3C66

Yeast poly(A) polymerase in complex with Fip1 residues 80-105


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of yeast poly(A) polymerase in complex with a peptide from Fip1, an intrinsically disordered protein.

Meinke, G.Ezeokonkwo, C.Balbo, P.Stafford, W.Moore, C.Bohm, A.

(2008) Biochemistry 47: 6859-6869

  • DOI: 10.1021/bi800204k
  • Primary Citation of Related Structures:  
    3C66

  • PubMed Abstract: 
  • In yeast, the mRNA processing enzyme poly(A) polymerase is tethered to the much larger 3'-end processing complex via Fip1, a 36 kDa protein of unknown structure. We report the 2.6 A crystal structure of yeast poly(A) polymerase in complex with a peptide containing residues 80-105 of Fip1 ...

    In yeast, the mRNA processing enzyme poly(A) polymerase is tethered to the much larger 3'-end processing complex via Fip1, a 36 kDa protein of unknown structure. We report the 2.6 A crystal structure of yeast poly(A) polymerase in complex with a peptide containing residues 80-105 of Fip1. The Fip1 peptide binds to the outside surface of the C-terminal domain of the polymerase. On the basis of this structure, we designed a mutant of the polymerase (V498Y, C485R) that is lethal to yeast. The mutant is unable to bind Fip1 but retains full polymerase activity. Fip1 is found in all eukaryotes and serves to connect poly(A) polymerase to pre-mRNA processing complexes in yeast, plants, and mammals. However, the Fip1 sequence is highly divergent, and residues on both Pap1 and Fip1 at the observed interaction surface are poorly conserved. Herein we demonstrate using analytical ultracentrifugation, circular dichroism, proteolytic studies, and other techniques that, in the absence of Pap1, Fip1 is largely, if not completely, unfolded. We speculate that flexibility may be important for Fip1's function as a molecular scaffold.


    Organizational Affiliation

    Department of Biochemistry, Tufts University, 136 Harrison Avenue, Boston, Massachusetts 02111, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Poly(A) polymeraseA, B537Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PAP1YKR002W
EC: 2.7.7.19
Find proteins for P29468 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P29468 
Go to UniProtKB:  P29468
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA polyadenylation factor FIP1C, D26N/AMutation(s): 0 
Find proteins for P45976 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P45976 
Go to UniProtKB:  P45976
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
E [auth A], K [auth B], L [auth B]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , M [auth B] , N [auth B] , O [auth B] , 
F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  M [auth B],  N [auth B],  O [auth B],  P [auth B],  Q [auth B],  R [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.124α = 90
b = 184.211β = 90
c = 73.534γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2008-02-02 
  • Released Date: 2008-05-20 
  • Deposition Author(s): Bohm, A., Meinke, G.

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2012-07-25
    Changes: Other
  • Version 1.3: 2017-10-25
    Changes: Refinement description