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PDBsum entry 2a6h

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
2a6h
Jmol
Contents
Protein chains
229 a.a. *
1119 a.a. *
1381 a.a. *
95 a.a. *
345 a.a. *
Ligands
STD ×2
Metals
_MG ×2
_ZN ×4
Waters ×7398
* Residue conservation analysis
PDB id:
2a6h
Name: Transferase
Title: Crystal structure of the t. Thermophilus RNA polymerase holoenzyme in complex with antibiotic sterptolydigin
Structure: DNA-directed RNA polymerase alpha chain. Chain: a, b, k, l. Synonym: rnap alpha subunit, transcriptase alpha chain, RNA polymerase alpha subunit. DNA-directed RNA polymerase beta chain. Chain: c, m. Synonym: rnap beta subunit, transcriptase beta chain, RNA polymerase beta subunit. DNA-directed RNA polymerase beta' chain.
Source: Thermus thermophilus. Organism_taxid: 274. Organism_taxid: 274
Biol. unit: Hexamer (from PQS)
Resolution:
2.40Å     R-factor:   0.230     R-free:   0.268
Authors: D.Temiakov,N.Zenkin,M.N.Vassylyeva,A.Perederina,T.H.Tahirov, M.Savkina,S.Zorov,V.Nikiforov,N.Igarashi,N.Matsugaki, S.Wakatsuki,K.Severinov,D.G.Vassylyev,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
D.Temiakov et al. (2005). Structural basis of transcription inhibition by antibiotic streptolydigin. Mol Cell, 19, 655-666. PubMed id: 16167380 DOI: 10.1016/j.molcel.2005.07.020
Date:
02-Jul-05     Release date:   20-Sep-05    
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.
1381 a.a.
Protein chains
Pfam   ArchSchema ?
Q8RQE7  (RPOZ_THET8) -  DNA-directed RNA polymerase subunit omega
Seq:
Struc:
99 a.a.
95 a.a.*
Protein chains
Pfam   ArchSchema ?
Q5SKW1  (Q5SKW1_THET8) -  RNA polymerase sigma factor SigA
Seq:
Struc:
423 a.a.
345 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 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!
  Cellular component     cytoplasm   1 term 
  Biological process     transcription initiation from bacterial-type RNA polymerase promoter   6 terms 
  Biochemical function     transferase activity     9 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.molcel.2005.07.020 Mol Cell 19:655-666 (2005)
PubMed id: 16167380  
 
 
Structural basis of transcription inhibition by antibiotic streptolydigin.
D.Temiakov, N.Zenkin, M.N.Vassylyeva, A.Perederina, T.H.Tahirov, E.Kashkina, M.Savkina, S.Zorov, V.Nikiforov, N.Igarashi, N.Matsugaki, S.Wakatsuki, K.Severinov, D.G.Vassylyev.
 
