1Q79

CRYSTAL STRUCTURE OF MAMMALIAN POLY(A) POLYMERASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Biochemical and structural insights into substrate binding and catalytic mechanism of mammalian poly(A) polymerase.

Martin, G.Moglich, A.Keller, W.Doublie, S.

(2004) J.Mol.Biol. 341: 911-925

  • DOI: 10.1016/j.jmb.2004.06.047
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Polyadenylation of messenger RNA precursors is an essential process in eukaryotes. Poly(A) polymerase (PAP), a member of the nucleotidyltransferase family that includes DNA polymerase beta, incorporates ATP at the 3' end of mRNAs in a template-indepe ...

    Polyadenylation of messenger RNA precursors is an essential process in eukaryotes. Poly(A) polymerase (PAP), a member of the nucleotidyltransferase family that includes DNA polymerase beta, incorporates ATP at the 3' end of mRNAs in a template-independent manner. Although the structures of mammalian and yeast PAPs are known, their mechanism of ATP selection has remained elusive. In a recent bovine PAP structure complexed with an analog of ATP and Mn2+, strictly conserved residues interact selectively with the adenine base, but the nucleotide was found in a "non-productive" conformation. Here we report a second bovine crystal structure, obtained in the presence of Mg2+, where 3'-dATP adopts a "productive" conformation similar to that seen in yeast PAP or DNA polymerase beta. Mutational analysis and activity assays with ATP analogs suggest a role in catalysis for one of the two adenine-binding sites revealed by our structural data. The other site might function to prevent futile hydrolysis of ATP. In order to investigate the role of metals in catalysis we performed steady state kinetics experiments under distributive polymerization conditions. These tests suggest a sequential random mechanism in vitro in the presence of ATP and RNA, without preference for a particular order of binding of the two substrates. In vivo, however, where polyadenylation is processive and the primer does not dissociate from the enzyme, an ordered mechanism with the primer as the leading substrate is more likely.


    Organizational Affiliation

    Department of Cell Biology Biozentrum, University of Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Poly(A) polymerase alpha
A
514Bos taurusMutation(s): 0 
Gene Names: PAPOLA (PAP)
EC: 2.7.7.19
Find proteins for P25500 (Bos taurus)
Go to Gene View: PAPOLA
Go to UniProtKB:  P25500
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
3AT
Query on 3AT

Download SDF File 
Download CCD File 
A
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
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
CSD
Query on CSD
A
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.640α = 90.00
b = 63.070β = 90.00
c = 181.340γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-07
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance