|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
|
|
|
|
Enzyme class:
|
|
Chain E:
E.C.3.4.21.81
- streptogrisin B.
|
|
|
|
|
|
|
Reaction:
|
|
Hydrolysis of proteins with specificity similar to trypsin.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
Biochemistry
22:4420-4433
(1983)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Structure of the complex of Streptomyces griseus protease B and the third domain of the turkey ovomucoid inhibitor at 1.8-A resolution.
|
|
R.J.Read,
M.Fujinaga,
A.R.Sielecki,
M.N.James.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
The structure of the complex between the serine protease Streptomyces griseus
protease B (SGPB) and the third domain of the Kazal-type ovomucoid inhibitor
from turkey has been solved at 1.8-A resolution and refined to a conventional R
factor of 0.125. As others have reported previously for analogous complexes of
proteases and protein inhibitors, the inhibitor binds in a fashion similar to
that of a substrate; it is not cleaved, but there is a close approach (2.7 A) of
the active site nucleophile Ser-195 O gamma to the carbonyl carbon of the
reactive peptide bond of the inhibitor. Contrary to the structural reports
regarding the other enzyme-inhibitor complexes, we conclude that there is no
evidence for a significant distortion of this peptide bond from planarity. The
mechanism of inhibition can be understood in terms of the equilibrium
thermodynamic parameters Ka, the enzyme-inhibitor association constant, and
Khyd, the equilibrium constant for inhibitor hydrolysis. These thermodynamic
parameters can be rationalized in terms of the observed structure.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
B.Kim,
J.Song,
and
X.Song
(2010).
Calculations of the binding affinities of protein-protein complexes with the fast multipole method.
|
| |
J Chem Phys,
133,
095101.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
N.J.Baxter,
A.Roetzer,
H.D.Liebig,
S.E.Sedelnikova,
A.M.Hounslow,
T.Skern,
and
J.P.Waltho
(2006).
Structure and dynamics of coxsackievirus B4 2A proteinase, an enyzme involved in the etiology of heart disease.
|
| |
J Virol,
80,
1451-1462.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
K.Nakamura,
Y.Someya,
T.Kumasaka,
G.Ueno,
M.Yamamoto,
T.Sato,
N.Takeda,
T.Miyamura,
and
N.Tanaka
(2005).
A norovirus protease structure provides insights into active and substrate binding site integrity.
|
| |
J Virol,
79,
13685-13693.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
M.Tian,
and
S.Kamoun
(2005).
A two disulfide bridge Kazal domain from Phytophthora exhibits stable inhibitory activity against serine proteases of the subtilisin family.
|
| |
BMC Biochem,
6,
15.
|
|
|
|
|
|
|
S.M.Truhlar,
and
D.A.Agard
(2005).
The folding landscape of an alpha-lytic protease variant reveals the role of a conserved beta-hairpin in the development of kinetic stability.
|
| |
Proteins,
61,
105-114.
|
|
|
|
|
|
|
A.M.Coros,
L.Swenson,
W.T.Wolodko,
and
M.E.Fraser
(2004).
Structure of the CoA transferase from pig heart to 1.7 A resolution.
|
| |
Acta Crystallogr D Biol Crystallogr,
60,
1717-1725.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
T.Z.Sen,
A.Kloczkowski,
R.L.Jernigan,
C.Yan,
V.Honavar,
K.M.Ho,
C.Z.Wang,
Y.Ihm,
H.Cao,
X.Gu,
and
D.Dobbs
(2004).
Predicting binding sites of hydrolase-inhibitor complexes by combining several methods.
|
| |
BMC Bioinformatics,
5,
205.
|
|
|
|
|
|
|
N.Foeger,
E.M.Schmid,
and
T.Skern
(2003).
Human rhinovirus 2 2Apro recognition of eukaryotic initiation factor 4GI. Involvement of an exosite.
|
| |
J Biol Chem,
278,
33200-33207.
|
|
|
|
|
|
|
D.M.Lorber,
M.K.Udo,
and
B.K.Shoichet
(2002).
Protein-protein docking with multiple residue conformations and residue substitutions.
|
| |
Protein Sci,
11,
1393-1408.
|
|
|
|
|
|
|
E.S.Radisky,
and
D.E.Koshland
(2002).
A clogged gutter mechanism for protease inhibitors.
|
| |
Proc Natl Acad Sci U S A,
99,
10316-10321.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
R.E.Georgescu,
E.G.Alexov,
and
M.R.Gunner
(2002).
Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins.
|
| |
Biophys J,
83,
1731-1748.
|
|
|
|
|
|
|
S.M.Lu,
W.Lu,
M.A.Qasim,
S.Anderson,
I.Apostol,
W.Ardelt,
T.Bigler,
Y.W.Chiang,
J.Cook,
M.N.James,
I.Kato,
C.Kelly,
W.Kohr,
T.Komiyama,
T.Y.Lin,
M.Ogawa,
J.Otlewski,
S.J.Park,
S.Qasim,
M.Ranjbar,
M.Tashiro,
N.Warne,
H.Whatley,
A.Wieczorek,
M.Wieczorek,
T.Wilusz,
R.Wynn,
W.Zhang,
and
M.Laskowski
(2001).
Predicting the reactivity of proteins from their sequence alone: Kazal family of protein inhibitors of serine proteinases.
|
| |
Proc Natl Acad Sci U S A,
98,
1410-1415.
|
|
|
|
|
|
|
K.S.Bateman,
S.Anderson,
W.Lu,
M.A.Qasim,
M.Laskowski,
and
M.N.James
(2000).
Deleterious effects of beta-branched residues in the S1 specificity pocket of Streptomyces griseus proteinase B (SGPB): crystal structures of the turkey ovomucoid third domain variants Ile18I, Val18I, Thr18I, and Ser18I in complex with SGPB.
|
| |
Protein Sci,
9,
83-94.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
W.R.Forsyth,
and
A.D.Robertson
(2000).
Insensitivity of perturbed carboxyl pK(a) values in the ovomucoid third domain to charge replacement at a neighboring residue.
|
| |
Biochemistry,
39,
8067-8072.
|
|
|
|
|
|
|
H.Czapinska,
and
J.Otlewski
(1999).
Structural and energetic determinants of the S1-site specificity in serine proteases.
|
| |
Eur J Biochem,
260,
571-595.
|
|
|
|
|
|
|
J.F.Petersen,
M.M.Cherney,
H.D.Liebig,
T.Skern,
E.Kuechler,
and
M.N.James
(1999).
The structure of the 2A proteinase from a common cold virus: a proteinase responsible for the shut-off of host-cell protein synthesis.
|
| |
EMBO J,
18,
5463-5475.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.V.Lehtonen,
K.Denessiouk,
A.C.May,
and
M.S.Johnson
(1999).
Finding local structural similarities among families of unrelated protein structures: a generic non-linear alignment algorithm.
|
| |
Proteins,
34,
341-355.
|
|
|
|
|
|
|
T.Asao,
K.Takahashi,
and
M.Tashiro
(1998).
Interaction of second and third domains of Japanese quail ovomucoid with ten mammalian trypsins.
|
| |
Biochim Biophys Acta,
1387,
415-421.
|
|
|
|
|
|
|
W.R.Forsyth,
M.K.Gilson,
J.Antosiewicz,
O.R.Jaren,
and
A.D.Robertson
(1998).
Theoretical and experimental analysis of ionization equilibria in ovomucoid third domain.
|
| |
Biochemistry,
37,
8643-8652.
|
|
|
|
|
|
|
E.M.Bergmann,
S.C.Mosimann,
M.M.Chernaia,
B.A.Malcolm,
and
M.N.James
(1997).
The refined crystal structure of the 3C gene product from hepatitis A virus: specific proteinase activity and RNA recognition.
|
| |
J Virol,
71,
2436-2448.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
G.T.DeKoster,
and
A.D.Robertson
(1997).
Thermodynamics of unfolding for Kazal-type serine protease inhibitors: entropic stabilization of ovomucoid first domain by glycosylation.
|
| |
Biochemistry,
36,
2323-2331.
|
|
|
|
|
|
|
J.Cavarelli,
G.Prévost,
W.Bourguet,
L.Moulinier,
B.Chevrier,
B.Delagoutte,
A.Bilwes,
L.Mourey,
S.Rifai,
Y.Piémont,
and
D.Moras
(1997).
The structure of Staphylococcus aureus epidermolytic toxin A, an atypic serine protease, at 1.7 A resolution.
|
| |
Structure,
5,
813-824.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
C.G.Hoogstraten,
S.Choe,
W.M.Westler,
and
J.L.Markley
(1995).
Comparison of the accuracy of protein solution structures derived from conventional and network-edited NOESY data.
|
| |
Protein Sci,
4,
2289-2299.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.Janin
(1995).
Elusive affinities.
|
| |
Proteins,
21,
30-39.
|
|
|
|
|
|
|
K.Huang,
W.Lu,
S.Anderson,
M.Laskowski,
and
M.N.James
(1995).
Water molecules participate in proteinase-inhibitor interactions: crystal structures of Leu18, Ala18, and Gly18 variants of turkey ovomucoid inhibitor third domain complexed with Streptomyces griseus proteinase B.
|
| |
Protein Sci,
4,
1985-1997.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.Abul Qasim,
M.R.Ranjbar,
R.Wynn,
S.Anderson,
and
M.Laskowski
(1995).
Ionizable P1 residues in serine proteinase inhibitors undergo large pK shifts on complex formation.
|
| |
J Biol Chem,
270,
27419-27422.
|
|
|
|
|
|
|
M.D.Cummings,
T.N.Hart,
and
R.J.Read
(1995).
Atomic solvation parameters in the analysis of protein-protein docking results.
|
| |
Protein Sci,
4,
2087-2099.
|
|
|
|
|
|
|
S.S.Sidhu,
G.B.Kalmar,
L.G.Willis,
and
T.J.Borgford
(1995).
Protease evolution in Streptomyces griseus. Discovery of a novel dimeric enzymes.
|
| |
J Biol Chem,
270,
7594-7600.
|
|
|
|
|
|
|
E.Pizzi,
A.Tramontano,
L.Tomei,
N.La Monica,
C.Failla,
M.Sardana,
T.Wood,
and
R.De Francesco
(1994).
Molecular model of the specificity pocket of the hepatitis C virus protease: implications for substrate recognition.
|
| |
Proc Natl Acad Sci U S A,
91,
888-892.
|
|
|
|
|
|
|
K.Huang,
N.C.Strynadka,
V.D.Bernard,
R.J.Peanasky,
and
M.N.James
(1994).
The molecular structure of the complex of Ascaris chymotrypsin/elastase inhibitor with porcine elastase.
|
| |
Structure,
2,
679-689.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.Zdanov,
S.Wu,
J.DiMaio,
Y.Konishi,
Y.Li,
X.Wu,
B.F.Edwards,
P.D.Martin,
and
M.Cygler
(1993).
Crystal structure of the complex of human alpha-thrombin and nonhydrolyzable bifunctional inhibitors, hirutonin-2 and hirutonin-6.
|
| |
Proteins,
17,
252-265.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
I.Apostol,
A.Giletto,
T.Komiyama,
W.Zhang,
and
M.Laskowski
(1993).
Amino acid sequences of ovomucoid third domains from 27 additional species of birds.
|
| |
J Protein Chem,
12,
419-433.
|
|
|
|
|
|
|
L.Swint,
and
A.D.Robertson
(1993).
Thermodynamics of unfolding for turkey ovomucoid third domain: thermal and chemical denaturation.
|
| |
Protein Sci,
2,
2037-2049.
|
|
|
|
|
|
|
T.L.Bigler,
W.Lu,
S.J.Park,
M.Tashiro,
M.Wieczorek,
R.Wynn,
and
M.Laskowski
(1993).
Binding of amino acid side chains to preformed cavities: interaction of serine proteinases with turkey ovomucoid third domains with coded and noncoded P1 residues.
|
| |
Protein Sci,
2,
786-799.
|
|
|
|
|
|
|
N.Horton,
and
M.Lewis
(1992).
Calculation of the free energy of association for protein complexes.
|
| |
Protein Sci,
1,
169-181.
|
|
|
|
|
|
|
R.R.Plaskon,
C.M.Kam,
E.M.Burgess,
J.C.Powers,
and
F.L.Suddath
(1992).
Michaelis complexes of porcine pancreatic elastase with 7-[(alkylcarbamoyl)amino]-4-chloro-3-ethoxyisocoumarins: translational sampling of inhibitor position and kinetic measurements.
|
| |
Proteins,
13,
141-151.
|
|
|
|
|
|
|
T.N.Hart,
and
R.J.Read
(1992).
A multiple-start Monte Carlo docking method.
|
| |
Proteins,
13,
206-222.
|
|
|
|
|
|
|
W.Bode,
and
R.Huber
(1992).
Natural protein proteinase inhibitors and their interaction with proteinases.
|
| |
Eur J Biochem,
204,
433-451.
|
|
|
|
|
|
|
Y.Takeuchi,
T.Nonaka,
K.T.Nakamura,
S.Kojima,
K.Miura,
and
Y.Mitsui
(1992).
Crystal structure of an engineered subtilisin inhibitor complexed with bovine trypsin.
|
| |
Proc Natl Acad Sci U S A,
89,
4407-4411.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.Rose,
and
F.Eisenmenger
(1991).
A fast unbiased comparison of protein structures by means of the Needleman-Wunsch algorithm.
|
| |
J Mol Evol,
32,
340-354.
|
|
|
|
|
|
|
O.Herzberg,
and
J.Moult
(1991).
Analysis of the steric strain in the polypeptide backbone of protein molecules.
|
| |
Proteins,
11,
223-229.
|
|
|
|
|
|
|
A.D.Robertson,
G.I.Rhyu,
W.M.Westler,
and
J.L.Markley
(1990).
Assignment of the 13C-NMR spectra of virgin and reactive-site modified turkey ovomucoid third domain.
|
| |
Biopolymers,
29,
461-467.
|
|
|
|
|
|
|
J.Greer
(1990).
Comparative modeling methods: application to the family of the mammalian serine proteases.
|
| |
Proteins,
7,
317-334.
|
|
|
|
|
|
|
M.Laskowski,
I.Apostol,
W.Ardelt,
J.Cook,
A.Giletto,
C.A.Kelly,
W.Y.Lu,
S.J.Park,
M.A.Qasim,
and
H.E.Whatley
(1990).
Amino acid sequences of ovomucoid third domain from 25 additional species of birds.
|
| |
J Protein Chem,
9,
715-725.
|
|
|
|
|
|
|
M.P.Williamson
(1990).
Secondary-structure dependent chemical shifts in proteins.
|
| |
Biopolymers,
29,
1423-1431.
|
|
|
|
|
|
|
P.Carter,
and
J.A.Wells
(1990).
Functional interaction among catalytic residues in subtilisin BPN'.
|
| |
Proteins,
7,
335-342.
|
|
|
|
|
|
|
L.B.Evnin,
and
C.S.Craik
(1988).
Development of an efficient method for generating and screening active trypsin and trypsin variants.
|
| |
Ann N Y Acad Sci,
542,
61-74.
|
|
|
|
|
|
|
M.E.Murphy,
J.Moult,
R.C.Bleackley,
H.Gershenfeld,
I.L.Weissman,
and
M.N.James
(1988).
Comparative molecular model building of two serine proteinases from cytotoxic T lymphocytes.
|
| |
Proteins,
4,
190-204.
|
|
|
|
|
|
|
H.Iijima,
J.B.Dunbar,
and
G.R.Marshall
(1987).
Calibration of effective van der Waals atomic contact radii for proteins and peptides.
|
| |
Proteins,
2,
330-339.
|
|
|
|
|
|
|
W.Bode,
E.Papamokos,
and
D.Musil
(1987).
The high-resolution X-ray crystal structure of the complex formed between subtilisin Carlsberg and eglin c, an elastase inhibitor from the leech Hirudo medicinalis. Structural analysis, subtilisin structure and interface geometry.
|
| |
Eur J Biochem,
166,
673-692.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
C.Chothia,
and
A.M.Lesk
(1986).
The relation between the divergence of sequence and structure in proteins.
|
| |
EMBO J,
5,
823-826.
|
|
|
|
|
|
|
J.Moult,
and
M.N.James
(1986).
An algorithm for determining the conformation of polypeptide segments in proteins by systematic search.
|
| |
Proteins,
1,
146-163.
|
|
|
|
|
|
|
W.Bode,
A.Z.Wei,
R.Huber,
E.Meyer,
J.Travis,
and
S.Neumann
(1986).
X-ray crystal structure of the complex of human leukocyte elastase (PMN elastase) and the third domain of the turkey ovomucoid inhibitor.
|
| |
EMBO J,
5,
2453-2458.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
W.Bode,
E.Papamokos,
D.Musil,
U.Seemueller,
and
H.Fritz
(1986).
Refined 1.2 A crystal structure of the complex formed between subtilisin Carlsberg and the inhibitor eglin c. Molecular structure of eglin and its detailed interaction with subtilisin.
|
| |
EMBO J,
5,
813-818.
|
|
|
|
|
|
|
C.A.McPhalen,
I.Svendsen,
I.Jonassen,
and
M.N.James
(1985).
Crystal and molecular structure of chymotrypsin inhibitor 2 from barley seeds in complex with subtilisin Novo.
|
| |
Proc Natl Acad Sci U S A,
82,
7242-7246.
|
|
|
|
|
|
|
W.Bode,
O.Epp,
R.Huber,
M.Laskowski,
and
W.Ardelt
(1985).
The crystal and molecular structure of the third domain of silver pheasant ovomucoid (OMSVP3).
|
| |
Eur J Biochem,
147,
387-395.
|
|
|
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
