 |
PDBsum entry 1r0r
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
|
|
|
|
Enzyme class:
|
|
Chain E:
E.C.3.4.21.62
- subtilisin.
|
|
|
|
|
|
|
Reaction:
|
|
Hydrolysis of proteins with broad specificity for peptide bonds, and a preference for a large uncharged residue in P1. Hydrolyzes peptide amides.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
J Mol Biol
331:497-508
(2003)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Structure and energetics of protein-protein interactions: the role of conformational heterogeneity in OMTKY3 binding to serine proteases.
|
|
J.R.Horn,
S.Ramaswamy,
K.P.Murphy.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
Proteins with flexible binding surfaces can interact with numerous binding
partners. However, this promiscuity is more difficult to understand in
"rigid-body" proteins, whose binding results in little, or no, change
in the position of backbone atoms. The binding of Kazal inhibitors to serine
proteases is considered a classic case of rigid-body binding, although they bind
to a wide range of proteases. We have studied the thermodynamics of binding of
the Kazal serine protease inhibitor, turkey ovomucoid third domain (OMTKY3), to
the serine protease subtilisin Carlsberg using isothermal titration calorimetry
and have determined the crystal structure of the complex at very high resolution
(1.1A). Comparison of the binding energetics and structure to other OMTKY3
interactions demonstrates that small changes in the position of side-chains can
make significant contributions to the binding thermodynamics, including the
enthalpy of binding. These effects emphasize that small, "rigid-body"
proteins are still dynamic structures, and these dynamics make contributions to
both the enthalpy and entropy of binding interactions.
|
|
|
|
|
|
| |
Selected figure(s)
|
|
|
|
| |
|
|
|
|
|
|
Figure 2.
Figure 2. Ribbon diagram of the crystal structure of the
complex between OMTKY3 and SC. OMTKY3 is colored tan and SC is
blue. The ion (calcium) binding sites are shown as yellow
spheres.
|
|
Figure 7.
Figure 7. Overlay of OMTKY3 from the SC complex, with
OMSVP3. The single site residue difference in OMSVP3 at position
18 is Leu to Met (2ovo.pdb).[22.] OMTKY3, blue; OMSVP3, green.
|
|
|
|
|
|
| |
The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2003,
331,
497-508)
copyright 2003.
|
|
| |
Figures were
selected
by an automated process.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
B.Aguilar,
R.Anandakrishnan,
J.Z.Ruscio,
and
A.V.Onufriev
(2010).
Statistics and physical origins of pK and ionization state changes upon protein-ligand binding.
|
| |
Biophys J,
98,
872-880.
|
|
|
|
|
|
|
R.Bourgeas,
M.J.Basse,
X.Morelli,
and
P.Roche
(2010).
Atomic analysis of protein-protein interfaces with known inhibitors: the 2P2I database.
|
| |
PLoS One,
5,
e9598.
|
|
|
|
|
|
|
A.C.Mason,
and
J.H.Jensen
(2008).
Protein-protein binding is often associated with changes in protonation state.
|
| |
Proteins,
71,
81-91.
|
|
|
|
|
|
|
J.W.Torrance,
M.W.Macarthur,
and
J.M.Thornton
(2008).
Evolution of binding sites for zinc and calcium ions playing structural roles.
|
| |
Proteins,
71,
813-830.
|
|
|
|
|
|
|
S.Bougouffa,
and
J.Warwicker
(2008).
Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfaces.
|
| |
BMC Bioinformatics,
9,
448.
|
|
|
|
|
|
|
K.M.Armstrong,
and
B.M.Baker
(2007).
A comprehensive calorimetric investigation of an entropically driven T cell receptor-peptide/major histocompatibility complex interaction.
|
| |
Biophys J,
93,
597-609.
|
|
|
|
|
|
|
R.Helland,
A.N.Larsen,
A.O.Smalås,
and
N.P.Willassen
(2006).
The 1.8 A crystal structure of a proteinase K-like enzyme from a psychrotroph Serratia species.
|
| |
FEBS J,
273,
61-71.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.L.Kouadio,
J.R.Horn,
G.Pal,
and
A.A.Kossiakoff
(2005).
Shotgun alanine scanning shows that growth hormone can bind productively to its receptor through a drastically minimized interface.
|
| |
J Biol Chem,
280,
25524-25532.
|
|
|
|
|
|
|
J.T.Maynes,
M.M.Cherney,
M.A.Qasim,
M.Laskowski,
and
M.N.James
(2005).
Structure of the subtilisin Carlsberg-OMTKY3 complex reveals two different ovomucoid conformations.
|
| |
Acta Crystallogr D Biol Crystallogr,
61,
580-588.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
M.J.Cliff,
A.Gutierrez,
and
J.E.Ladbury
(2004).
A survey of the year 2003 literature on applications of isothermal titration calorimetry.
|
| |
J Mol Recognit,
17,
513-523.
|
|
|
|
|
|
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
