 |
PDBsum entry 9rnt
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Hydrolase(endoribonuclease)
|
PDB id
|
|
|
|
9rnt
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
|
|
|
|
|
Enzyme class:
|
|
E.C.4.6.1.24
- ribonuclease T1.
|
|
|
|
|
|
|
Reaction:
|
|
[RNA] containing guanosine + H2O = an [RNA fragment]-3'-guanosine- 3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA fragment]
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
|
J Mol Biol
222:335-352
(1991)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Ribonuclease T1 with free recognition and catalytic site: crystal structure analysis at 1.5 A resolution.
|
|
J.Martinez-Oyanedel,
H.W.Choe,
U.Heinemann,
W.Saenger.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
The free form of ribonuclease T1 (RNase T1) has been crystallized at neutral pH,
and the three-dimensional structure of the enzyme has been determined at 1.5 A
nominal resolution. Restrained least-squares refinement yielded an R value of
14.3% for 12,623 structure amplitudes. The high resolution of the structure
analysis permits a detailed description of the solvent structure around RNase
T1, the reliable rotational setting of several side-chain amide and imidazole
groups and the identification of seven disordered residues. Among these, the
disordered and completely internal Val78 residue is noteworthy. In the RNase T1
crystal structures determined thus far it is always disordered in the absence of
bound guanosine, but not in its presence. A systematic analysis of hydrogen
bonding reveals the presence in RNase T1 of 40 three-center and an additional
seven four-center hydrogen bonds. Three-center hydrogen bonds occur
predominantly in the alpha-helix, where their minor components close 3(10)-type
turns, and in beta-sheets, where their minor components connect the peptide
nitrogen and carbonyl functions of the same residue. The structure of the free
form is compared with complexes of RNase T1 with filled base recognition site
and/or catalytic site. Several structural rearrangements occurring upon
inhibitor or substrate binding are clearly apparent. In conjunction with the
available biochemical knowledge, they are used to describe probable steps
occurring early during RNase T1-catalyzed phosphate transesterification.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
F.Pavelcík,
and
J.Václavík
(2010).
Performance of phased rotation, conformation and translation function: accurate protein model building with tripeptidic and tetrapeptidic fragments.
|
| |
Acta Crystallogr D Biol Crystallogr,
66,
1012-1023.
|
|
|
|
|
|
|
H.Fu,
G.R.Grimsley,
A.Razvi,
J.M.Scholtz,
and
C.N.Pace
(2009).
Increasing protein stability by improving beta-turns.
|
| |
Proteins,
77,
491-498.
|
|
|
|
|
|
|
J.M.Schmidt,
M.J.Howard,
M.Maestre-Martínez,
C.S.Pérez,
and
F.Löhr
(2009).
Variation in protein C(alpha)-related one-bond J couplings.
|
| |
Magn Reson Chem,
47,
16-30.
|
|
|
|
|
|
|
B.A.Kerwin,
K.H.Aoki,
M.Gonelli,
and
G.B.Strambini
(2008).
Differentiation of the local structure around tryptophan 51 and 64 in recombinant human erythropoietin by tryptophan phosphorescence.
|
| |
Photochem Photobiol,
84,
1172-1181.
|
|
|
|
|
|
|
J.Lu,
A.Esberg,
B.Huang,
and
A.S.Byström
(2008).
Kluyveromyces lactis gamma-toxin, a ribonuclease that recognizes the anticodon stem loop of tRNA.
|
| |
Nucleic Acids Res,
36,
1072-1080.
|
|
|
|
|
|
|
S.Shimotakahara,
K.Furihata,
and
M.Tashiro
(2005).
Application of NMR screening techniques for observing ligand binding with a protein receptor.
|
| |
Magn Reson Chem,
43,
69-72.
|
|
|
|
|
|
|
Y.Sei,
S.Shimotakahara,
J.Ishii,
H.Shindo,
H.Seki,
K.Yamaguchi,
and
M.Tashiro
(2005).
