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PDBsum entry 1eos
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* Residue conservation analysis
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Enzyme class:
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E.C.4.6.1.18
- pancreatic ribonuclease.
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Reaction:
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1.
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an [RNA] containing cytidine + H2O = an [RNA]-3'-cytidine- 3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]
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2.
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an [RNA] containing uridine + H2O = an [RNA]-3'-uridine-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]
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DOI no:
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Protein Sci
9:1217-1225
(2000)
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PubMed id:
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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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L.Vitagliano,
A.Merlino,
A.Zagari,
L.Mazzarella.
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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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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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N.Thiyagarajan,
B.D.Smith,
R.T.Raines,
and
K.R.Acharya
(2011).
Functional and structural analyses of N-acylsulfonamide-linked dinucleoside inhibitors of RNase A.
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FEBS J,
278,
541-549.
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PDB codes:
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E.Pizzo,
A.Merlino,
M.Turano,
I.Russo Krauss,
F.Coscia,
A.Zanfardino,
M.Varcamonti,
A.Furia,
C.Giancola,
L.Mazzarella,
F.Sica,
and
G.D'Alessio
(2010).
A new RNase sheds light on the RNase/angiogenin subfamily from zebrafish.
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Biochem J,
433,
345-355.
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PDB codes:
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A.Merlino,
I.Russo Krauss,
M.Perillo,
C.A.Mattia,
C.Ercole,
D.Picone,
A.Vergara,
and
F.Sica
(2009).
Toward an antitumor form of bovine pancreatic ribonuclease: The crystal structure of three noncovalent dimeric mutants.
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Biopolymers,
91,
1029-1037.
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PDB codes:
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A.T.Torelli,
R.C.Spitale,
J.Krucinska,
and
J.E.Wedekind
(2008).
Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme.
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Biochem Biophys Res Commun,
371,
154-158.
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PDB code:
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S.B.Larson,
J.S.Day,
R.Cudney,
and
A.McPherson
(2007).
A new crystal form of bovine pancreatic RNase A in complex with 2'-deoxyguanosine-5'-monophosphate.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
63,
728-733.
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PDB code:
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A.A.Moosavi-Movahedi,
M.Gharanfoli,
S.Jalili,
F.Ahmad,
J.Chamani,
G.H.Hakimelahi,
M.Sadeghi,
M.Amani,
and
A.A.Saboury
(2006).
The correlation of RNase A enzymatic activity with the changes in the distance between Nepsilon2-His12 and N delta1-His119 upon addition of stabilizing and destabilizing salts.
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Protein J,
25,
117-125.
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A.Merlino,
M.A.Ceruso,
L.Vitagliano,
and
L.Mazzarella
(2005).
Open interface and large quaternary structure movements in 3D domain swapped proteins: insights from molecular dynamics simulations of the C-terminal swapped dimer of ribonuclease A.
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Biophys J,
88,
2003-2012.
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G.N.Hatzopoulos,
D.D.Leonidas,
R.Kardakaris,
J.Kobe,
and
N.G.Oikonomakos
(2005).
The binding of IMP to ribonuclease A.
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FEBS J,
272,
3988-4001.
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PDB codes:
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A.Merlino,
L.Vitagliano,
F.Sica,
A.Zagari,
and
L.Mazzarella
(2004).
Population shift vs induced fit: the case of bovine seminal ribonuclease swapping dimer.
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Biopolymers,
73,
689-695.
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PDB codes:
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A.Merlino,
L.Vitagliano,
M.A.Ceruso,
and
L.Mazzarella
(2004).
Dynamic properties of the N-terminal swapped dimer of ribonuclease A.
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Biophys J,
86,
2383-2391.
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N.G.Beloglazova,
M.M.Fabani,
M.A.Zenkova,
E.V.Bichenkova,
N.N.Polushin,
V.V.Sil'nikov,
K.T.Douglas,
and
V.V.Vlassov
(2004).
Sequence-specific artificial ribonucleases. I. Bis-imidazole-containing oligonucleotide conjugates prepared using precursor-based strategy.
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Nucleic Acids Res,
32,
3887-3897.
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A.Merlino,
L.Vitagliano,
M.A.Ceruso,
A.Di Nola,
and
L.Mazzarella
(2002).
Global and local motions in ribonuclease A: a molecular dynamics study.
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Biopolymers,
65,
274-283.
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L.Vitagliano,
A.Merlino,
A.Zagari,
and
L.Mazzarella
(2002).
Reversible substrate-induced domain motions in ribonuclease A.
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Proteins,
46,
97.
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PDB codes:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
