 |
PDBsum entry 1s6h
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
|
|
|
|
|
Enzyme class:
|
|
E.C.3.4.21.4
- trypsin.
|
|
|
|
|
|
|
Reaction:
|
|
Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
Biochemistry
43:2829-2839
(2004)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
X-ray and NMR characterization of covalent complexes of trypsin, borate, and alcohols.
|
|
T.R.Transue,
J.M.Krahn,
S.A.Gabel,
E.F.DeRose,
R.E.London.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
An understanding of the physiological and toxicological properties of borate and
the utilization of boronic acids in drug development require a basic
understanding of borate-enzyme chemistry. We report here the extension of our
recent NMR studies indicating the formation of a ternary borate-alcohol-trypsin
complex. Crystallographic and solution state NMR studies of porcine trypsin were
performed in the presence of borate and either of three alcohols designed to
bind to the S1 affinity subsite: 4-aminobutanol, guanidine-3-propanol, and
4-hydroxymethylbenzamidine. Quaternary complexes of trypsin, borate, S1-binding
alcohol, and ethylene glycol (a cryoprotectant), as well as a ternary trypsin,
borate, and ethylene glycol complex have been observed in the crystalline state.
Borate forms ester bonds to Ser195, ethylene glycol (two bonds), and the
S1-binding alcohol (if present). Spectra from (1)H and (11)B NMR studies confirm
that these complexes also exist in solution and also provide evidence for the
formation of ternary trypsin, borate, and S1-subsite alcohol complexes which are
not observed in the crystals using our experimental protocols. Analysis of eight
crystal structures indicates that formation of an active site borate complex is
in all cases accompanied by a significant (approximately 4%) increase in the
b-axis dimension of the unit cell. Presumably, our inability to observe the
ternary complexes in the crystalline state arises from the lower stability of
these complexes and consequent inability to overcome the constraints imposed by
the lattice contacts. A mechanism for the coupling of the lattice contacts with
the active site that involves a conformational rearrangement of Gln192 is
suggested. The structures presented here represent the first crystallographic
demonstration of covalent binding of an enzyme by borate.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
C.Haupt,
M.Bereza,
S.T.Kumar,
B.Kieninger,
I.Morgado,
P.Hortschansky,
G.Fritz,
C.Röcken,
U.Horn,
and
M.Fändrich
(2011).
Pattern recognition with a fibril-specific antibody fragment reveals the surface variability of natural amyloid fibrils.
|
| |
J Mol Biol,
408,
529-540.
|
|
|
|
|
|
|
F.Casadonte,
L.Pasqua,
R.Savino,
and
R.Terracciano
(2010).
Smart trypsin adsorption into N-(2-aminoethyl)-3-aminopropyl-modified mesoporous silica for ultra fast protein digestion.
|
| |
Chemistry,
16,
8998-9001.
|
|
|
|
|
|
|
P.A.Osmulski,
M.Hochstrasser,
and
M.Gaczynska
(2009).
A tetrahedral transition state at the active sites of the 20S proteasome is coupled to opening of the alpha-ring channel.
|
| |
Structure,
17,
1137-1147.
|
|
|
|
|
|
|
K.Park,
and
D.Kim
(2008).
Binding similarity network of ligand.
|
| |
Proteins,
71,
960-971.
|
|
|
|
|
|
|
S.A.Gabel,
and
R.E.London
(2008).
Ternary borate-nucleoside complex stabilization by ribonuclease A demonstrates phosphate mimicry.
|
| |
J Biol Inorg Chem,
13,
207-217.
|
|
|
|
|
|
|
A.Moulin,
J.H.Bell,
R.F.Pratt,
and
D.Ringe
(2007).
Inhibition of chymotrypsin by a complex of ortho-vanadate and benzohydroxamic acid: structure of the inert complex and its mechanistic interpretation.
|
| |
Biochemistry,
46,
5982-5990.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
B.Ozbas,
K.Rajagopal,
L.Haines-Butterick,
J.P.Schneider,
and
D.J.Pochan
(2007).
Reversible stiffening transition in beta-hairpin hydrogels induced by ion complexation.
|
| |
J Phys Chem B,
111,
13901-13908.
|
|
|
|
|
|
|
M.Groll,
C.R.Berkers,
H.L.Ploegh,
and
H.Ovaa
(2006).
Crystal structure of the boronic acid-based proteasome inhibitor bortezomib in complex with the yeast 20S proteasome.
|
| |
Structure,
14,
451-456.
|
|
|
PDB code:
|
|
|
|
|
|
|
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
code is
shown on the right.
|
|
Links
