    Nucleic Acids Res 37:5803-9. 2009
    ..Comparison with published data suggests that the architecture of the complete EC is conserved from bacteria to eukaryotes and that upstream DNA is relocated during the initiation-elongation transition...
  32. pmc Crystallization of RNA polymerase I subcomplex A14/A43 by iterative prediction, probing and removal of flexible regions
    Sebastian R Geiger
    Gene Center Munich, Center for Integrated Protein Science CIPSM and Department of Chemistry and Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Acta Crystallogr Sect F Struct Biol Cryst Commun 64:413-8. 2008
    ..This strategy should enable the crystallization of other proteins and subcomplexes with multiple flexibilities, as required for hybrid structure solution of large macromolecular assemblies...
  33. pmc Structure-system correlation identifies a gene regulatory Mediator submodule
    Laurent Lariviere
    Gene Center Munich and Center for Integrated Protein Science CIPSM, Department of Chemistry and Biochemistry, Ludwig Maximilians Universitat Munchen, 81377 Munich, Germany
    Genes Dev 22:872-7. 2008
    ..The presented structure-based system perturbation is superior to gene deletion analysis of gene regulation...
  34. doi request reprint Uniform transitions of the general RNA polymerase II transcription complex
    Andreas Mayer
    Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science, Ludwig Maximilians Universitat Munchen, Munich, Germany
    Nat Struct Mol Biol 17:1272-8. 2010
    ..Transitions are uniform and independent of gene length, type and expression...
  35. doi request reprint Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA
    Jasmin F Sydow
    Department of Chemistry and Biochemistry, Gene Center Munich and Center for Integrated Protein Science CIPSM, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Mol Cell 34:710-21. 2009
    ....
  36. ncbi request reprint Structure and mechanism of RNA polymerase II CTD phosphatases
    Tomislav Kamenski
    Department of Chemistry and Biochemistry, Gene Center, University of Munich, Feodor Lynen Str 25, 81377 Munich, Germany
    Mol Cell 15:399-407. 2004
    ..Fcp1 specificity may additionally arise from phosphatase recruitment near the CTD via the Pol II subcomplex Rpb4/7, which is shown to be required for binding of Fcp1 to the polymerase in vitro...
  37. ncbi request reprint Structure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs
    Hubert Kettenberger
    Gene Center, University of Munich, Department of Chemistry and Biochemistry, Feodor Lynen Str 25, 81377 Munich, Germany
    Nat Struct Mol Biol 13:44-8. 2006
    ..The structure also indicates that A-form RNA could interact with Pol II similarly to a B-form DNA promoter, as suggested for the bacterial transcription inhibitor 6S RNA...
  38. ncbi request reprint Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage
    Hubert Kettenberger
    Institute of Biochemistry, Gene Center, University of Munich, Feodor Lynen Str 25, 81377 Munich, Germany
    Cell 114:347-57. 2003
    ..Our results support the idea that Pol II contains a single tunable active site for RNA polymerization and cleavage, in contrast to DNA polymerases with two separate active sites for DNA polymerization and cleavage...
  39. ncbi request reprint The dynamic machinery of mRNA elongation
    Karim Jean Armache
    Department of Chemistry and Biochemistry, Gene Center, Ludwig Maximilians University of Munich, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Curr Opin Struct Biol 15:197-203. 2005
    ....
  40. ncbi request reprint A structural perspective of CTD function
    Anton Meinhart
    Department of Chemistry and Biochemistry, Gene Center, University of Munich LMU, 81377 Munich, Germany
    Genes Dev 19:1401-15. 2005
    ..The catalytic mechanisms of CTD kinases and phosphatases are known, but the basis for CTD specificity of these enzymes remains to be understood...
  41. ncbi request reprint DNA photodamage recognition by RNA polymerase II
    Florian Brueckner
    Gene Center Munich, Department of Chemistry and Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, D 81377 Munich, Germany
    FEBS Lett 581:2757-60. 2007
    ..The study provided the molecular basis for recognition of a damaged DNA by Pol II, which is the first step in transcription-coupled DNA repair (TCR). The results have general implications for damage recognition and the TCR mechanism...
  42. doi request reprint A nano-positioning system for macromolecular structural analysis
    Adam Muschielok
    Department of Chemistry and Biochemistry and Center for Integrated Protein Science München, Ludwig Maximilians Universitat Munchen, Butenandtstrasse 11, 81377 Munchen, Germany
    Nat Methods 5:965-71. 2008
    ....
  43. ncbi request reprint Structural biology of RNA polymerase III: subcomplex C17/25 X-ray structure and 11 subunit enzyme model
    Anna J Jasiak
    Department of Chemistry and Biochemistry, Gene Center, Ludwig Maximilians University of Munich, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Mol Cell 23:71-81. 2006
    ..During elongation, C17/25 may bind Pol III transcripts emerging from the adjacent exit pore, because the subcomplex binds to tRNA in vitro...
