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PDBsum entry 2o5j

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protein dna_rna ligands metals Protein-protein interface(s) links
Transferase/DNA-RNA hybrid PDB id
2o5j
Jmol
Contents
Protein chains
229 a.a. *
1119 a.a. *
1264 a.a. *
95 a.a. *
DNA/RNA
Ligands
APC ×2
Metals
_ZN ×4
_MG ×4
Waters ×2633
* Residue conservation analysis
PDB id:
2o5j
Name: Transferase/DNA-RNA hybrid
Title: Crystal structure of the t. Thermophilus rnap polymerase elo complex with the ntp substrate analog
Structure: 5'-d(p Cp Cp Cp Tp Gp Tp Cp Tp Gp Gp Cp Gp Tp Tp P Cp Gp Cp Cp G)-3'. Chain: g, x. Engineered: yes. Other_details: DNA template strand. 5'-r(p Gp Ap Gp Up Cp Up Gp Cp Gp Gp Cp Gp Cp Gp Chain: h, y. Engineered: yes. Other_details: RNA transcript.
Source: Synthetic: yes. Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Strain: hb8
Resolution:
3.00Å     R-factor:   0.225     R-free:   0.257
Authors: D.G.Vassylyev,M.N.Vassylyeva
Key ref:
D.G.Vassylyev et al. (2007). Structural basis for substrate loading in bacterial RNA polymerase. Nature, 448, 163-168. PubMed id: 17581591 DOI: 10.1038/nature05931
Date:
06-Dec-06     Release date:   03-Jul-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q5SHR6  (RPOA_THET8) -  DNA-directed RNA polymerase subunit alpha
Seq:
Struc:
315 a.a.
229 a.a.
Protein chains
Pfam   ArchSchema ?
Q8RQE9  (RPOB_THET8) -  DNA-directed RNA polymerase subunit beta
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1119 a.a.
1119 a.a.
Protein chains
Pfam   ArchSchema ?
Q8RQE8  (RPOC_THET8) -  DNA-directed RNA polymerase subunit beta'
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1524 a.a.
1264 a.a.
Protein chains
Pfam   ArchSchema ?
Q8RQE7  (RPOZ_THET8) -  DNA-directed RNA polymerase subunit omega
Seq:
Struc:
99 a.a.
95 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, K, L, M, N, O: E.C.2.7.7.6  - DNA-directed Rna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Nucleoside triphosphate
+ RNA(n)
= diphosphate
+ RNA(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA repair   2 terms 
  Biochemical function     transferase activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1038/nature05931 Nature 448:163-168 (2007)
PubMed id: 17581591  
 
 
Structural basis for substrate loading in bacterial RNA polymerase.
D.G.Vassylyev, M.N.Vassylyeva, J.Zhang, M.Palangat, I.Artsimovitch, R.Landick.
 
  ABSTRACT  
 
The mechanism of substrate loading in multisubunit RNA polymerase is crucial for understanding the general principles of transcription yet remains hotly debated. Here we report the 3.0-A resolution structures of the Thermus thermophilus elongation complex (EC) with a non-hydrolysable substrate analogue, adenosine-5'-[(alpha,beta)-methyleno]-triphosphate (AMPcPP), and with AMPcPP plus the inhibitor streptolydigin. In the EC/AMPcPP structure, the substrate binds to the active ('insertion') site closed through refolding of the trigger loop (TL) into two alpha-helices. In contrast, the EC/AMPcPP/streptolydigin structure reveals an inactive ('preinsertion') substrate configuration stabilized by streptolydigin-induced displacement of the TL. Our structural and biochemical data suggest that refolding of the TL is vital for catalysis and have three main implications. First, despite differences in the details, the two-step preinsertion/insertion mechanism of substrate loading may be universal for all RNA polymerases. 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.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: Structures of the substrate complexes. The same colour scheme is used in all figures. The DNA template, non-template and RNA strands are in red, blue and yellow, respectively. The BH, the TH and the rest of the RNAP molecule are in magenta, cyan and grey, respectively. The insertion and preinsertion NTP analogues and Stl are designated by green, orange and black, respectively. The catalytic Mg^2+ ions (MgI and MgII) are shown as magenta spheres. a, b, Overall views of the ttEC/AMPcPP (a) and EC/AMPcPP/Stl (b) complexes. CC, coiled coil. c, d, Superposition of the NTPs (c, d) and TH (d) in the insertion (green, NTP; cyan, TH) and preinsertion (orange, NTP; blue, TH) complexes.
Figure 5.
Figure 5: Nucleotide addition cycle. The substrate loading pathway in bacterial RNAP.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2007, 448, 163-168) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23151482 S.Sainsbury, J.Niesser, and P.Cramer (2013).
Structure and function of the initially transcribing RNA polymerase II-TFIIB complex.
  Nature, 493, 437-440.
PDB codes: 4bbr 4bbs
21346759 A.C.Cheung, and P.Cramer (2011).
Structural basis of RNA polymerase II backtracking, arrest and reactivation.
  Nature, 471, 249-253.
PDB codes: 3po2 3po3
  21435034 G.Swapna, A.Chakraborty, V.Kumari, R.Sen, and V.Nagaraja (2011).
Mutations in β' subunit of Escherichia coli RNA polymerase perturb the activator polymerase functional interaction required for promoter clearance.
  Mol Microbiol, 80, 1169-1185.  
21321236 M.L.Gleghorn, E.K.Davydova, R.Basu, L.B.Rothman-Denes, and K.S.Murakami (2011).
X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides.
  Proc Natl Acad Sci U S A, 108, 3566-3571.
PDB codes: 3q0a 3q22 3q23 3q24
21447716 S.R.Kennedy, and D.A.Erie (2011).
Templated nucleoside triphosphate binding to a noncatalytic site on RNA polymerase regulates transcription.
  Proc Natl Acad Sci U S A, 108, 6079-6084.  
21562494 T.Tsukazaki, H.Mori, Y.Echizen, R.Ishitani, S.Fukai, T.Tanaka, A.Perederina, D.G.Vassylyev, T.Kohno, A.D.Maturana, K.Ito, and O.Nureki (2011).
Structure and function of a membrane component SecDF that enhances protein export.
  Nature, 474, 235-238.
PDB codes: 2rrn 3aqo 3aqp
21071662 B.Pan, Y.Xiong, and T.A.Steitz (2010).
How the CCA-adding enzyme selects adenine over cytosine at position 76 of tRNA.
  Science, 330, 937-940.
PDB codes: 3ouy 3ov7 3ova 3ovb 3ovs
20598112 C.D.Kaplan (2010).
The architecture of RNA polymerase fidelity.
  BMC Biol, 8, 85.  
20457751 D.Pupov, N.Miropolskaya, A.Sevostyanova, I.Bass, I.Artsimovitch, and A.Kulbachinskiy (2010).
Multiple roles of the RNA polymerase {beta}' SW2 region in transcription initiation, promoter escape, and RNA elongation.
  Nucleic Acids Res, 38, 5784-5796.  
20360047 G.Ruprich-Robert, and P.Thuriaux (2010).
Non-canonical DNA transcription enzymes and the conservation of two-barrel RNA polymerases.
  Nucleic Acids Res, 38, 4559-4569.  
20127927 J.C.Carlson, J.L.Fortman, Y.Anzai, S.Li, D.A.Burr, and D.H.Sherman (2010).
Identification of the tirandamycin biosynthetic gene cluster from Streptomyces sp. 307-9.
  Chembiochem, 11, 564-572.  
  20856905 N.Opalka, J.Brown, W.J.Lane, K.A.Twist, R.Landick, F.J.Asturias, and S.A.Darst (2010).
Complete structural model of Escherichia coli RNA polymerase from a hybrid approach.
  PLoS Biol, 8, 0.
PDB codes: 3lti 3lu0
20482321 P.Cramer (2010).
Towards molecular systems biology of gene transcription and regulation.
  Biol Chem, 391, 731-735.  
21114873 P.P.Hein, and R.Landick (2010).
The bridge helix coordinates movements of modules in RNA polymerase.
  BMC Biol, 8, 141.  
20030589 R.Wurm, T.Neusser, and R.Wagner (2010).
6S RNA-dependent inhibition of RNA polymerase is released by RNA-dependent synthesis of small de novo products.
  Biol Chem, 391, 187-196.  
21124318 S.Tagami, S.Sekine, T.Kumarevel, N.Hino, Y.Murayama, S.Kamegamori, M.Yamamoto, K.Sakamoto, and S.Yokoyama (2010).
Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein.
  Nature, 468, 978-982.
PDB codes: 3aoh 3aoi
19895816 W.J.Lane, and S.A.Darst (2010).
Molecular evolution of multisubunit RNA polymerases: structural analysis.
  J Mol Biol, 395, 686-704.  
19895820 W.J.Lane, and S.A.Darst (2010).
Molecular evolution of multisubunit RNA polymerases: sequence analysis.
  J Mol Biol, 395, 671-685.  
20798057 X.Huang, D.Wang, D.R.Weiss, D.A.Bushnell, R.D.Kornberg, and M.Levitt (2010).
RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription.
  Proc Natl Acad Sci U S A, 107, 15745-15750.  
20459653 Y.Yuzenkova, A.Bochkareva, V.R.Tadigotla, M.Roghanian, S.Zorov, K.Severinov, and N.Zenkin (2010).
Stepwise mechanism for transcription fidelity.
  BMC Biol, 8, 54.  
