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2q66, resolution 1.80Å ()
Ligands: , ,
Gene: PAP1 (Saccharomyces cerevisiae)
Activity: Polynucleotide adenylyltransferase, with EC number
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml


Structure of Yeast Poly(A) Polymerase with ATP and oligo(A)

Publication Abstract from PubMed

We report the 1.8 A structure of yeast poly(A) polymerase (PAP) trapped in complex with ATP and a five residue poly(A) by mutation of the catalytically required aspartic acid 154 to alanine. The enzyme has undergone significant domain movement and reveals a closed conformation with extensive interactions between the substrates and all three polymerase domains. Both substrates and 31 buried water molecules are enclosed within a central cavity that is open at both ends. Four PAP mutants were subjected to detailed kinetic analysis, and studies of the adenylyltransfer (forward), pyrophosphorolysis (reverse), and nucleotidyltransfer reaction utilizing CTP for the mutants are presented. The results support a model in which binding of both poly(A) and the correct nucleotide, MgATP, induces a conformational change, resulting in formation of a stable, closed enzyme state. Thermodynamic considerations of the data are discussed as they pertain to domain closure, substrate specificity, and catalytic strategies utilized by PAP.

Mechanism of poly(A) polymerase: structure of the enzyme-MgATP-RNA ternary complex and kinetic analysis., Balbo PB, Bohm A, Structure. 2007 Sep;15(9):1117-31. PMID:17850751

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

2q66 is a 2 chain structure with sequence from Saccharomyces cerevisiae. The October 2008 RCSB PDB Molecule of the Month feature on Poly(A) Polymerase by David Goodsell is 10.2210/rcsb_pdb/mom_2008_10. Full crystallographic information is available from OCA.

See Also


  • Balbo PB, Bohm A. Mechanism of poly(A) polymerase: structure of the enzyme-MgATP-RNA ternary complex and kinetic analysis. Structure. 2007 Sep;15(9):1117-31. PMID:17850751 doi:S0969-2126(07)00283-3
  • Meinke G, Ezeokonkwo C, Balbo P, Stafford W, Moore C, Bohm A. Structure of yeast poly(A) polymerase in complex with a peptide from Fip1, an intrinsically disordered protein. Biochemistry. 2008 Jul 1;47(26):6859-69. Epub 2008 Jun 7. PMID:18537269 doi:10.1021/bi800204k

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