  44. pmc Torpedo nuclease Rat1 is insufficient to terminate RNA polymerase II in vitro
    Stefan Dengl
    Gene Center and Center for Integrated Protein Science Munich, Department of Chemistry and Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, 81377 Munich, Germany
    J Biol Chem 284:21270-9. 2009
    ..Thus, pol II termination apparently requires a factor or several factors in addition to Rat1, Rai1, and Rtt103, post-translational modifications of these factors, or unusual reaction conditions...
  45. ncbi request reprint Structure of a bifunctional DNA primase-polymerase
    Georg Lipps
    Institute of Biochemistry, University of Bayreuth, Universitatsstrasse 30, D 95447 Bayreuth, Germany
    Nat Struct Mol Biol 11:157-62. 2004
    ..We propose that archaeal and eukaryotic primases and the prim-pol domain have a common evolutionary ancestor, a bifunctional replicase for small DNA genomes...
  46. pmc Single-molecule tracking of mRNA exiting from RNA polymerase II
    Joanna Andrecka
    Munich Center for Integrated Protein Science CiPS and Center for Nanoscience CeNS, Ludwig Maximilians Universitat Munchen, 81377 Munich, Germany
    Proc Natl Acad Sci U S A 105:135-40. 2008
    ..RNA further extends toward the linker connecting to the polymerase C-terminal repeat domain (CTD), which binds the 5'-capping enzyme and other RNA processing factors...
  47. pmc Genome-associated RNA polymerase II includes the dissociable Rpb4/7 subcomplex
    Anna J Jasiak
    Gene Center and Center for Integrated Protein Science Munich CIPSM, Department of Chemistry and Biochemistry, Ludwig Maximilians University of Munich, Feodor Lynen Strasse 25, D 81377 Munich, Germany
    J Biol Chem 283:26423-7. 2008
    ..Thus, the complete Pol II associates with DNA in vivo, consistent with functional roles of Rpb4/7 throughout the transcription cycle...
  48. ncbi request reprint A conserved mediator hinge revealed in the structure of the MED7.MED21 (Med7.Srb7) heterodimer
    Sonja Baumli
    Gene Center, University of Munich Ludwig Maximilians Universität, Department of Chemistry and Biochemistry, Feodor Lynen Strasse 25, 81377 Munich, Germany
    J Biol Chem 280:18171-8. 2005
    ..MED21 hinge could account for changes in overall Mediator structure upon binding to Pol II or activators. Our results support the idea that transcription regulation involves conformational changes within the general machinery...
  49. ncbi request reprint Structures of complete RNA polymerase II and its subcomplex, Rpb4/7
    Karim Jean Armache
    Gene Center, University of Munich LMU, Department of Chemistry and Biochemistry, Feodor Lynen Strasse 25, 81377 Munich, Germany
    J Biol Chem 280:7131-4. 2005
    ....
  50. doi request reprint Molecular basis of RNA polymerase III transcription repression by Maf1
    Alessandro Vannini
    Gene Center and Department of Biochemistry, Center for Integrated Protein Science Munich CIPSM, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Cell 143:59-70. 2010
    ..These results explain how Maf1 specifically represses transcription initiation from Pol III promoters and indicate that Maf1 also prevents reinitiation by binding Pol III during transcription elongation...
  51. doi request reprint RNA polymerase II-TFIIB structure and mechanism of transcription initiation
    Dirk Kostrewa
    Gene Center Munich and Center for Integrated Protein Science Munich CIPSM, Department of Chemistry and Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Nature 462:323-30. 2009
    ..Synthesis of the RNA chain and rewinding of upstream DNA displace the B-reader and B-linker, respectively, to trigger B release and elongation complex formation...
  52. doi request reprint A movie of the RNA polymerase nucleotide addition cycle
    Florian Brueckner
    Gene Center and Center for Integrated Protein Science Munich CIPSM, Department of Chemistry and Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Curr Opin Struct Biol 19:294-9. 2009
    ..The movie facilitates teaching and a mechanistic analysis of transcription and can be downloaded from http://www.lmb.uni-muenchen.de/cramer/pr-materials...
  53. ncbi request reprint Structure of the mediator subunit cyclin C and its implications for CDK8 function
    Sabine Hoeppner
    Gene Center, University of Munich LMU, Department of Chemistry and Biochemistry, Feodor Lynen Str 25, 81377 Munich, Germany
    J Mol Biol 350:833-42. 2005
    ..In CDK8, this loop is longer and the threonine is absent, suggesting an alternative mechanism of activation that we discuss based on a CDK8-cyclin C model...