20534498 Y.Yuzenkova, and N.Zenkin (2010).
Central role of the RNA polymerase trigger loop in intrinsic RNA hydrolysis.
  Proc Natl Acad Sci U S A, 107, 10878-10883.  
20497334 Z.Baharoglu, R.Lestini, S.Duigou, and B.Michel (2010).
RNA polymerase mutations that facilitate replication progression in the rep uvrD recF mutant lacking two accessory replicative helicases.
  Mol Microbiol, 77, 324-336.  
19605532 A.C.Rhee, B.H.Somerlot, N.Parimi, and J.M.Gott (2009).
Distinct roles for sequences upstream of and downstream from Physarum editing sites.
  RNA, 15, 1753-1765.  
19903881 B.P.Hudson, J.Quispe, S.Lara-González, Y.Kim, H.M.Berman, E.Arnold, R.H.Ebright, and C.L.Lawson (2009).
Three-dimensional EM structure of an intact activator-dependent transcription initiation complex.
  Proc Natl Acad Sci U S A, 106, 19830-19835.
PDB code: 3iyd
19489723 E.Nudler (2009).
RNA polymerase active center: the molecular engine of transcription.
  Annu Rev Biochem, 78, 335-361.  
19481445 F.Brueckner, J.Ortiz, and P.Cramer (2009).
A movie of the RNA polymerase nucleotide addition cycle.
  Curr Opin Struct Biol, 19, 294-299.  
19171965 F.Brueckner, K.J.Armache, A.Cheung, G.E.Damsma, H.Kettenberger, E.Lehmann, J.Sydow, and P.Cramer (2009).
Structure-function studies of the RNA polymerase II elongation complex.
  Acta Crystallogr D Biol Crystallogr, 65, 112-120.  
18946472 G.A.Belogurov, M.N.Vassylyeva, A.Sevostyanova, J.R.Appleman, A.X.Xiang, R.Lira, S.E.Webber, S.Klyuyev, E.Nudler, I.Artsimovitch, and D.G.Vassylyev (2009).
Transcription inactivation through local refolding of the RNA polymerase structure.
  Nature, 457, 332-335.
PDB code: 3eql
19458260 H.Spåhr, G.Calero, D.A.Bushnell, and R.D.Kornberg (2009).
Schizosacharomyces pombe RNA polymerase II at 3.6-A resolution.
  Proc Natl Acad Sci U S A, 106, 9185-9190.
PDB code: 3h0g
19560423 J.F.Sydow, F.Brueckner, A.C.Cheung, G.E.Damsma, S.Dengl, E.Lehmann, D.Vassylyev, and P.Cramer (2009).
Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA.
  Mol Cell, 34, 710-721.
PDB codes: 3hou 3hov 3how 3hox 3hoy 3hoz
19416863 M.L.Kireeva, and M.Kashlev (2009).
Mechanism of sequence-specific pausing of bacterial RNA polymerase.
  Proc Natl Acad Sci U S A, 106, 8900-8905.  
19659121 M.Voliotis, N.Cohen, C.Molina-París, and T.B.Liverpool (2009).
Backtracking and proofreading in DNA transcription.
  Phys Rev Lett, 102, 258101.  
19926275 M.X.Ho, B.P.Hudson, K.Das, E.Arnold, and R.H.Ebright (2009).
Structures of RNA polymerase-antibiotic complexes.
  Curr Opin Struct Biol, 19, 715-723.  
19855007 N.Miropolskaya, I.Artsimovitch, S.Klimasauskas, V.Nikiforov, and A.Kulbachinskiy (2009).
Allosteric control of catalysis by the F loop of RNA polymerase.
  Proc Natl Acad Sci U S A, 106, 18942-18947.  
19470457 R.Landick (2009).
Transcriptional pausing without backtracking.
  Proc Natl Acad Sci U S A, 106, 8797-8798.  
19278646 R.Landick (2009).
Functional divergence in the growing family of RNA polymerases.
  Structure, 17, 323-325.  
19171784 S.T.Rutherford, C.L.Villers, J.H.Lee, W.Ross, and R.L.Gourse (2009).
Allosteric control of Escherichia coli rRNA promoter complexes by DksA.
  Genes Dev, 23, 236-248.  
18022639 A.Dimitri, A.K.Goodenough, F.P.Guengerich, S.Broyde, and D.A.Scicchitano (2008).
Transcription processing at 1,N2-ethenoguanine by human RNA polymerase II and bacteriophage T7 RNA polymerase.
  J Mol Biol, 375, 353-366.  
18235446 A.Hirata, B.J.Klein, and K.S.Murakami (2008).
The X-ray crystal structure of RNA polymerase from Archaea.
  Nature, 451, 851-854.
PDB codes: 2pa8 2pmz 3hkz
18538653 C.D.Kaplan, K.M.Larsson, and R.D.Kornberg (2008).
The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin.
  Mol Cell, 30, 547-556.
PDB code: 3cqz
19090964 C.D.Kaplan, and R.D.Kornberg (2008).
A bridge to transcription by RNA polymerase.
  J Biol, 7, 39.  
18272182 C.E.Vrentas, T.Gaal, M.B.Berkmen, S.T.Rutherford, S.P.Haugen, D.G.Vassylyev, W.Ross, and R.L.Gourse (2008).
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.
  J Mol Biol, 377, 551-564.  
18482981 D.Dutta, J.Chalissery, and R.Sen (2008).
Transcription termination factor rho prefers catalytically active elongation complexes for releasing RNA.
  J Biol Chem, 283, 20243-20251.  
18552824 F.Brueckner, and P.Cramer (2008).
Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation.
  Nat Struct Mol Biol, 15, 811-818.
PDB code: 2vum
18468900 F.Werner (2008).
Structural evolution of multisubunit RNA polymerases.
  Trends Microbiol, 16, 247-250.  
18729732 J.W.Roberts, S.Shankar, and J.J.Filter (2008).
RNA polymerase elongation factors.
  Annu Rev Microbiol, 62, 211-233.  
18358810 M.H.Larson, W.J.Greenleaf, R.Landick, and S.M.Block (2008).
Applied force reveals mechanistic and energetic details of transcription termination.
  Cell, 132, 971-982.  
18538654 M.L.Kireeva, Y.A.Nedialkov, G.H.Cremona, Y.A.Purtov, L.Lubkowska, F.Malagon, Z.F.Burton, J.N.Strathern, and M.Kashlev (2008).
Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation.
  Mol Cell, 30, 557-566.  
18573085 P.Cramer, K.J.Armache, S.Baumli, S.Benkert, F.Brueckner, C.Buchen, G.E.Damsma, S.Dengl, S.R.Geiger, A.J.Jasiak, A.Jawhari, S.Jennebach, T.Kamenski, H.Kettenberger, C.D.Kuhn, E.Lehmann, K.Leike, J.F.Sydow, and A.Vannini (2008).
Structure of eukaryotic RNA polymerases.
  Annu Rev Biophys, 37, 337-352.  
18280161 S.Borukhov, and E.Nudler (2008).
RNA polymerase: the vehicle of transcription.
  Trends Microbiol, 16, 126-134.  
18669632 T.F.Cheng, X.Hu, A.Gnatt, and P.J.Brooks (2008).
Differential Blocking Effects of the Acetaldehyde-derived DNA Lesion N2-Ethyl-2'-deoxyguanosine on Transcription by Multisubunit and Single Subunit RNA Polymerases.
  J Biol Chem, 283, 27820-27828.  
18923527 T.Tsukazaki, H.Mori, S.Fukai, R.Ishitani, T.Mori, N.Dohmae, A.Perederina, Y.Sugita, D.G.Vassylyev, K.Ito, and O.Nureki (2008).
Conformational transition of Sec machinery inferred from bacterial SecYE structures.
  Nature, 455, 988-991.
PDB codes: 2zjs 2zqp
18679430 V.Svetlov, and E.Nudler (2008).
Jamming the ratchet of transcription.
  Nat Struct Mol Biol, 15, 777-779.  
18647607 Y.X.Mejia, H.Mao, N.R.Forde, and C.Bustamante (2008).
Thermal probing of E. coli RNA polymerase off-pathway mechanisms.
  J Mol Biol, 382, 628-637.  
17697097 F.Werner (2007).
Structure and function of archaeal RNA polymerases.
  Mol Microbiol, 65, 1395-1404.  
18059450 I.Artsimovitch, and D.G.Vassylyev (2007).
Merging the RNA and DNA worlds.
  Nat Struct Mol Biol, 14, 1122-1123.  
17679091 I.Toulokhonov, J.Zhang, M.Palangat, and R.Landick (2007).
A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing.
  Mol Cell, 27, 406-419.  
17625551 P.Cramer (2007).
Gene transcription: extending the message.
  Nature, 448, 142-143.  
18158897 V.Epshtein, C.J.Cardinale, A.E.Ruckenstein, S.Borukhov, and E.Nudler (2007).
An allosteric path to transcription termination.
  Mol Cell, 28, 991.  
17711918 V.Svetlov, G.A.Belogurov, E.Shabrova, D.G.Vassylyev, and I.Artsimovitch (2007).
Allosteric control of the RNA polymerase by the elongation factor RfaH.
  Nucleic Acids Res, 35, 5694-5705.  
17875640 Y.Xiong, and Z.F.Burton (2007).
A tunable ratchet driving human RNA polymerase II translocation adjusted by accurately templated nucleoside triphosphates loaded at downstream sites and by elongation factors.
  J Biol Chem, 282, 36582-36592.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.