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PDBsum entry 1r3m
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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 the dimeric unswapped form of bovine seminal ribonuclease.
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Authors
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R.Berisio,
F.Sica,
C.De lorenzo,
A.Di fiore,
R.Piccoli,
A.Zagari,
L.Mazzarella.
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Ref.
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FEBS Lett, 2003,
554,
105-110.
[DOI no: ]
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PubMed id
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Abstract
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Bovine seminal ribonuclease is a unique case of protein dimorphism, since it
exists in two dimeric forms, with different biological and kinetic behavior,
which interconvert into one another through three-dimensional swapping. Here we
report the crystal structure, at 2.2 A resolution, of the unswapped form of
bovine seminal ribonuclease. Besides completing the structural definition of
bovine seminal ribonuclease conformational dimorphism, this study provides the
structural basis to explain the dependence of the enzyme cooperative effects on
its swapping state.
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Figure 2.
Fig. 2. a: Omit (Fo−Fc) map around a portion of the
N-terminal helix including the catalytic His12. b: Omit
(Fo−Fc) electron density around the hinge loop of one of the
two subunits in the M=M crystal structure. Residues Ser20 and
Ser21, which are fully disordered, are modeled (light gray) to
show the hinge connectivity. c: Stereo diagram showing the hinge
region after the superposition of a subunit of M=M (dark gray)
with RNase A (medium gray) and hRNase (light gray).
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Figure 3.
Fig. 3. Superposition of the C^α trace of one MxM subunit
(PDB code 1BSR) (dark gray) with the corresponding M=M subunit
(light gray). a: View along the approximate two-fold axis. b: A
view of the C^α traces rotated by 90°.
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The above figures are
reprinted
by permission from the Federation of European Biochemical Societies:
FEBS Lett
(2003,
554,
105-110)
copyright 2003.
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Secondary reference #1
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Title
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Bovine seminal ribonuclease: structure at 1.9 a resolution.
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Authors
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L.Mazzarella,
S.Capasso,
D.Demasi,
G.Di lorenzo,
C.A.Mattia,
A.Zagari.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 1993,
49,
389-402.
[DOI no: ]
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PubMed id
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Figure 13.
Fig. 13. Histogram showing the distribution of the thermal factors
for water molecules.
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Figure 14.
Fig. 14. A group of highly conserved water molecules for S1.
Broken lines indicate hydrogen bonds involving water
molecules. The same pattern is also observed for $2 and for
RNase A.
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The above figures are
reproduced from the cited reference
with permission from the IUCr
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Secondary reference #2
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Title
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The unswapped chain of bovine seminal ribonuclease: crystal structure of the free and liganded monomeric derivative.
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Authors
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F.Sica,
A.Di fiore,
A.Zagari,
L.Mazzarella.
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Ref.
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Proteins, 2003,
52,
263-271.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. Ribbon representation of the MCAM peptide fold. The
carboxamidomethylated sidechains of Cys31 and Cys32 are drawn in
ball-and-stick.
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Figure 3.
Figure 3. The active site region in the liganded MCAM. (a)
Isomorphous difference map (see text) contoured at 2.0 for 3
 -UMP.
(b) Isomorphous difference map contoured at 1.8 for adenosine.
(c) Hydrogen-bonding network (dotted lines) between 3 -UMP
and the protein matrix. (d) Superimposed structures of the 3
-UMP
complexes with MCAM (cyan) and with a RNase A mutant (magenta;
PDB code: 4RSK). The His119 sidechain adopts the A conformation
in MCAM and the B conformation in the RNase A mutant. The H-bond
distances are given in angstrom units. The figure was drawn with
BOBSCRIPT[22] (a and b) and MOLSCRIPT[21] (c and d).
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The above figures are
reproduced from the cited reference
with permission from John Wiley & Sons, Inc.
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