Observation of water molecules bound to a protein using cold-spray ionization mass spectrometry.
|
| |
Anal Sci,
21,
449-451.
|
|
|
|
|
|
|
R.W.Alston,
L.Urbanikova,
J.Sevcik,
M.Lasagna,
G.D.Reinhart,
J.M.Scholtz,
and
C.N.Pace
(2004).
Contribution of single tryptophan residues to the fluorescence and stability of ribonuclease Sa.
|
| |
Biophys J,
87,
4036-4047.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
S.Shimotakahara,
S.Hojo,
K.Furihata,
and
M.Tashiro
(2004).
Computational and NMR analyses for the identification of bound water molecules in ribonuclease T1.
|
| |
Anal Sci,
20,
1471-1474.
|
|
|
|
|
|
|
K.Hatano,
M.Kojima,
E.Suzuki,
M.Tanokura,
and
K.Takahashi
(2003).
Determination of the NMR structure of Gln25-ribonuclease T1.
|
| |
Biol Chem,
384,
1173-1183.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
M.Torrez,
M.Schultehenrich,
and
D.R.Livesay
(2003).
Conferring thermostability to mesophilic proteins through optimized electrostatic surfaces.
|
| |
Biophys J,
85,
2845-2853.
|
|
|
|
|
|
|
A.Koumanov,
H.Rüterjans,
and
A.Karshikoff
(2002).
Continuum electrostatic analysis of irregular ionization and proton allocation in proteins.
|
| |
Proteins,
46,
85-96.
|
|
|
|
|
|
|
K.M.Polyakov,
A.A.Lebedev,
A.L.Okorokov,
K.I.Panov,
A.A.Schulga,
A.G.Pavlovsky,
M.Y.Karpeisky,
and
G.G.Dodson
(2002).
The structure of substrate-free microbial ribonuclease binase and of its complexes with 3'GMP and sulfate ions.
|
| |
Acta Crystallogr D Biol Crystallogr,
58,
744-750.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
R.Moritz,
D.Reinstädler,
H.Fabian,
and
D.Naumann
(2002).
Time-resolved FTIR difference spectroscopy as tool for investigating refolding reactions of ribonuclease T1 synchronized with trans --> cis prolyl isomerization.
|
| |
Biopolymers,
67,
145-155.
|
|
|
|
|
|
|
C.N.Schutz,
and
A.Warshel
(2001).
What are the dielectric "constants" of proteins and how to validate electrostatic models?
|
| |
Proteins,
44,
400-417.
|
|
|
|
|
|
|
D.Peters,
and
J.Peters
(2001).
The pseudomolecule method and the structure of globular proteins. II. The example of ribonuclease F1 and T1.
|
| |
Biopolymers,
59,
402-410.
|
|
|
|
|
|
|
R.Pinard,
K.J.Hampel,
J.E.Heckman,
D.Lambert,
P.A.Chan,
F.Major,
and
J.M.Burke
(2001).
Functional involvement of G8 in the hairpin ribozyme cleavage mechanism.
|
| |
EMBO J,
20,
6434-6442.
|
|
|
|
|
|
|
E.S.Courtenay,
M.W.Capp,
C.F.Anderson,
and
M.T.Record
(2000).
Vapor pressure osmometry studies of osmolyte-protein interactions: implications for the action of osmoprotectants in vivo and for the interpretation of "osmotic stress" experiments in vitro.
|
| |
Biochemistry,
39,
4455-4471.
|
|
|
|
|
|
|
J.Foadi,
M.M.Woolfson,
E.J.Dodson,
K.S.Wilson,
Y.Jia-xing,
and
Z.Chao-de
(2000).
A flexible and efficient procedure for the solution and phase refinement of protein structures.
|
| |
Acta Crystallogr D Biol Crystallogr,
56,
1137-1147.
|
|
|
|
|
|
|
L.Hwu,
K.Huang,
D.Chen,
and
A.Lin
(2000).
The action mode of the ribosome-inactivating protein alpha-sarcin.
|
| |
J Biomed Sci,
7,
420-428.
|
|
|
|
|
|
|
B.M.Huyghues-Despointes,
U.Langhorst,
J.Steyaert,
C.N.Pace,
and
J.M.Scholtz
(1999).
Hydrogen-exchange stabilities of RNase T1 and variants with buried and solvent-exposed Ala --> Gly mutations in the helix.
|
| |
Biochemistry,
38,
16481-16490.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
D.Reinstädler,
H.Fabian,
and
D.Naumann
(1999).
New structural insights into the refolding of ribonuclease T1 as seen by time-resolved Fourier-transform infrared spectroscopy.
|
| |
Proteins,
34,
303-316.
|
|
|
|
|
|
|
G.R.Grimsley,
K.L.Shaw,
L.R.Fee,
R.W.Alston,
B.M.Huyghues-Despointes,
R.L.Thurlkill,
J.M.Scholtz,
and
C.N.Pace
(1999).
Increasing protein stability by altering long-range coulombic interactions.
|
| |
Protein Sci,
8,
1843-1849.
|
|
|
|
|
|
|
U.Langhorst,
R.Loris,
V.P.Denisov,
J.Doumen,
P.Roose,
D.Maes,
B.Halle,
and
J.Steyaert
(1999).
Dissection of the structural and functional role of a conserved hydration site in RNase T1.
|
| |
Protein Sci,
8,
722-730.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
I.Zegers,
R.Loris,
G.Dehollander,
A.Fattah Haikal,
F.Poortmans,
J.Steyaert,
and
L.Wyns
(1998).
Hydrolysis of a slow cyclic thiophosphate substrate of RNase T1 analyzed by time-resolved crystallography.
|
| |
Nat Struct Biol,
5,
280-283.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.K.Myers,
C.N.Pace,
and
J.M.Scholtz
(1997).
A direct comparison of helix propensity in proteins and peptides.
|
| |
Proc Natl Acad Sci U S A,
94,
2833-2837.
|
|
|
|
|
|
|
J.K.Myers,
C.N.Pace,
and
J.M.Scholtz
(1997).
Helix propensities are identical in proteins and peptides.
|
| |
Biochemistry,
36,
10923-10929.
|
|
|
|
|
|
|
J.Steyaert
(1997).
A decade of protein engineering on ribonuclease T1--atomic dissection of the enzyme-substrate interactions.
|
| |
Eur J Biochem,
247,
1.
|
|
|
|
|
|
|
L.S.Mullins,
C.N.Pace,
and
F.M.Raushel
(1997).
Conformational stability of ribonuclease T1 determined by hydrogen-deuterium exchange.
|
| |
Protein Sci,
6,
1387-1395.
|
|
|
|
|
|
|
M.H.Zehfus
(1997).
Identification of compact, hydrophobically stabilized domains and modules containing multiple peptide chains.
|
| |
Protein Sci,
6,
1210-1219.
|
|
|
|
|
|
|
T.Liu,
M.Ryan,
F.W.Dahlquist,
and
O.H.Griffith
(1997).
Determination of pKa values of the histidine side chains of phosphatidylinositol-specific phospholipase C from Bacillus cereus by NMR spectroscopy and site-directed mutagenesis.
|
| |
Protein Sci,
6,
1937-1944.
|
|
|
|
|
|
|
J.B.Garrett,
L.S.Mullins,
and
F.M.Raushel
(1996).
Are turns required for the folding of ribonuclease T1?
|
| |
Protein Sci,
5,
204-211.
|
|
|
|
|
|
|
K.Ishikawa,
E.Suzuki,
M.Tanokura,
and
K.Takahashi
(1996).
Crystal structure of ribonuclease T1 carboxymethylated at Glu58 in complex with 2'-GMP.
|
| |
Biochemistry,
35,
8329-8334.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
L.M.Mayr,
C.Odefey,
M.Schutkowski,
and
F.X.Schmid
(1996).
Kinetic analysis of the unfolding and refolding of ribonuclease T1 by a stopped-flow double-mixing technique.
|
| |
Biochemistry,
35,
5550-5561.
|
|
|
|
|
|
|
T.Schindler,
L.M.Mayr,
O.Landt,
U.Hahn,
and
F.X.Schmid
(1996).
The role of a trans-proline in the folding mechanism of ribonuclease T1.
|
| |
Eur J Biochem,
241,
516-524.
|
|
|
|
|
|
|
V.J.Hilser,
J.Gómez,
and
E.Freire
(1996).
The enthalpy change in protein folding and binding: refinement of parameters for structure-based calculations.
|
| |
Proteins,
26,
123-133.
|
|
|
|
|
|
|
X.Yang,
and
K.Moffat
(1996).
Insights into specificity of cleavage and mechanism of cell entry from the crystal structure of the highly specific Aspergillus ribotoxin, restrictocin.
|
| |
Structure,
4,
837-852.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
C.Frech,
and
F.X.Schmid
(1995).
DsbA-mediated disulfide bond formation and catalyzed prolyl isomerization in oxidative protein folding.
|
| |
J Biol Chem,
270,
5367-5374.
|
|
|
|
|
|
|
C.N.Pace,
F.Vajdos,
L.Fee,
G.Grimsley,
and
T.Gray
(1995).
How to measure and predict the molar absorption coefficient of a protein.
|
| |
Protein Sci,
4,
2411-2423.
|
|
|
|
|
|
|
M.F.Haun,
M.Wirth,
and
H.Rüterjans
(1995).
Calorimetric investigation of thermal stability and ligand-binding characteristics of disulfide-bond-cleaved ribonuclease T1.
|
| |
Eur J Biochem,
227,
516-523.
|
|
|
|
|
|
|
M.H.Zehfus
(1995).
Automatic recognition of hydrophobic clusters and their correlation with protein folding units.
|
| |
Protein Sci,
4,
1188-1202.
|
|
|
|
|
|
|
S.Ganguli,
H.Wang,
P.Matsumura,
and
K.Volz
(1995).
Uncoupled phosphorylation and activation in bacterial chemotaxis. The 2.1-A structure of a threonine to isoleucine mutant at position 87 of CheY.
|
| |
J Biol Chem,
270,
17386-17393.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
L.M.Mayr,
D.Willbold,
O.Landt,
and
F.X.Schmid
(1994).
Role of the Cys 2-Cys 10 disulfide bond for the structure, stability, and folding kinetics of ribonuclease T1.
|
| |
Protein Sci,
3,
227-239.
|
|
|
|
|
|
|
S.Vuilleumier,
and
A.R.Fersht
(1994).
Insertion in barnase of a loop sequence from ribonuclease T1. Investigating sequence and structure alignments by protein engineering.
|
| |
Eur J Biochem,
221,
1003-1012.
|
|
|
|
|
|
|
A.Elofsson,
T.Kulinski,
R.Rigler,
and
L.Nilsson
(1993).
Site specific point mutation changes specificity: a molecular modeling study by free energy simulations and enzyme kinetics of the thermodynamics in ribonuclease T1 substrate interactions.
|
| |
Proteins,
17,
161-175.
|
|
|
|
|
|
|
A.Heydenreich,
G.Koellner,
H.W.Choe,
F.Cordes,
C.Kisker,
H.Schindelin,
R.Adamiak,
U.Hahn,
and
W.Saenger
(1993).
The complex between ribonuclease T1 and 3'GMP suggests geometry of enzymic reaction path. An X-ray study.
|
| |
Eur J Biochem,
218,
1005-1012.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
C.A.Orengo,
and
J.M.Thornton
(1993).
Alpha plus beta folds revisited: some favoured motifs.
|
| |
Structure,
1,
105-120.
|
|
|
|
|
|
|
T.Nakai,
W.Yoshikawa,
H.Nakamura,
and
H.Yoshida
(1992).
The three-dimensional structure of guanine-specific ribonuclease F1 in solution determined by NMR spectroscopy and distance geometry.
|
| |
Eur J Biochem,
208,
41-51.
|
|
|
PDB codes:
|
|
|
|
|
|
|
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.
|
|
Links
