1FA0 | pdb_00001fa0

STRUCTURE OF YEAST POLY(A) POLYMERASE BOUND TO MANGANATE AND 3'-DATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.278 (Depositor) 
  • R-Value Work: 
    0.233 (Depositor) 
  • R-Value Observed: 
    0.233 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1FA0

This is version 1.3 of the entry. See complete history

Literature

Structure of yeast poly(A) polymerase alone and in complex with 3'-dATP.

Bard, J.Zhelkovsky, A.M.Helmling, S.Earnest, T.N.Moore, C.L.Bohm, A.

(2000) Science 289: 1346-1349

  • DOI: https://doi.org/10.1126/science.289.5483.1346
  • Primary Citation Related Structures: 
    1FA0

  • PubMed Abstract: 

    Polyadenylate [poly(A)] polymerase (PAP) catalyzes the addition of a polyadenosine tail to almost all eukaryotic messenger RNAs (mRNAs). The crystal structure of the PAP from Saccharomyces cerevisiae (Pap1) has been solved to 2.6 angstroms, both alone and in complex with 3'-deoxyadenosine triphosphate (3'-dATP). Like other nucleic acid polymerases, Pap1 is composed of three domains that encircle the active site. The arrangement of these domains, however, is quite different from that seen in polymerases that use a template to select and position their incoming nucleotides. The first two domains are functionally analogous to polymerase palm and fingers domains. The third domain is attached to the fingers domain and is known to interact with the single-stranded RNA primer. In the nucleotide complex, two molecules of 3'-dATP are bound to Pap1. One occupies the position of the incoming base, prior to its addition to the mRNA chain. The other is believed to occupy the position of the 3' end of the mRNA primer.


  • Organizational Affiliation
    • Boston Biomedical Research Institute, 64 Grove Street, Watertown, MA 02472, USA.

Macromolecule Content 

  • Total Structure Weight: 124.76 kDa 
  • Atom Count: 8,250 
  • Modeled Residue Count: 1,020 
  • Deposited Residue Count: 1,074 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
POLY(A)-POLYMERASE
A, B
537Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.19
UniProt
Find proteins for P29468 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P29468 
Go to UniProtKB:  P29468
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29468
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3AT

Query on 3AT



Download:Ideal Coordinates CCD File
E [auth A],
J [auth B]
3'-DEOXYADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
NLIHPCYXRYQPSD-BAJZRUMYSA-N
3AD

Query on 3AD



Download:Ideal Coordinates CCD File
F [auth A],
K [auth B]
3'-DEOXYADENOSINE
C10 H13 N5 O3
OFEZSBMBBKLLBJ-BAJZRUMYSA-N
POP

Query on POP



Download:Ideal Coordinates CCD File
G [auth A]PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
MN

Query on MN



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
H [auth B],
I [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.278 (Depositor) 
  • R-Value Work:  0.233 (Depositor) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.8α = 90
b = 109.1β = 90
c = 238.5γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-08-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations