1S0V

Structural basis for substrate selection by T7 RNA polymerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural basis for substrate selection by t7 RNA polymerase.

Temiakov, D.Patlan, V.Anikin, M.McAllister, W.T.Yokoyama, S.Vassylyev, D.G.

(2004) Cell 116: 381-391

  • DOI: 10.1016/s0092-8674(04)00059-5
  • Primary Citation of Related Structures:  
    1S0V

  • PubMed Abstract: 
  • The mechanism by which nucleotide polymerases select the correct substrate is of fundamental importance to the fidelity of DNA replication and transcription. During the nucleotide addition cycle, pol I DNA polymerases undergo the transition from a catalytically inactive "open" to an active "closed" conformation ...

    The mechanism by which nucleotide polymerases select the correct substrate is of fundamental importance to the fidelity of DNA replication and transcription. During the nucleotide addition cycle, pol I DNA polymerases undergo the transition from a catalytically inactive "open" to an active "closed" conformation. All known determinants of substrate selection are associated with the "closed" state. To elucidate if this mechanism is conserved in homologous single subunit RNA polymerases (RNAPs), we have determined the structure of T7 RNAP elongation complex with the incoming substrate analog. Surprisingly, the substrate specifically binds to RNAP in the "open" conformation, where it is base paired with the acceptor template base, while Tyr639 provides discrimination of ribose versus deoxyribose substrates. The structure therefore suggests a novel mechanism, in which the substrate selection occurs prior to the isomerization to the catalytically active conformation. Modeling of multisubunit RNAPs suggests that this mechanism might be universal for all RNAPs.


    Related Citations: 
    • Structure of a T7 RNA polymerase elongation complex at 2.9 A resolution.
      Tahirov, T.H., Temiakov, D., Anikin, M., Patlan, V., G Vassylyev, D., McAllister, W.T., Yokoyama, S.
      (2002) Nature 420: 43
    • Crystallization and preliminary crystallographic analysis of T7 RNA polymerase elongation complex
      Temiakov, D., Tahirov, T.H., Anikin, M., McAllister, W.T., Vassylyev, D.G., Yokoyama, S.
      (2003) Acta Crystallogr D Biol Crystallogr 59: 185

    Organizational Affiliation

    Morse Institute for Molecular Genetics, Department of Microbiology, SUNY Health Science Center, 450 Clarkson Avenue, Brooklyn, New York 11203, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymeraseM [auth A],
N [auth B],
O [auth C],
P [auth D]
883Escherichia phage T7Mutation(s): 0 
Gene Names: 1
EC: 2.7.7.6
UniProt
Find proteins for P00573 (Escherichia phage T7)
Explore P00573 
Go to UniProtKB:  P00573
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00573
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*G*GP*GP*AP*AP*TP*CP*GP*AP*TP*AP*TP*CP*GP*CP*CP*GP*C)-3'A [auth E],
D [auth H],
G [auth K],
J [auth N]
18N/A
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-R(*AP*AP*CP*U*GP*CP*GP*GP*CP*GP*AP*U)-3'B [auth F],
E [auth I],
H [auth L],
K [auth O]
12N/A
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChainsLengthOrganismImage
5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*C)-3'C [auth G],
F [auth J],
I [auth M],
L [auth P]
10N/A
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.133α = 91.93
b = 87.703β = 91.02
c = 206.531γ = 110.66
Software Package:
Software NamePurpose
DENZOdata reduction
TRUNCATEdata reduction
CNSrefinement
CCP4data scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-24
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Data collection