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 
  • R-Value Observed: 0.208 

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Ligand Structure Quality Assessment 


This is version 1.3 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:  
    3ER8, 3ER9, 3ERC

  • 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 polyadenylation primer around the polymerase during translocation ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cap-specific mRNA (nucleoside-2'-O-)-methyltransferaseA297Vaccinia virus WRMutation(s): 3 
Gene Names: PAPSVACWR095F9J3R
EC: 2.1.1.57
UniProt
Find proteins for P07617 (Vaccinia virus (strain Western Reserve))
Explore P07617 
Go to UniProtKB:  P07617
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07617
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Poly(A) polymerase catalytic subunitB479Vaccinia virus WRMutation(s): 1 
Gene Names: PAPLVACWR057E1L
EC: 2.7.7.19
UniProt
Find proteins for P23371 (Vaccinia virus (strain Western Reserve))
Explore P23371 
Go to UniProtKB:  P23371
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23371
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChainsLengthOrganismImage
5'-R(UP*U)-3'C [auth D]2N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3AT
Query on 3AT

Download Ideal Coordinates CCD File 
G [auth B]3'-DEOXYADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
NLIHPCYXRYQPSD-BAJZRUMYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
H [auth B],
I [auth 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 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.531α = 90
b = 91.977β = 90
c = 133.734γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations