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PDBsum entry 1eos
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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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Productive and nonproductive binding to ribonuclease a: X-Ray structure of two complexes with uridylyl(2',5')Guanosine.
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Authors
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L.Vitagliano,
A.Merlino,
A.Zagari,
L.Mazzarella.
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Ref.
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Protein Sci, 2000,
9,
1217-1225.
[DOI no: ]
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PubMed id
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Abstract
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Guanine-containing mono- and dinucleotides bind to the active site of
ribonuclease A in a nonproductive mode (retro-binding) (Aguilar CF, Thomas PJ,
Mills A, Moss DS, Palmer RA. 1992. J Mol Biol 224:265-267). Guanine binds to the
highly specific pyrimidine site by forming hydrogen bonds with Thr45 and with
the sulfate anion located in the P1 site. To investigate the influence of the
anion present in the P1 site on retro-binding, we determined the structure of
two new complexes of RNase A with uridylyl(2',5')guanosine obtained by soaking
two different forms of pre-grown RNase A crystals. In one case, RNase A was
crystallized without removing the sulfate anion strongly bound to the active
site; in the other, the protein was first equilibrated with a basic solution to
displace the anion from the P1 site. The X-ray structures of the complexes with
and without sulfate in P1 were refined using diffraction data up to 1.8 A
(R-factor 0.192) and 2.0 A (R-factor 0.178), respectively. The binding mode of
the substrate analogue to the protein differs markedly in the two complexes.
When the sulfate is located in P1, we observe retro-binding; whereas when the
anion is removed from the active site, the uridine is productively bound at the
B1 site. In the productive complex, the electron density is very well defined
for the uridine moiety, whereas the downstream guanine is disordered. This
finding indicates that the interactions of guanine in the B2 site are rather
weak and that this site is essentially adenine preferring. In this crystal form,
there are two molecules per asymmetric unit, and due to crystal packing, only
the active site of one molecule is accessible to the ligand. Thus, in the same
crystal we have a ligand-bound and a ligand-free RNase A molecule. The
comparison of these two structures furnishes a detailed and reliable picture of
the structural alterations induced by the binding of the substrate. These
results provide structural information to support the hypotheses on the role of
RNase A active site residues that have recently emerged from site-directed
mutagenesis studies.
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Secondary reference #1
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Title
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A potential allosteric subsite generated by domain swapping in bovine seminal ribonuclease.
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Authors
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L.Vitagliano,
S.Adinolfi,
F.Sica,
A.Merlino,
A.Zagari,
L.Mazzarella.
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Ref.
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J Mol Biol, 1999,
293,
569-577.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. Omit electron density map calculated with
Fourier coefficients Fo
-
Fc of the dinucleotide bound at
one active site contoured to 2.2s. This picture was
generated using the program O (Jones et al., 1991).
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Figure 6.
Figure 6. Space-filling representation of the dimer and
the substrate analogue bound at the interface site.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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