3ER9

Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase complex with UU and 3'-deoxy ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Polymerase Translocation with Respect to Single-Stranded Nucleic Acid: Looping or Wrapping of Primer around a Poly(A) Polymerase

Li, C.Li, H.Zhou, S.Sun, E.Yoshizawa, J.Poulos, T.L.Gershon, P.D.

(2009) Structure 17: 680-689

  • DOI: 10.1016/j.str.2009.03.012
  • Primary Citation of Related Structures:  
  • Also Cited By: 3OWG

  • PubMed Abstract: 
  • Vaccinia virus protein VP55 translocates continuously with respect to single-stranded nucleic acid while extending its 3'end. Here, all key sites of polymerase-primer interaction were identified, demonstrating the wrapping or looping of polyadenylati ...

    Vaccinia virus protein VP55 translocates continuously with respect to single-stranded nucleic acid while extending its 3'end. Here, all key sites of polymerase-primer interaction were identified, demonstrating the wrapping or looping of polyadenylation primer around the polymerase during translocation. Side-chain substitutions at one of the sites indicated its requirement for tail extension beyond approximately 12 nucleotides in length, and conformational changes observed upon oligonucleotide binding suggested allosteric connectivity during translocation. Conformational changes in VP39 upon VP55 binding suggested that, within the VP55-VP39 complex, VP39's mRNA 5' cap binding site closes. The crystallographic structure showed a PAPase catalytic center without side-chain substitutions, possessing two metal ions and with all known reactive and catalytic groups represented, fitting a classical two-metal ion mechanism for phosphoryl transfer.


    Related Citations: 
    • Crystal structure of the vaccinia virus polyadenylate polymerase heterodimer: insight into ATP selecttivity and processivity
      Moure, C.M.,Bowman, B.R.,Gershon, P.D.,Quiocho, F.A.
      (2006) Mol.Cell 22: 339


    Organizational Affiliation

    Department of Chemistry, Xinxiang Medical University, Xinxiang, Henan, PR China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
A
297Vaccinia virus (strain Western Reserve)Mutation(s): 3 
Gene Names: PAPS
EC: 2.1.1.57
Find proteins for P07617 (Vaccinia virus (strain Western Reserve))
Go to UniProtKB:  P07617
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Poly(A) polymerase catalytic subunit
B
479Vaccinia virus (strain Western Reserve)Mutation(s): 1 
Gene Names: PAPL
EC: 2.7.7.19
Find proteins for P23371 (Vaccinia virus (strain Western Reserve))
Go to UniProtKB:  P23371
Entity ID: 3
MoleculeChainsLengthOrganism
5'-R(UP*U)-3'D2N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3AT
Query on 3AT

Download SDF File 
Download CCD File 
B
3'-DEOXYADENOSINE-5'-TRIPHOSPHATE
CORDYCEPIN TRIPHOSPHATE
C10 H16 N5 O12 P3
NLIHPCYXRYQPSD-BAJZRUMYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 69.531α = 90.00
b = 91.977β = 90.00
c = 133.734γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
ADSCdata collection
CNSrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2018-01-24
    Type: Structure summary