  ABSTRACT  
 
Streptolydigin (Stl) is a potent inhibitor of bacterial RNA polymerases (RNAPs). The 2.4 A resolution structure of the Thermus thermophilus RNAP-Stl complex showed that, in full agreement with the available genetic data, the inhibitor binding site is located 20 A away from the RNAP active site and encompasses the bridge helix and the trigger loop, two elements that are considered to be crucial for RNAP catalytic center function. Structure-based biochemical experiments revealed additional determinants of Stl binding and demonstrated that Stl does not affect NTP substrate binding, DNA translocation, and phosphodiester bond formation. The RNAP-Stl complex structure, its comparison with the closely related substrate bound eukaryotic transcription elongation complexes, and biochemical analysis suggest an inhibitory mechanism in which Stl stabilizes catalytically inactive (preinsertion) substrate bound transcription intermediate, thereby blocking structural isomerization of RNAP to an active configuration. The results provide a basis for a design of new antibiotics utilizing the Stl-like mechanism.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The RNAP-Stl Complex Structure
Figure 5.
Figure 5. Substrate Loading in the IS and Plausible Mechanism of Stl Action
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2005, 19, 655-666) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
20598112 C.D.Kaplan (2010).
The architecture of RNA polymerase fidelity.
  BMC Biol, 8, 85.  
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.  
19966797 J.Zhang, M.Palangat, and R.Landick (2010).
Role of the RNA polymerase trigger loop in catalysis and pausing.
  Nat Struct Mol Biol, 17, 99.  
20176899 M.Sánchez-Hidalgo, L.E.Núñez, C.Méndez, and J.A.Salas (2010).
Involvement of the beta subunit of RNA polymerase in resistance to streptolydigin and streptovaricin in the producer organisms Streptomyces lydicus and Streptomyces spectabilis.
  Antimicrob Agents Chemother, 54, 1684-1692.  
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.  
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.  
19875077 C.Olano, C.Gómez, M.Pérez, M.Palomino, A.Pineda-Lucena, R.J.Carbajo, A.F.Braña, C.Méndez, and J.A.Salas (2009).
Deciphering biosynthesis of the RNA polymerase inhibitor streptolydigin and generation of glycosylated derivatives.
  Chem Biol, 16, 1031-1044.  
19896365 D.G.Vassylyev (2009).
Elongation by RNA polymerase: a race through roadblocks.
  Curr Opin Struct Biol, 19, 691-700.  
19489723 E.Nudler (2009).
RNA polymerase active center: the molecular engine of transcription.
  Annu Rev Biochem, 78, 335-361.  
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
19883065 J.C.Carlson, S.Li, D.A.Burr, and D.H.Sherman (2009).
Isolation and characterization of tirandamycins from a marine-derived Streptomyces sp.
  J Nat Prod, 72, 2076-2079.  
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.  
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
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.  
19055851 L.Tan, S.Wiesler, D.Trzaska, H.C.Carney, and R.O.Weinzierl (2008).
Bridge helix and trigger loop perturbations generate superactive RNA polymerases.
  J Biol, 7, 40.  
18280161 S.Borukhov, and E.Nudler (2008).
RNA polymerase: the vehicle of transcription.
  Trends Microbiol, 16, 126-134.  
17581591 D.G.Vassylyev, M.N.Vassylyeva, J.Zhang, M.Palangat, I.Artsimovitch, and R.Landick (2007).
Structural basis for substrate loading in bacterial RNA polymerase.
  Nature, 448, 163-168.
PDB codes: 2o5j 2ppb
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.  
17917675 M.N.Vassylyeva, V.Svetlov, A.D.Dearborn, S.Klyuyev, I.Artsimovitch, and D.G.Vassylyev (2007).
The carboxy-terminal coiled-coil of the RNA polymerase beta'-subunit is the main binding site for Gre factors.
  EMBO Rep, 8, 1038-1043.
PDB code: 2p4v
17502377 S.Kyzer, K.S.Ha, R.Landick, and M.Palangat (2007).
Direct versus limited-step reconstitution reveals key features of an RNA hairpin-stabilized paused transcription complex.
  J Biol Chem, 282, 19020-19028.  
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.  
17129781 D.Wang, D.A.Bushnell, K.D.Westover, C.D.Kaplan, and R.D.Kornberg (2006).
Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis.
  Cell, 127, 941-954.
PDB codes: 2e2h 2e2i 2e2j 2nvq 2nvs 2nvt 2nvx 2nvy 2nvz 2yu9
16914440 E.Kashkina, M.Anikin, T.H.Tahirov, S.N.Kochetkov, D.G.Vassylyev, and D.Temiakov (2006).
Elongation complexes of Thermus thermophilus RNA polymerase that possess distinct translocation conformations.
  Nucleic Acids Res, 34, 4036-4045.  
16873663 N.Zenkin, Y.Yuzenkova, and K.Severinov (2006).
Transcript-assisted transcriptional proofreading.
  Science, 313, 518-520.  
16621791 S.F.Holmes, T.J.Santangelo, C.K.Cunningham, J.W.Roberts, and D.A.Erie (2006).
Kinetic investigation of Escherichia coli RNA polymerase mutants that influence nucleotide discrimination and transcription fidelity.
  J Biol Chem, 281, 18677-18683.  
16524917 V.Trinh, M.F.Langelier, J.Archambault, and B.Coulombe (2006).
Structural perspective on mutations affecting the function of multisubunit RNA polymerases.
  Microbiol Mol Biol Rev, 70, 12-36.  
16360025 D.G.Vassylyev, and I.Artsimovitch (2005).
Tracking RNA polymerase, one step at a time.
  Cell, 123, 977-979.  
16273103 D.G.Vassylyev, V.Svetlov, M.N.Vassylyeva, A.Perederina, N.Igarashi, N.Matsugaki, S.Wakatsuki, and I.Artsimovitch (2005).
Structural basis for transcription inhibition by tagetitoxin.
  Nat Struct Mol Biol, 12, 1086-1093.
PDB code: 2be5
16284617 E.A.Abbondanzieri, W.J.Greenleaf, J.W.Shaevitz, R.Landick, and S.M.Block (2005).
Direct observation of base-pair stepping by RNA polymerase.
  Nature, 438, 460-465.  
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.