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PDBsum entry 1f5a
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Crystal structure of mammalian poly(a) polymerase in complex with an analog of ATP.
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Authors
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G.Martin,
W.Keller,
S.Doublié.
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Ref.
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EMBO J, 2000,
19,
4193-4203.
[DOI no: ]
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PubMed id
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Abstract
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In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the
initiation step of protein synthesis, as well as in the export and stability of
mRNAs. Poly(A) polymerase, the enzyme at the heart of the polyadenylation
machinery, is a template-independent RNA polymerase which specifically
incorporates ATP at the 3' end of mRNA. We have solved the crystal structure of
bovine poly(A) polymerase bound to an ATP analog at 2.5 A resolution. The
structure revealed expected and unexpected similarities to other proteins. As
expected, the catalytic domain of poly(A) polymerase shares substantial
structural homology with other nucleotidyl transferases such as DNA polymerase
beta and kanamycin transferase. The C-terminal domain unexpectedly folds into a
compact domain reminiscent of the RNA-recognition motif fold. The three
invariant aspartates of the catalytic triad ligate two of the three active site
metals. One of these metals also contacts the adenine ring. Furthermore,
conserved, catalytically important residues contact the nucleotide. These
contacts, taken together with metal coordination of the adenine base, provide a
structural basis for ATP selection by poly(A) polymerase.
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Figure 1.
Figure 1 (A) Ribbon diagram of the bovine PAP complex with
3'-dATP. The catalytic domain (residues 60–173) is shown in
orange, the central domain in blue (residues 20–59 and
174–352) and the C-terminal RNA-binding domain in purple
(residues 353–498). The 3'-dATP molecule bound in the active
site is shown in magenta, and the three metals ions are shown as
yellow spheres. Helices are designated with letters,  -strands
with numbers. (B) Stereo view of the PAP complex in the same
orientation as in (A). Every 20 residues are labeled. Secondary
structure elements were determined by Procheck (Laskowski et
al., 1993). Figures 1, 3, 4 and 5 were generated with SETOR
(Evans, 1993).
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Figure 3.
Figure 3 PAP active site showing the major interacting residues.
The secondary structure elements are color-coded as in Figure 1.
Residues are shown in blue, except when they share structural
homology with other proteins: orange (pol and
KanNt), green (KanNt) and purple (T7 DNA polymerase). Hydrogen
bonds are shown as dashed gray lines.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2000,
19,
4193-4203)
copyright 2000.
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Secondary reference #1
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Title
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Mutational analysis of mammalian poly(a) polymerase identifies a region for primer binding and catalytic domain, Homologous to the family X polymerases, And to other nucleotidyltransferases.
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Authors
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G.Martin,
W.Keller.
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Ref.
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Embo J, 1996,
15,
2593-2603.
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PubMed id
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Secondary reference #2
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Title
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Mapping of ATP binding regions in poly(a) polymerases by photoaffinity labeling and by mutational analysis identifies a domain conserved in many nucleotidyltransferases.
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Authors
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G.Martin,
P.Jenö,
W.Keller.
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Ref.
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Protein Sci, 1999,
8,
2380-2391.
[DOI no: ]
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PubMed id
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