1S0V

Structural basis for substrate selection by T7 RNA polymerase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.255 

wwPDB Validation 3D Report Full Report


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


  • 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 ca ...

    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: 
    • 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.,Sect.D 59: 185
    • 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

    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: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase
A, B, C, D
883Enterobacteria phage T7Mutation(s): 0 
Find proteins for P00573 (Enterobacteria phage T7)
Go to UniProtKB:  P00573
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*G*GP*GP*AP*AP*TP*CP*GP*AP*TP*AP*TP*CP*GP*CP*CP*GP*C)-3'E,H,K,N18N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*AP*AP*CP*U*GP*CP*GP*GP*CP*GP*AP*U)-3'F,I,L,O12N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*C)-3'G,J,M,P10N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APC
Query on APC
Download SDF File 
Download CCD File 
A, B, C, D
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
A, B, C, D, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.307 
  • R-Value Work: 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
CNSrefinement
TRUNCATEdata reduction
CNSphasing
DENZOdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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