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 

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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

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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
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  • Reference Sequence

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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
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  • Reference Sequence

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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
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  • Reference Sequence

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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
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  • 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

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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