  54. ncbi request reprint The mRNA transcription/processing factor Ssu72 is a potential tyrosine phosphatase
    Anton Meinhart
    Institute of Biochemistry, Gene Center, University of Munich, Feodor Lynen Strasse 25, 81377 Munich, Germany
    J Biol Chem 278:15917-21. 2003
    ..The novel Ssu72 activity may regulate coupling events during mRNA biogenesis...
  55. pmc The archaeo-eukaryotic primase of plasmid pRN1 requires a helix bundle domain for faithful primer synthesis
    Kirsten Beck
    Institute of Biochemistry, University of Bayreuth, Universitatsstrasse 30, 95447 Bayreuth, Germany
    Nucleic Acids Res 38:6707-18. 2010
    ..Furthermore, we identified mutants of the C-terminal domain, which are defective in template binding, dinucleotide formation and conformation change prior to DNA extension...
  56. pmc Preparation and topology of the Mediator middle module
    Tobias Koschubs
    Department of Biochemistry, Gene Center Munich and Center for Integrated Protein Science Munich, Ludwig Maximilians Universitat Munchen, Feodor Lynen St 25, 81377 Munich, Germany
    Nucleic Acids Res 38:3186-95. 2010
    ..The subunits, Med1 and Med10, which bridge to the Mediator tail module, bind to both Med7 and Med4...
  57. ncbi request reprint Gene transcription: extending the message
    Patrick Cramer
    Nature 448:142-3. 2007
  58. ncbi request reprint Multisubunit RNA polymerases melt only a single DNA base pair downstream of the active site
    Ekaterina Kashkina
    Department of Cell Biology, University of Medicine and Dentistry of New Jersey, School of Osteopathic Medicine, Stratford, NJ 08084, USA
    J Biol Chem 282:21578-82. 2007
    ..These data argue against a model in which multiple NTPs are lined up downstream of the active site...
  59. ncbi request reprint Finding the right spot to start transcription
    Patrick Cramer
    Nat Struct Mol Biol 14:686-7. 2007
  60. pmc Structural basis of transcription: alpha-amanitin-RNA polymerase II cocrystal at 2.8 A resolution
    David A Bushnell
    Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305 5126, USA
    Proc Natl Acad Sci U S A 99:1218-22. 2002
    ..The structure of the complex indicates the likely basis of inhibition and gives unexpected insight into the transcription mechanism...
  61. pmc Structure-function analysis of the RNA polymerase cleft loops elucidates initial transcription, DNA unwinding and RNA displacement
    Souad Naji
    Lehrstuhl fur Mikrobiologie und Archaeenzentrum, Universitat Regensburg, Universitatsstrasse 31, D 93053 Regensburg, Germany
    Nucleic Acids Res 36:676-87. 2008
    ..During elongation, downstream DNA strand separation required template strand binding to an invariant arginine in switch 2, and apparently interaction of an invariant arginine in fork 2 with the non-template strand...
  62. ncbi request reprint Template misalignment in multisubunit RNA polymerases and transcription fidelity
    Ekaterina Kashkina
    Department of Cell Biology, School of Osteopathic Medicine, University of Medicine and Dentistry of New Jersey, 42 East Laurel Road, Stratford, New Jersey 08084, USA
    Mol Cell 24:257-66. 2006
    ..Analysis of the effects of different template topologies on misincorporation indicates that the duplex DNA immediately downstream of the active site plays an important role in transcription fidelity...
  63. ncbi request reprint Structural biology of RNA polymerase III: mass spectrometry elucidates subcomplex architecture
    Kristina Lorenzen
    Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Chemistry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
    Structure 15:1237-45. 2007
    ..These data suggest that Pol III consists of a 10 subunit Pol II-like core; the peripheral heterodimers C17/25, C53/37, and C82/34; and subunit C31, which bridges between C82/34, C17/25, and the core...
  64. pmc Archaeal transcription: function of an alternative transcription factor B from Pyrococcus furiosus
    Michael Micorescu
    Department of Biology, Portland State University, P O Box 751, Portland, OR 97207, USA
    J Bacteriol 190:157-67. 2008
    ..The results indicate that the TFB N-terminal region, containing conserved Zn ribbon and B-finger motifs, is important in promoter opening and that TFE can compensate for defects in the N terminus through enhancement of promoter opening...
  65. doi request reprint Multiplexed proteomics mapping of yeast RNA polymerase II and III allows near-complete sequence coverage and reveals several novel phosphorylation sites
    Shabaz Mohammed
    Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Chemistry, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
    Anal Chem 80:3584-92. 2008
    ..The described multiplexed proteomics approach is generic and reveals that it is possible to map a protein complex to near completion while applying less than 5 mug (approximately 10 pmol) of total starting material...