1UVK

The structural basis for RNA specificity and Ca2 inhibition of an RNA-dependent RNA polymerase phi6p2 dead-end complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The structural basis for RNA specificity and Ca2+ inhibition of an RNA-dependent RNA polymerase.

Salgado, P.S.Makeyev, E.V.Butcher, S.J.Bamford, D.H.Stuart, D.I.Grimes, J.M.

(2004) Structure 12: 307-316

  • DOI: 10.1016/j.str.2004.01.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The RNA-dependent RNA polymerase of bacteriophage phi6 transcribes mRNA from the three segments of the dsRNA viral genome. We have cocrystallized RNA oligonucleotides with the polymerase, revealing the mode of binding of RNA templates. This binding i ...

    The RNA-dependent RNA polymerase of bacteriophage phi6 transcribes mRNA from the three segments of the dsRNA viral genome. We have cocrystallized RNA oligonucleotides with the polymerase, revealing the mode of binding of RNA templates. This binding is somewhat different from that previously seen for DNA oligomers, leading to additional RNA-protein hydrogen bonds, consistent with a preference for RNA. Activation of the RNA/polymerase complex by the addition of substrate and Mg2+ initiates a single round of reaction within the crystal to form a dead-end complex that partially collapses within the enzyme active site. By replacing Mg2+ with Ca2+, we have been able to capture the inhibited complex which shows distortion that explains the structural basis for the inhibition of such polymerases by Ca2+.


    Organizational Affiliation

    Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford, OX3 7BN, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase
A, C, E
664Pseudomonas phage phi6Mutation(s): 0 
Gene Names: P2
EC: 2.7.7.48
Find proteins for P11124 (Pseudomonas phage phi6)
Go to UniProtKB:  P11124
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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Download CCD File 
A, C, E
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
POP
Query on POP

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Download CCD File 
A, C, E
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
GTP
Query on GTP

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Download CCD File 
A, C, E
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, C, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
G
Query on G

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Download CCD File 
A, C, E
GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.243 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 106.290α = 90.00
b = 93.800β = 101.35
c = 140.770γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-02-19
    Type: Initial release
  • Version 1.1: 2014-04-09
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2017-07-12
    Type: Derived calculations
  • Version 1.3: 2018-03-07
    Type: Database references, Derived calculations, Source and taxonomy