2PI4

T7RNAP complexed with a phi10 protein and initiating GTPs.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.265 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanism for de novo RNA synthesis and initiating nucleotide specificity by t7 RNA polymerase.

Kennedy, W.P.Momand, J.R.Yin, Y.W.

(2007) J.Mol.Biol. 370: 256-268

  • DOI: 10.1016/j.jmb.2007.03.041
  • Primary Citation of Related Structures:  2PI5

  • PubMed Abstract: 
  • DNA-directed RNA polymerases are capable of initiating synthesis of RNA without primers, the first catalytic stage of initiation is referred to as de novo RNA synthesis. De novo synthesis is a unique phase in the transcription cycle where the RNA pol ...

    DNA-directed RNA polymerases are capable of initiating synthesis of RNA without primers, the first catalytic stage of initiation is referred to as de novo RNA synthesis. De novo synthesis is a unique phase in the transcription cycle where the RNA polymerase binds two nucleotides rather than a nascent RNA polymer and a single nucleotide. For bacteriophage T7 RNA polymerase, transcription begins with a marked preference for GTP at the +1 and +2 positions. We determined the crystal structures of T7 RNA polymerase complexes captured during the de novo RNA synthesis. The DNA substrates in the structures in the complexes contain a common Phi 10 duplex promoter followed by a unique five base single-stranded extension of template DNA whose sequences varied at positions +1 and +2, thereby allowing for different pairs of initiating nucleotides GTP, ATP, CTP or UTP to bind. The structures show that the initiating nucleotides bind RNA polymerase in locations distinct from those described previously for elongation complexes. Selection bias in favor of GTP as an initiating nucleotide is accomplished by shape complementarity, extensive protein side-chain and strong base-stacking interactions for the guanine moiety in the enzyme active site. Consequently, an initiating GTP provides the largest stabilization force for the open promoter conformation.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase
A
878Enterobacteria phage T7EC: 2.7.7.6
Find proteins for P00573 (Enterobacteria phage T7)
Go to UniProtKB:  P00573
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*TP*TP*CP*CP*TP*AP*TP*AP*GP*TP*GP*AP*GP*TP*CP*GP*TP*AP*TP*TP*A)-3'T22N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*TP*AP*AP*TP*AP*CP*GP*AP*CP*TP*CP*AP*CP*T)-3'P14N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GH3
Query on GH3

Download SDF File 
Download CCD File 
A
3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
QGYIFQKZZSSUCR-OBXARNEKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.265 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 224.450α = 90.00
b = 73.791β = 90.00
c = 80.315γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance