 |
PDBsum entry 1gmr
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Hydrolase(guanyloribonuclease)
|
PDB id
|
|
|
|
1gmr
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Complex of ribonuclease from streptomyces aureofaciens with 2'-Gmp at 1.7 a resolution.
|
|
|
Authors
|
|
J.Sevcik,
C.P.Hill,
Z.Dauter,
K.S.Wilson.
|
|
|
Ref.
|
|
Acta Crystallogr D Biol Crystallogr, 1993,
49,
257-271.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
94%.
|
|
|
|
Abstract
|
|
|
The crystal structure of a complex of ribonuclease from Streptomyces
aureofaciens (RNase Sa) with guanosine-2'-monophosphate (2'-GMP) has been
refined against synchrotron data recorded from a single crystal using radiation
from beamline X31 at EMBL, Hamburg, and an imaging plate scanner. The crystals
are in space group P2(1)2(1)2(1) with cell dimensions a = 64.7, b = 78.8 and c =
39.1 A. The structure has two enzyme molecules in the asymmetric unit, complexed
with 2'-GMP inhibitor with occupancies of 1 and 2/3 (different to the 3'-GMP
complex crystal structure where only one of the two independent RNase Sa
molecules binds nucleotide), 492 associated water molecules and one sulfate ion,
and was refined using all data between 10.0 and 1.7 A to a final
crystallographic R factor of 13.25%. Binding of the base to the enzyme confirms
the basis for the guanine specificity but the structural results still do not
provide direct evidence of the identity and role of the particular residues
involved in the catalytic process. New native RNase Sa data to 1.8 A were
recorded to provide a reference set measured under comparable experimental
conditions. The crystals are in the same space group and have the same lattice
as those of the 2'-GMP complex. The native structure with 423 water molecules
was refined in a similar manner to the complex to a final R factor of 13.87%.
1.77 A resolution data were independently measured on a 2'-GMP complex crystal
at UCLA using an R-AXIS II image plate scanner mounted on a conventional source.
The cell dimensions were essentially the same as above. 2'-GMP was bound more
fully to molecule A than to molecule B of the RNase Sa. The structure was
refined to an R factor of 14.64% with 388 water molecules. This work follows on
from the structure determination of native RNase Sa and its complex with 3'-GMP
[Sevcik, Dodson & Dodson (1991). Acta Cryst. B47, 240-253].
|
|
|
|
|
|
|
|
|
|
Figure 11.
Fig. 11. The hydrogen-bonding network formed between the
enzyme and guanine base of the EMBL 2'-GMP inhibitor in the
B molecule.
|
|
Figure 13.
Fig. 13. Binding of the 2'-GMP phosphate group to molecule A.
The hydrogen bonds to the hosphate oxygens are shown as
thin lines.
|
|
Figure 31.
Ser 31A, Gin 32A and the side chain of Glu 54A in
relation to the native enzyme. These changes are not
observed n the 2'-GMP complex as the ribose ring
of the inhibitor is directed towards the outside of he
enzyme molecule and less structural change is neces-
sary for 2'-GMP to bind t the enzyme. The largest
changes caused by 2'-GMP binding are observed in
the positions of residues His 85 and Tyr 86 which
move towards the phosphate group in order to bind
to it. These two residues are very flexible and show a
degree of disorder in the native structure also.
The puckers adopted by the ribose moiety in the A
an B molecules in EMBL 2'-GMP and the A mol-
ecule in the UCLA '-GMP are essentially identical.
They are not ideal C(3')-endo conformations, ut
closely similar, with the C2' atom lyng slightly
above the plane of the CI', 04' and C4' atoms rather
than somewhat below as in th ideal conformation
(Fig. 12a). The torsion angle around the glycosyl link
is in the syn conformation, in contrast to the 3'-GMP
complex where a C(2')-endo pucker and the anti
conformation was adopted (Fig. 12b). Indeed the
riboses lie in distinctly different positions in the 2'-
and 3'-GMP complexes (Fig. 10h). The pucker for
the 2'-GMP in the B molecule of the UCLA model
refines much closer to the ideal C(3')-endo conforma-
tion (Fig. 12c). This is almost certainly a esult of the
low occupacy (~) and overall higher B factor for this
structure, rather than a real structral difference.
The occuancy of 2'-GMP is 1 in both A molecules,
and ~ m the EMBL B molecule. This again
emphasizes the need of accurate high-resolution data
for such detailed analyses.
The binding of the phosphate group is not so
specific as the binding of the base. The phosphate
binding ligands are the side chains of Glu 54, Arg 65,
Arg 69, His 85 and Tyr 86 (Fig. 13), which lie in a
relatively flexible part of the structure equipped with
a nmber of potential binding sites capable of
|
|
|
|
|
|
The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(1993,
49,
257-271)
copyright 1993.
|
|
|
Secondary reference #1
|
|
|
Title
|
|
Determination and restrained least-Squares refinement of the structures of ribonuclease sa and its complex with 3'-Guanylic acid at 1.8 a resolution.
|
|
|
Authors
|
|
J.Sevcik,
E.J.Dodson,
G.G.Dodson.
|
|
|
Ref.
|
|
Acta Crystallogr B, 1991,
47,
240-253.
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
|
|
|
|
